Starting phenix.real_space_refine
on Thu Jul  2 14:40:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y91_39066/07_2026/8y91_39066.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y91_39066/07_2026/8y91_39066.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.13
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y91_39066/07_2026/8y91_39066.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y91_39066/07_2026/8y91_39066.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y91_39066/07_2026/8y91_39066.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y91_39066/07_2026/8y91_39066.map"
  }
  resolution = 3.13
  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=   0.057
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     Cl      2      4.86       5
     Na      2      4.78       5
     C    6084      2.51       5
     N    1416      2.21       5
     O    1528      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9072
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "D"
      Number of atoms: 4516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 565, 4516
          Classifications: {'peptide': 565}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 544}
    Chain: "A"
      Number of atoms: 4516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 565, 4516
          Classifications: {'peptide': 565}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 544}
    Chain: "D"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 18
          Ad-hoc single atom residues: {' NA': 1, ' CL': 1}
          Unusual residues: {'A1LX5': 1}
          Classifications: {'undetermined': 1}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 18
          Ad-hoc single atom residues: {' NA': 1, ' CL': 1}
          Unusual residues: {'A1LX5': 1}
          Classifications: {'undetermined': 1}
          Chain breaks: 2
  Time building chain proxies: 2.15, per 1000 atoms: 0.24
  Number of scatterers: 9072
  At special positions: 0
  Unit cell: (78.11, 120.45, 89.79, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      2     17.00
     S      40     16.00
     Na      2     11.00
     O    1528      8.00
     N    1416      7.00
     C    6084      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: 0.84
  Conformation dependent library (CDL) restraints added in 325.2 milliseconds
  

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2076

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 0 sheets defined
      78.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'D' and resid 61 through 74
      removed outlier: 3.669A  pdb=" N   PHE D  65 " --> pdb=" O   LYS D  61 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 75 through 81
      removed outlier: 3.621A  pdb=" N   VAL D  79 " --> pdb=" O   ASP D  75 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 81 through 89
    Processing helix  chain 'D' and resid 90 through 93
    Processing helix  chain 'D' and resid 94 through 107
      removed outlier: 3.905A  pdb=" N   LEU D 100 " --> pdb=" O   ILE D  96 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 107 through 120
    Processing helix  chain 'D' and resid 124 through 133
      removed outlier: 3.835A  pdb=" N   VAL D 127 " --> pdb=" O   ALA D 124 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   TRP D 128 " --> pdb=" O   ALA D 125 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   LYS D 129 " --> pdb=" O   THR D 126 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   ILE D 130 " --> pdb=" O   VAL D 127 " (cutoff:3.500A)
      Proline residue:  D 132  - end of helix
    Processing helix  chain 'D' and resid 134 through 151
      removed outlier: 3.761A  pdb=" N   ILE D 142 " --> pdb=" O   GLY D 138 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLY D 149 " --> pdb=" O   ALA D 145 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   TYR D 151 " --> pdb=" O   TYR D 147 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 151 through 166
      removed outlier: 3.641A  pdb=" N   ILE D 156 " --> pdb=" O   TYR D 152 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   TYR D 162 " --> pdb=" O   TRP D 158 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 208 through 219
      removed outlier: 4.013A  pdb=" N   TYR D 214 " --> pdb=" O   ALA D 210 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   GLU D 215 " --> pdb=" O   ALA D 211 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 220 through 224
    Processing helix  chain 'D' and resid 234 through 253
    Processing helix  chain 'D' and resid 255 through 267
      removed outlier: 3.769A  pdb=" N   SER D 259 " --> pdb=" O   GLY D 255 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   LYS D 261 " --> pdb=" O   LYS D 257 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   TRP D 264 " --> pdb=" O   GLY D 260 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   ILE D 265 " --> pdb=" O   LYS D 261 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 268 through 283
      removed outlier: 3.554A  pdb=" N   PHE D 272 " --> pdb=" O   THR D 268 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   THR D 283 " --> pdb=" O   VAL D 279 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 286 through 295
      removed outlier: 3.652A  pdb=" N   GLY D 290 " --> pdb=" O   GLY D 286 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 303 through 320
