Starting phenix.real_space_refine
on Fri Aug 22 21:34:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uvi_42621/08_2025/8uvi_42621.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uvi_42621/08_2025/8uvi_42621.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uvi_42621/08_2025/8uvi_42621.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uvi_42621/08_2025/8uvi_42621.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uvi_42621/08_2025/8uvi_42621.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uvi_42621/08_2025/8uvi_42621.cif"
  }
  resolution = 2.53
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.033
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: 5
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     Na      2      4.78       5
     C    5634      2.51       5
     N    1226      2.21       5
     O    1300      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 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: 8212
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 497, 3887
          Classifications: {'peptide': 497}
          Link IDs: {'PTRANS': 33, 'TRANS': 463}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 3887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 497, 3887
          Classifications: {'peptide': 497}
          Link IDs: {'PTRANS': 33, 'TRANS': 463}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 219
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 219
          Unusual residues: {' NA': 1, 'C14': 3, 'CLR': 6, 'SIN': 1}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
    Chain: "B"
      Number of atoms: 219
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 219
          Unusual residues: {' NA': 1, 'C14': 3, 'CLR': 6, 'SIN': 1}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
  Time building chain proxies: 1.91, per 1000 atoms: 0.23
  Number of scatterers: 8212
  At special positions: 0
  Unit cell: (87.45, 97.35, 90.75, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      50     16.00
     Na      2     11.00
     O    1300      8.00
     N    1226      7.00
     C    5634      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: 0.53
  Conformation dependent library (CDL) restraints added in 393.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1860

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 0 sheets defined
      83.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 14
    Processing helix  chain 'A' and resid 14 through 34
      Proline residue:  A  24  - end of helix
      Proline residue:  A  29  - end of helix
      removed outlier: 3.906A  pdb=" N   PHE A  32 " --> pdb=" O   LEU A  28 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU A  34 " --> pdb=" O   VAL A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 55
    Processing helix  chain 'A' and resid 58 through 64
    Processing helix  chain 'A' and resid 64 through 73
      removed outlier: 3.902A  pdb=" N   VAL A  68 " --> pdb=" O   LEU A  64 " (cutoff:3.500A)
      Proline residue:  A  71  - end of helix
    Processing helix  chain 'A' and resid 77 through 82
    Processing helix  chain 'A' and resid 83 through 86
    Processing helix  chain 'A' and resid 87 through 106
      removed outlier: 3.940A  pdb=" N   PHE A  91 " --> pdb=" O   LEU A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 121
      removed outlier: 3.605A  pdb=" N   ARG A 111 " --> pdb=" O   ASN A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 140
    Processing helix  chain 'A' and resid 143 through 163
      Proline residue:  A 153  - end of helix
    Processing helix  chain 'A' and resid 225 through 246
      removed outlier: 4.543A  pdb=" N   ILE A 238 " --> pdb=" O   PHE A 234 " (cutoff:3.500A)
      Proline residue:  A 239  - end of helix
    Processing helix  chain 'A' and resid 253 through 267
      removed outlier: 3.828A  pdb=" N   LEU A 257 " --> pdb=" O   THR A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 301
      Proline residue:  A 284  - end of helix
    Processing helix  chain 'A' and resid 320 through 336
      removed outlier: 3.539A  pdb=" N   GLY A 336 " --> pdb=" O   TYR A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 359
    Processing helix  chain 'A' and resid 366 through 371
    Processing helix  chain 'A' and resid 377 through 390
      removed outlier: 3.612A  pdb=" N   THR A 381 " --> pdb=" O   SER A 377 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ILE A 388 " --> pdb=" O   ALA A 384 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   LEU A 389 " --> pdb=" O   ILE A 385 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   PHE A 390 " --> pdb=" O   VAL A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 404
      removed outlier: 4.013A  pdb=" N   PHE A 403 " --> pdb=" O   LEU A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 425
    Processing helix  chain 'A' and resid 426 through 446
      removed outlier: 3.653A  pdb=" N   ILE A 430 " --> pdb=" O   PRO A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 456
    Processing helix  chain 'A' and resid 463 through 479
    Processing helix  chain 'A' and resid 483 through 502
      Proline residue:  A 493  - end of helix
      removed outlier: 3.552A  pdb=" N   ILE A 500 " --> pdb=" O   ALA A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 518
      Proline residue:  A 512  - end of helix
      removed outlier: 3.963A  pdb=" N   SER A 518 " --> pdb=" O   THR A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 526
    Processing helix  chain 'A' and resid 527 through 535
    Processing helix  chain 'A' and resid 540 through 566
      removed outlier: 4.071A  pdb=" N   LEU A 550 " --> pdb=" O   ARG A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 571
      removed outlier: 3.558A  pdb=" N   ILE A 570 " --> pdb=" O   TRP A 566 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 14
    Processing helix  chain 'B' and resid 14 through 34
      Proline residue:  B  24  - end of helix
      Proline residue:  B  29  - end of helix
      removed outlier: 3.906A  pdb=" N   PHE B  32 " --> pdb=" O   LEU B  28 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU B  34 " --> pdb=" O   VAL B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 55
    Processing helix  chain 'B' and resid 58 through 64
    Processing helix  chain 'B' and resid 64 through 73
      removed outlier: 3.902A  pdb=" N   VAL B  68 " --> pdb=" O   LEU B  64 " (cutoff:3.500A)
      Proline residue:  B  71  - end of helix
    Processing helix  chain 'B' and resid 77 through 82
    Processing helix  chain 'B' and resid 83 through 86
    Processing helix  chain 'B' and resid 87 through 106
      removed outlier: 3.807A  pdb=" N   PHE B  91 " --> pdb=" O   LEU B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 121
      removed outlier: 3.605A  pdb=" N   ARG B 111 " --> pdb=" O   ASN B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 140
    Processing helix  chain 'B' and resid 143 through 163
      Proline residue:  B 153  - end of helix
    Processing helix  chain 'B' and resid 225 through 246
      removed outlier: 4.544A  pdb=" N   ILE B 238 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      Proline residue:  B 239  - end of helix
    Processing helix  chain 'B' and resid 253 through 267
      removed outlier: 3.829A  pdb=" N   LEU B 257 " --> pdb=" O   THR B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 301
      Proline residue:  B 284  - end of helix
    Processing helix  chain 'B' and resid 320 through 336
      removed outlier: 3.539A  pdb=" N   GLY B 336 " --> pdb=" O   TYR B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 359
    Processing helix  chain 'B' and resid 366 through 371
    Processing helix  chain 'B' and resid 377 through 390
      removed outlier: 3.612A  pdb=" N   THR B 381 " --> pdb=" O   SER B 377 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ILE B 388 " --> pdb=" O   ALA B 384 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   LEU B 389 " --> pdb=" O   ILE B 385 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   PHE B 390 " --> pdb=" O   VAL B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 404
      removed outlier: 4.012A  pdb=" N   PHE B 403 " --> pdb=" O   LEU B 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 425
    Processing helix  chain 'B' and resid 426 through 446
      removed outlier: 3.653A  pdb=" N   ILE B 430 " --> pdb=" O   PRO B 426 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 456
    Processing helix  chain 'B' and resid 463 through 479
    Processing helix  chain 'B' and resid 483 through 502
      Proline residue:  B 493  - end of helix
      removed outlier: 3.552A  pdb=" N   ILE B 500 " --> pdb=" O   ALA B 496 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 518
      Proline residue:  B 512  - end of helix
      removed outlier: 3.963A  pdb=" N   SER B 518 " --> pdb=" O   THR B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 523 through 526
    Processing helix  chain 'B' and resid 527 through 535
    Processing helix  chain 'B' and resid 540 through 566
      removed outlier: 4.071A  pdb=" N   LEU B 550 " --> pdb=" O   ARG B 546 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 566 through 571
      removed outlier: 3.559A  pdb=" N   ILE B 570 " --> pdb=" O   TRP B 566 " (cutoff:3.500A)

    522 hydrogen bonds defined for protein.
    1536 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.25

  Time building geometry restraints manager: 0.69 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1160
        1.30 -     1.43: 2123
        1.43 -     1.55: 5074
        1.55 -     1.68: 21
        1.68 -     1.81: 86
  Bond restraints: 8464
  Sorted by residual:
  bond pdb=" C   CYS A  82 "
       pdb=" O   CYS A  82 "
    ideal  model  delta    sigma   weight residual
    1.244  1.189  0.055 1.00e-02 1.00e+04 2.97e+01
  bond pdb=" C   PRO A  83 "
       pdb=" O   PRO A  83 "
    ideal  model  delta    sigma   weight residual
    1.237  1.173  0.064 1.32e-02 5.74e+03 2.34e+01
  bond pdb=" C   GLN B  84 "
       pdb=" O   GLN B  84 "
    ideal  model  delta    sigma   weight residual
    1.236  1.175  0.061 1.28e-02 6.10e+03 2.27e+01
  bond pdb=" C   PHE B  86 "
       pdb=" O   PHE B  86 "
    ideal  model  delta    sigma   weight residual
    1.235  1.172  0.063 1.41e-02 5.03e+03 1.99e+01
  bond pdb=" C   ASP B  88 "
       pdb=" O   ASP B  88 "
    ideal  model  delta    sigma   weight residual
    1.236  1.185  0.051 1.25e-02 6.40e+03 1.70e+01
  ... (remaining 8459 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.53: 11380
        2.53 -     5.07: 169
        5.07 -     7.60: 24
        7.60 -    10.14: 6
       10.14 -    12.67: 1
  Bond angle restraints: 11580
  Sorted by residual:
  angle pdb=" C   THR A  89 "
        pdb=" CA  THR A  89 "
        pdb=" CB  THR A  89 "
      ideal   model   delta    sigma   weight residual
     110.68  123.35  -12.67 1.70e+00 3.46e-01 5.56e+01
  angle pdb=" C   LYS A  80 "
        pdb=" CA  LYS A  80 "
        pdb=" CB  LYS A  80 "
      ideal   model   delta    sigma   weight residual
     109.02  118.32   -9.30 1.68e+00 3.54e-01 3.06e+01
  angle pdb=" C   ASP A  88 "
        pdb=" CA  ASP A  88 "
        pdb=" CB  ASP A  88 "
      ideal   model   delta    sigma   weight residual
     110.63  119.94   -9.31 1.85e+00 2.92e-01 2.53e+01
  angle pdb=" CA  ASP A  88 "
        pdb=" CB  ASP A  88 "
        pdb=" CG  ASP A  88 "
      ideal   model   delta    sigma   weight residual
     112.60  117.17   -4.57 1.00e+00 1.00e+00 2.09e+01
  angle pdb=" C   LEU A  87 "
        pdb=" N   ASP A  88 "
        pdb=" CA  ASP A  88 "
      ideal   model   delta    sigma   weight residual
     120.28  126.80   -6.52 1.44e+00 4.82e-01 2.05e+01
  ... (remaining 11575 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.62: 5228
       24.62 -    49.24: 230
       49.24 -    73.85: 42
       73.85 -    98.47: 8
       98.47 -   123.09: 8
  Dihedral angle restraints: 5516
    sinusoidal: 2654
      harmonic: 2862
  Sorted by residual:
  dihedral pdb=" C   THR A  89 "
           pdb=" N   THR A  89 "
           pdb=" CA  THR A  89 "
           pdb=" CB  THR A  89 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -137.51   15.51     0      2.50e+00 1.60e-01 3.85e+01
  dihedral pdb=" C   PHE A  86 "
           pdb=" N   PHE A  86 "
           pdb=" CA  PHE A  86 "
           pdb=" CB  PHE A  86 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -135.34   12.74     0      2.50e+00 1.60e-01 2.60e+01
  dihedral pdb=" N   PHE A  86 "
           pdb=" C   PHE A  86 "
           pdb=" CA  PHE A  86 "
           pdb=" CB  PHE A  86 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  133.98  -11.18     0      2.50e+00 1.60e-01 2.00e+01
  ... (remaining 5513 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.093: 1314
       0.093 -    0.187: 57
       0.187 -    0.280: 7
       0.280 -    0.373: 1
       0.373 -    0.467: 3
  Chirality restraints: 1382
  Sorted by residual:
  chirality pdb=" CA  PHE A  86 "
            pdb=" N   PHE A  86 "
            pdb=" C   PHE A  86 "
            pdb=" CB  PHE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.44e+00
  chirality pdb=" CA  PHE B  86 "
            pdb=" N   PHE B  86 "
            pdb=" C   PHE B  86 "
            pdb=" CB  PHE B  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.35e+00
  chirality pdb=" CA  THR A  89 "
            pdb=" N   THR A  89 "
            pdb=" C   THR A  89 "
            pdb=" CB  THR A  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.12    0.40 2.00e-01 2.50e+01 4.09e+00
  ... (remaining 1379 not shown)

  Planarity restraints: 1334
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B  88 "    0.014 2.00e-02 2.50e+03   2.98e-02 8.87e+00
        pdb=" C   ASP B  88 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   ASP B  88 "    0.019 2.00e-02 2.50e+03
        pdb=" N   THR B  89 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 528 "    0.046 5.00e-02 4.00e+02   6.92e-02 7.66e+00
        pdb=" N   PRO B 529 "   -0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO B 529 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 529 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 528 "   -0.046 5.00e-02 4.00e+02   6.91e-02 7.64e+00
        pdb=" N   PRO A 529 "    0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO A 529 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 529 "   -0.039 5.00e-02 4.00e+02
  ... (remaining 1331 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 70
        2.65 -     3.22: 7838
        3.22 -     3.78: 13014
        3.78 -     4.34: 18417
        4.34 -     4.90: 29602
  Nonbonded interactions: 68941
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 479 "
            pdb="NA    NA B 701 "
     model   vdw
     2.093 2.470
  nonbonded pdb=" O   THR A 479 "
            pdb="NA    NA A 701 "
     model   vdw
     2.209 2.470
  nonbonded pdb=" OD1 ASN B 484 "
            pdb="NA    NA B 701 "
     model   vdw
     2.209 2.470
  nonbonded pdb=" O   THR B 479 "
            pdb="NA    NA B 701 "
     model   vdw
     2.242 2.470
  nonbonded pdb=" OG1 THR A 479 "
            pdb="NA    NA A 701 "
     model   vdw
     2.256 2.470
  ... (remaining 68936 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.410
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   8464  Z= 0.253
  Angle     :  0.745  12.674  11580  Z= 0.393
  Chirality :  0.051   0.467   1382
  Planarity :  0.007   0.069   1334
  Dihedral  : 14.601 123.090   3656
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  0.36 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.43 %
  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:  1.41 (0.28), residues: 982
  helix:  1.26 (0.19), residues: 756
  sheet:  None (None), residues: 0
  loop :  0.09 (0.46), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 227 
 TYR   0.022   0.003   TYR B  85 
 PHE   0.025   0.002   PHE A 234 
 TRP   0.039   0.002   TRP A 231 
 HIS   0.001   0.000   HIS B 538 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 8464)
  covalent geometry    : angle       0.74544 (11580)
  hydrogen bonds       : bond        0.12876 (  522)
  hydrogen bonds       : angle       5.39806 ( 1536)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 185
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
REVERT: A  251 THR cc_start: 0.7592 (p) cc_final: 0.7385 (p)
REVERT: A  299 PHE cc_start: 0.8115 (t80) cc_final: 0.7776 (t80)
REVERT: A  510 MET cc_start: 0.7254 (mmt) cc_final: 0.5813 (mmt)
REVERT: B  510 MET cc_start: 0.7396 (mmt) cc_final: 0.7044 (mpt)
  outliers start: 6
  outliers final: 2
  residues processed: 188
  average time/residue: 0.4427
  time to fit residues: 89.2309
Evaluate side-chains
  141 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 139
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain B residue   86 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0970
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A 395 GLN
A 422 GLN
B 422 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.179059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.138187 restraints weight = 9352.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3600 rms_B_bonded: 1.67
r_work: 0.3499 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3395 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.1772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8464  Z= 0.138
  Angle     :  0.635   7.589  11580  Z= 0.304
  Chirality :  0.042   0.170   1382
  Planarity :  0.006   0.076   1334
  Dihedral  :  7.982  59.390   1894
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  :  9.93 %
    Favored  : 87.32 %
  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:  2.01 (0.28), residues: 982
  helix:  1.66 (0.19), residues: 758
  sheet:  None (None), residues: 0
  loop :  0.41 (0.48), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 227 
 TYR   0.014   0.001   TYR B 508 
 PHE   0.014   0.001   PHE A 478 
 TRP   0.016   0.002   TRP B 418 
 HIS   0.002   0.001   HIS B 538 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 8464)
  covalent geometry    : angle       0.63471 (11580)
  hydrogen bonds       : bond        0.03878 (  522)
  hydrogen bonds       : angle       4.14858 ( 1536)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 0.307 
Fit side-chains
REVERT: A   73 MET cc_start: 0.9012 (mtt) cc_final: 0.8759 (mtt)
REVERT: A   86 PHE cc_start: 0.9071 (OUTLIER) cc_final: 0.7854 (t80)
REVERT: A  131 MET cc_start: 0.7408 (mtp) cc_final: 0.7038 (mtm)
REVERT: A  299 PHE cc_start: 0.8088 (t80) cc_final: 0.7883 (t80)
REVERT: A  510 MET cc_start: 0.7348 (mmt) cc_final: 0.7016 (mpt)
REVERT: A  534 PHE cc_start: 0.6786 (m-80) cc_final: 0.6189 (m-80)
REVERT: A  546 ARG cc_start: 0.7222 (mtm110) cc_final: 0.5467 (mmm160)
REVERT: B   73 MET cc_start: 0.9014 (mtt) cc_final: 0.8804 (mtt)
REVERT: B   86 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.7788 (t80)
REVERT: B  259 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6894 (tp)
REVERT: B  444 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.7039 (pm20)
REVERT: B  510 MET cc_start: 0.7458 (mmt) cc_final: 0.7214 (mpt)
REVERT: B  540 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6969 (mp)
  outliers start: 23
  outliers final: 8
  residues processed: 149
  average time/residue: 0.4355
  time to fit residues: 69.9524
Evaluate side-chains
  136 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  286 MET
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  286 MET
Chi-restraints excluded: chain B residue  439 MET
Chi-restraints excluded: chain B residue  444 GLU
Chi-restraints excluded: chain B residue  461 ASN
Chi-restraints excluded: chain B residue  540 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 15 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 256 ASN
A 395 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.172726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.131735 restraints weight = 9376.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 1.65
r_work: 0.3411 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3305 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.2464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8464  Z= 0.174
  Angle     :  0.675  10.026  11580  Z= 0.324
  Chirality :  0.045   0.184   1382
  Planarity :  0.006   0.075   1334
  Dihedral  :  8.436  58.790   1894
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 12.56 %
    Favored  : 83.97 %
  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:  2.11 (0.28), residues: 982
  helix:  1.70 (0.19), residues: 754
  sheet:  None (None), residues: 0
  loop :  0.58 (0.48), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 227 
 TYR   0.012   0.001   TYR A 508 
 PHE   0.017   0.002   PHE A 534 
 TRP   0.019   0.002   TRP B 418 
 HIS   0.002   0.001   HIS A 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 8464)
  covalent geometry    : angle       0.67453 (11580)
  hydrogen bonds       : bond        0.04299 (  522)
  hydrogen bonds       : angle       4.09664 ( 1536)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 137
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A  118 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.6857 (mpp)
REVERT: A  131 MET cc_start: 0.7667 (mtp) cc_final: 0.7096 (mtm)
REVERT: A  228 ARG cc_start: 0.7062 (mtm-85) cc_final: 0.6588 (mpp80)
REVERT: A  299 PHE cc_start: 0.7929 (t80) cc_final: 0.7618 (t80)
REVERT: A  546 ARG cc_start: 0.7455 (mtm110) cc_final: 0.5618 (mmm160)
REVERT: B   86 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.7355 (t80)
REVERT: B  259 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6831 (tp)
REVERT: B  444 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7237 (pm20)
REVERT: B  510 MET cc_start: 0.7356 (mmt) cc_final: 0.7052 (mpt)
REVERT: B  546 ARG cc_start: 0.7181 (mtm110) cc_final: 0.5502 (mmm160)
  outliers start: 29
  outliers final: 9
  residues processed: 149
  average time/residue: 0.4195
  time to fit residues: 67.3867
Evaluate side-chains
  143 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 130
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  118 MET
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  286 MET
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  286 MET
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  444 GLU
Chi-restraints excluded: chain B residue  461 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 65 optimal weight:    4.9990
   chunk 12 optimal weight:    0.8980
   chunk 86 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 54 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 395 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.173495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.132894 restraints weight = 9472.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 1.66
r_work: 0.3429 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3324 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8464  Z= 0.146
  Angle     :  0.633   8.883  11580  Z= 0.303
  Chirality :  0.042   0.154   1382
  Planarity :  0.006   0.073   1334
  Dihedral  :  8.191  58.528   1894
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 14.83 %
    Favored  : 82.54 %
  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:  2.20 (0.28), residues: 982
  helix:  1.78 (0.19), residues: 756
  sheet:  None (None), residues: 0
  loop :  0.55 (0.48), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 329 
 TYR   0.010   0.001   TYR A 508 
 PHE   0.024   0.001   PHE B 234 
 TRP   0.020   0.002   TRP A 418 
 HIS   0.001   0.000   HIS B 538 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 8464)
  covalent geometry    : angle       0.63302 (11580)
  hydrogen bonds       : bond        0.03858 (  522)
  hydrogen bonds       : angle       3.95897 ( 1536)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A   34 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7918 (pt)
REVERT: A  118 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.6858 (mpp)
REVERT: A  131 MET cc_start: 0.7677 (mtp) cc_final: 0.7024 (mtm)
REVERT: A  227 ARG cc_start: 0.7255 (mtt180) cc_final: 0.6903 (mtt90)
REVERT: A  228 ARG cc_start: 0.7064 (mtm-85) cc_final: 0.6580 (mpp80)
REVERT: A  299 PHE cc_start: 0.7929 (t80) cc_final: 0.7651 (t80)
REVERT: A  510 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.6530 (mpt)
REVERT: A  546 ARG cc_start: 0.7544 (mtm110) cc_final: 0.5866 (mmm160)
REVERT: B   86 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.7328 (t80)
REVERT: B  259 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6796 (tp)
REVERT: B  280 ILE cc_start: 0.7111 (OUTLIER) cc_final: 0.6837 (tp)
REVERT: B  510 MET cc_start: 0.7363 (mmt) cc_final: 0.6988 (mpt)
REVERT: B  534 PHE cc_start: 0.6440 (m-80) cc_final: 0.6122 (m-80)
REVERT: B  544 MET cc_start: 0.6692 (ptm) cc_final: 0.6038 (ptm)
REVERT: B  546 ARG cc_start: 0.7193 (mtm110) cc_final: 0.5512 (mmm160)
  outliers start: 22
  outliers final: 11
  residues processed: 142
  average time/residue: 0.4045
  time to fit residues: 61.8336
Evaluate side-chains
  138 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  118 MET
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  286 MET
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain A residue  461 ASN
Chi-restraints excluded: chain A residue  510 MET
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  286 MET
Chi-restraints excluded: chain B residue  287 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 67 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0870
   chunk 96 optimal weight:    4.9990
   chunk 64 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 55 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.6158

-------------------------------------------------------------------------------
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 = 0.4003 r_free = 0.4003 target = 0.174185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.133414 restraints weight = 9426.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 1.68
r_work: 0.3442 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3336 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.2721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8464  Z= 0.132
  Angle     :  0.602   9.035  11580  Z= 0.288
  Chirality :  0.041   0.153   1382
  Planarity :  0.006   0.072   1334
  Dihedral  :  8.038  59.202   1894
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 15.55 %
    Favored  : 81.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.40 (0.28), residues: 982
  helix:  1.92 (0.19), residues: 758
  sheet:  None (None), residues: 0
  loop :  0.63 (0.48), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 227 
 TYR   0.012   0.001   TYR A 508 
 PHE   0.022   0.001   PHE B 234 
 TRP   0.019   0.002   TRP B 418 
 HIS   0.002   0.000   HIS A 538 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 8464)
  covalent geometry    : angle       0.60186 (11580)
  hydrogen bonds       : bond        0.03671 (  522)
  hydrogen bonds       : angle       3.86318 ( 1536)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 131
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A  118 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.6833 (mpp)
REVERT: A  131 MET cc_start: 0.7679 (mtp) cc_final: 0.7041 (mtm)
REVERT: A  227 ARG cc_start: 0.7264 (mtt180) cc_final: 0.6882 (mtt90)
REVERT: A  299 PHE cc_start: 0.7906 (t80) cc_final: 0.7654 (t80)
REVERT: A  503 ARG cc_start: 0.7273 (pmt-80) cc_final: 0.6896 (pmt-80)
REVERT: A  510 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.6543 (mpt)
REVERT: A  546 ARG cc_start: 0.7479 (mtm110) cc_final: 0.5623 (mmm160)
REVERT: B  259 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6872 (tp)
REVERT: B  280 ILE cc_start: 0.7147 (OUTLIER) cc_final: 0.6897 (tp)
REVERT: B  510 MET cc_start: 0.7469 (mmt) cc_final: 0.7194 (mpt)
REVERT: B  544 MET cc_start: 0.6287 (ptm) cc_final: 0.5959 (ptm)
REVERT: B  546 ARG cc_start: 0.7137 (mtm110) cc_final: 0.5522 (mmm160)
  outliers start: 26
  outliers final: 12
  residues processed: 140
  average time/residue: 0.3609
  time to fit residues: 55.0096
Evaluate side-chains
  140 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  118 MET
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  286 MET
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  461 ASN
Chi-restraints excluded: chain A residue  510 MET
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  286 MET
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  550 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 55 optimal weight:    1.9990
   chunk 96 optimal weight:    4.9990
   chunk 72 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.3975 r_free = 0.3975 target = 0.171396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.130670 restraints weight = 9332.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 1.65
r_work: 0.3400 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3293 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.2950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   8464  Z= 0.170
  Angle     :  0.661   9.240  11580  Z= 0.316
  Chirality :  0.044   0.169   1382
  Planarity :  0.006   0.072   1334
  Dihedral  :  8.409  59.283   1894
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.03 %
    Favored  : 81.10 %
  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:  2.25 (0.28), residues: 982
  helix:  1.80 (0.19), residues: 758
  sheet:  None (None), residues: 0
  loop :  0.62 (0.48), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 329 
 TYR   0.013   0.001   TYR A 508 
 PHE   0.027   0.002   PHE B 234 
 TRP   0.020   0.002   TRP B 418 
 HIS   0.001   0.000   HIS B 538 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 8464)
  covalent geometry    : angle       0.66144 (11580)
  hydrogen bonds       : bond        0.04035 (  522)
  hydrogen bonds       : angle       3.95814 ( 1536)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A  118 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.6804 (mpp)
REVERT: A  131 MET cc_start: 0.7795 (mtp) cc_final: 0.6951 (mtm)
REVERT: A  227 ARG cc_start: 0.7254 (mtt180) cc_final: 0.6773 (mtt90)
REVERT: A  234 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7716 (t80)
REVERT: A  299 PHE cc_start: 0.7936 (t80) cc_final: 0.7675 (t80)
REVERT: A  329 ARG cc_start: 0.7249 (mtm110) cc_final: 0.6977 (mtm110)
REVERT: A  510 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.6592 (mpt)
REVERT: A  546 ARG cc_start: 0.7792 (mtm110) cc_final: 0.6130 (mmm160)
REVERT: B   86 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.7417 (t80)
REVERT: B  259 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6756 (tp)
REVERT: B  280 ILE cc_start: 0.7187 (OUTLIER) cc_final: 0.6945 (tp)
REVERT: B  546 ARG cc_start: 0.7403 (mtm110) cc_final: 0.5723 (mmm160)
  outliers start: 24
  outliers final: 10
  residues processed: 140
  average time/residue: 0.3388
  time to fit residues: 51.6242
Evaluate side-chains
  139 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  118 MET
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  234 PHE
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  286 MET
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  461 ASN
Chi-restraints excluded: chain A residue  510 MET
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  286 MET
Chi-restraints excluded: chain B residue  287 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 83 optimal weight:    0.4980
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 73 optimal weight:    8.9990
   chunk 26 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   overall best weight:    1.2186

-------------------------------------------------------------------------------
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 = 0.3967 r_free = 0.3967 target = 0.170652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.129509 restraints weight = 9420.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 1.67
r_work: 0.3390 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3284 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.3083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   8464  Z= 0.181
  Angle     :  0.681   9.856  11580  Z= 0.327
  Chirality :  0.045   0.176   1382
  Planarity :  0.007   0.073   1334
  Dihedral  :  8.593  58.967   1894
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 16.27 %
    Favored  : 80.26 %
  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:  2.17 (0.28), residues: 982
  helix:  1.74 (0.19), residues: 756
  sheet:  None (None), residues: 0
  loop :  0.63 (0.48), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 329 
 TYR   0.016   0.002   TYR A 508 
 PHE   0.026   0.002   PHE B 234 
 TRP   0.021   0.002   TRP B 418 
 HIS   0.002   0.001   HIS A 538 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 8464)
  covalent geometry    : angle       0.68078 (11580)
  hydrogen bonds       : bond        0.04184 (  522)
  hydrogen bonds       : angle       4.01090 ( 1536)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 123
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A  118 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.6835 (mpp)
REVERT: A  131 MET cc_start: 0.7699 (mtp) cc_final: 0.6849 (mtm)
REVERT: A  227 ARG cc_start: 0.7193 (mtt180) cc_final: 0.6721 (mtt90)
REVERT: A  234 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.7747 (t80)
REVERT: A  510 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.6674 (mpt)
REVERT: A  546 ARG cc_start: 0.7694 (mtm110) cc_final: 0.6045 (mmm160)
REVERT: B    9 LYS cc_start: 0.7646 (mmmt) cc_final: 0.7014 (mppt)
REVERT: B   86 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.7382 (t80)
REVERT: B  259 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6745 (tp)
REVERT: B  280 ILE cc_start: 0.7128 (OUTLIER) cc_final: 0.6892 (tp)
REVERT: B  510 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.6660 (mpt)
REVERT: B  546 ARG cc_start: 0.7506 (mtm110) cc_final: 0.5871 (mmm160)
  outliers start: 29
  outliers final: 13
  residues processed: 139
  average time/residue: 0.4016
  time to fit residues: 60.8078
Evaluate side-chains
  137 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 SER
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  118 MET
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  234 PHE
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  286 MET
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  461 ASN
Chi-restraints excluded: chain A residue  510 MET
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  286 MET
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain B residue  510 MET
Chi-restraints excluded: chain B residue  522 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 81 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 29 optimal weight:    0.2980
   chunk 51 optimal weight:    0.6980
   chunk 48 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 5 optimal weight:    0.2980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3998 r_free = 0.3998 target = 0.173596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.132814 restraints weight = 9449.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3538 rms_B_bonded: 1.68
r_work: 0.3437 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3332 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.3022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8464  Z= 0.132
  Angle     :  0.629  10.168  11580  Z= 0.302
  Chirality :  0.043   0.234   1382
  Planarity :  0.006   0.074   1334
  Dihedral  :  8.287  59.339   1894
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 16.51 %
    Favored  : 80.14 %
  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:  2.33 (0.28), residues: 982
  helix:  1.84 (0.19), residues: 762
  sheet:  None (None), residues: 0
  loop :  0.70 (0.49), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 329 
 TYR   0.008   0.001   TYR B 508 
 PHE   0.026   0.001   PHE A 534 
 TRP   0.020   0.002   TRP B 418 
 HIS   0.001   0.000   HIS B 538 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 8464)
  covalent geometry    : angle       0.62861 (11580)
  hydrogen bonds       : bond        0.03698 (  522)
  hydrogen bonds       : angle       3.93515 ( 1536)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 132
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.6827 (mpp)
REVERT: A  131 MET cc_start: 0.7681 (mtp) cc_final: 0.6904 (mtm)
REVERT: A  227 ARG cc_start: 0.7275 (mtt180) cc_final: 0.6780 (mtt90)
REVERT: A  329 ARG cc_start: 0.7253 (mtm110) cc_final: 0.7007 (mtm110)
REVERT: A  503 ARG cc_start: 0.7405 (pmt-80) cc_final: 0.7081 (pmt-80)
REVERT: A  510 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.6581 (mpt)
REVERT: A  546 ARG cc_start: 0.7671 (mtm110) cc_final: 0.5992 (mmm160)
REVERT: B    9 LYS cc_start: 0.7607 (mmmt) cc_final: 0.6988 (mppt)
REVERT: B  280 ILE cc_start: 0.7219 (OUTLIER) cc_final: 0.6984 (tp)
REVERT: B  546 ARG cc_start: 0.7239 (mtm110) cc_final: 0.5630 (mmm160)
  outliers start: 28
  outliers final: 15
  residues processed: 148
  average time/residue: 0.4650
  time to fit residues: 74.4259
Evaluate side-chains
  143 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   60 SER
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  118 MET
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  286 MET
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  461 ASN
Chi-restraints excluded: chain A residue  510 MET
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  286 MET
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  544 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 7 optimal weight:    0.0980
   chunk 55 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 91 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9980
   chunk 72 optimal weight:    0.7980
   chunk 28 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.173065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.132729 restraints weight = 9407.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 1.66
r_work: 0.3428 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3323 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.3112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8464  Z= 0.142
  Angle     :  0.655   8.847  11580  Z= 0.313
  Chirality :  0.043   0.181   1382
  Planarity :  0.006   0.074   1334
  Dihedral  :  8.367  58.926   1894
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 17.46 %
    Favored  : 79.31 %
  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:  2.33 (0.28), residues: 982
  helix:  1.83 (0.19), residues: 760
  sheet:  None (None), residues: 0
  loop :  0.72 (0.49), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 329 
 TYR   0.009   0.001   TYR B 508 
 PHE   0.027   0.001   PHE A 534 
 TRP   0.021   0.002   TRP A 418 
 HIS   0.001   0.000   HIS A 538 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 8464)
  covalent geometry    : angle       0.65461 (11580)
  hydrogen bonds       : bond        0.03802 (  522)
  hydrogen bonds       : angle       3.98551 ( 1536)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 127
  time to evaluate  : 0.213 
Fit side-chains
REVERT: A  118 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.6874 (mpp)
REVERT: A  227 ARG cc_start: 0.7281 (mtt180) cc_final: 0.6803 (mtt90)
REVERT: A  280 ILE cc_start: 0.7290 (OUTLIER) cc_final: 0.6942 (tp)
REVERT: A  329 ARG cc_start: 0.7238 (mtm110) cc_final: 0.6982 (mtm110)
REVERT: A  423 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7666 (mt-10)
REVERT: A  503 ARG cc_start: 0.7421 (pmt-80) cc_final: 0.7091 (pmt-80)
REVERT: A  510 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.6571 (mpt)
REVERT: A  546 ARG cc_start: 0.7699 (mtm110) cc_final: 0.6020 (mmm160)
REVERT: B    9 LYS cc_start: 0.7597 (mmmt) cc_final: 0.6993 (mppt)
REVERT: B  280 ILE cc_start: 0.7282 (OUTLIER) cc_final: 0.7031 (tp)
REVERT: B  534 PHE cc_start: 0.6649 (m-80) cc_final: 0.6394 (m-80)
REVERT: B  546 ARG cc_start: 0.7128 (mtm110) cc_final: 0.5560 (mmm160)
  outliers start: 27
  outliers final: 14
  residues processed: 142
  average time/residue: 0.4390
  time to fit residues: 67.1099
Evaluate side-chains
  141 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   60 SER
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  118 MET
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  286 MET
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  461 ASN
Chi-restraints excluded: chain A residue  510 MET
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  286 MET
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  386 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 63 optimal weight:    0.5980
   chunk 5 optimal weight:    0.4980
   chunk 65 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 96 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 79 optimal weight:    0.8980
   chunk 82 optimal weight:    0.8980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3994 r_free = 0.3994 target = 0.173048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.131993 restraints weight = 9426.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 1.68
r_work: 0.3432 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3327 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.3111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8464  Z= 0.143
  Angle     :  0.679  12.345  11580  Z= 0.324
  Chirality :  0.044   0.272   1382
  Planarity :  0.006   0.075   1334
  Dihedral  :  8.407  59.738   1894
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 17.70 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.29 (0.28), residues: 982
  helix:  1.80 (0.19), residues: 762
  sheet:  None (None), residues: 0
  loop :  0.74 (0.50), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 329 
 TYR   0.009   0.001   TYR B 508 
 PHE   0.030   0.002   PHE B 478 
 TRP   0.020   0.002   TRP A 418 
 HIS   0.001   0.000   HIS A 538 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 8464)
  covalent geometry    : angle       0.67947 (11580)
  hydrogen bonds       : bond        0.03826 (  522)
  hydrogen bonds       : angle       4.02739 ( 1536)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A  118 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.6916 (mpp)
REVERT: A  227 ARG cc_start: 0.7279 (mtt180) cc_final: 0.6814 (mtt90)
REVERT: A  280 ILE cc_start: 0.7299 (OUTLIER) cc_final: 0.6961 (tp)
REVERT: A  329 ARG cc_start: 0.7227 (mtm110) cc_final: 0.6965 (mtm110)
REVERT: A  503 ARG cc_start: 0.7427 (pmt-80) cc_final: 0.7090 (pmt-80)
REVERT: A  510 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.6627 (mpt)
REVERT: A  546 ARG cc_start: 0.7757 (mtm110) cc_final: 0.6080 (mmm160)
REVERT: B    9 LYS cc_start: 0.7588 (mmmt) cc_final: 0.6970 (mppt)
REVERT: B  280 ILE cc_start: 0.7205 (OUTLIER) cc_final: 0.6965 (tp)
REVERT: B  546 ARG cc_start: 0.7106 (mtm110) cc_final: 0.5522 (mmm160)
  outliers start: 23
  outliers final: 16
  residues processed: 133
  average time/residue: 0.3752
  time to fit residues: 54.1098
Evaluate side-chains
  139 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   60 SER
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  118 MET
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  286 MET
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  461 ASN
Chi-restraints excluded: chain A residue  510 MET
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   86 PHE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  286 MET
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  386 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 81 optimal weight:    0.2980
   chunk 28 optimal weight:    4.9990
   chunk 69 optimal weight:    0.0470
   chunk 94 optimal weight:    0.8980
   chunk 40 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.6078

-------------------------------------------------------------------------------
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 = 0.4002 r_free = 0.4002 target = 0.173738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.133291 restraints weight = 9439.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 1.67
r_work: 0.3443 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3341 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.3158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8464  Z= 0.140
  Angle     :  0.682  19.397  11580  Z= 0.323
  Chirality :  0.043   0.173   1382
  Planarity :  0.006   0.075   1334
  Dihedral  :  8.367  59.540   1894
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 17.82 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.28 (0.28), residues: 982
  helix:  1.79 (0.19), residues: 762
  sheet:  None (None), residues: 0
  loop :  0.72 (0.50), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 329 
 TYR   0.008   0.001   TYR B 508 
 PHE   0.030   0.001   PHE B 478 
 TRP   0.020   0.002   TRP A 418 
 HIS   0.001   0.000   HIS A 538 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 8464)
  covalent geometry    : angle       0.68211 (11580)
  hydrogen bonds       : bond        0.03831 (  522)
  hydrogen bonds       : angle       4.02994 ( 1536)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3106.18 seconds
wall clock time: 53 minutes 30.72 seconds (3210.72 seconds total)