      removed outlier: 4.838A  pdb=" N   ILE D 309 " --> pdb=" O   ALA D 305 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   ASP D 310 " --> pdb=" O   THR D 306 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   GLY D 320 " --> pdb=" O   PHE D 316 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 324 through 331
    Processing helix  chain 'D' and resid 338 through 372
      removed outlier: 3.610A  pdb=" N   ASP D 342 " --> pdb=" O   ASN D 338 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 375 through 380
      removed outlier: 3.930A  pdb=" N   VAL D 379 " --> pdb=" O   ASN D 375 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 383 through 389
      removed outlier: 3.730A  pdb=" N   VAL D 387 " --> pdb=" O   GLY D 383 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 390 through 398
      removed outlier: 3.684A  pdb=" N   THR D 397 " --> pdb=" O   GLU D 393 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU D 398 " --> pdb=" O   ALA D 394 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 400 through 435
      removed outlier: 3.704A  pdb=" N   TRP D 404 " --> pdb=" O   GLY D 400 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   SER D 419 " --> pdb=" O   LEU D 415 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 435 through 441
      removed outlier: 3.812A  pdb=" N   LYS D 439 " --> pdb=" O   PHE D 435 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 441 through 456
    Processing helix  chain 'D' and resid 464 through 494
      removed outlier: 3.866A  pdb=" N   VAL D 468 " --> pdb=" O   GLY D 464 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 497 through 509
    Processing helix  chain 'D' and resid 514 through 523
      removed outlier: 3.505A  pdb=" N   ARG D 518 " --> pdb=" O   GLY D 514 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 524 through 529
    Processing helix  chain 'D' and resid 530 through 539
    Processing helix  chain 'D' and resid 551 through 579
      removed outlier: 3.811A  pdb=" N   ASN D 555 " --> pdb=" O   PRO D 551 " (cutoff:3.500A)
      Proline residue:  D 570  - end of helix
    Processing helix  chain 'D' and resid 583 through 589
    Processing helix  chain 'D' and resid 598 through 604
      removed outlier: 3.929A  pdb=" N   ALA D 602 " --> pdb=" O   HIS D 598 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 610 through 615
      removed outlier: 4.030A  pdb=" N   TRP D 614 " --> pdb=" O   GLN D 610 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 74
      removed outlier: 3.661A  pdb=" N   PHE A  65 " --> pdb=" O   LYS A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 81
      removed outlier: 3.632A  pdb=" N   VAL A  79 " --> pdb=" O   ASP A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 89
    Processing helix  chain 'A' and resid 90 through 93
    Processing helix  chain 'A' and resid 94 through 107
      removed outlier: 3.914A  pdb=" N   LEU A 100 " --> pdb=" O   ILE A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 120
    Processing helix  chain 'A' and resid 124 through 128
      removed outlier: 3.824A  pdb=" N   VAL A 127 " --> pdb=" O   ALA A 124 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   TRP A 128 " --> pdb=" O   ALA A 125 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 124 through 128'
    Processing helix  chain 'A' and resid 131 through 133
      No H-bonds generated for 'chain 'A' and resid 131 through 133'
    Processing helix  chain 'A' and resid 134 through 151
      removed outlier: 3.764A  pdb=" N   ILE A 142 " --> pdb=" O   GLY A 138 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLY A 149 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   TYR A 151 " --> pdb=" O   TYR A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 166
      removed outlier: 3.640A  pdb=" N   ILE A 156 " --> pdb=" O   TYR A 152 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   TYR A 162 " --> pdb=" O   TRP A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 219
      removed outlier: 4.012A  pdb=" N   TYR A 214 " --> pdb=" O   ALA A 210 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLU A 215 " --> pdb=" O   ALA A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 224
    Processing helix  chain 'A' and resid 234 through 253
    Processing helix  chain 'A' and resid 255 through 267
      removed outlier: 3.762A  pdb=" N   SER A 259 " --> pdb=" O   GLY A 255 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   LYS A 261 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   TRP A 264 " --> pdb=" O   GLY A 260 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   ILE A 265 " --> pdb=" O   LYS A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 283
      removed outlier: 3.557A  pdb=" N   PHE A 272 " --> pdb=" O   THR A 268 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   THR A 283 " --> pdb=" O   VAL A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 295
      removed outlier: 3.653A  pdb=" N   GLY A 290 " --> pdb=" O   GLY A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 320
      removed outlier: 3.511A  pdb=" N   VAL A 307 " --> pdb=" O   LYS A 303 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   ILE A 309 " --> pdb=" O   ALA A 305 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   ASP A 310 " --> pdb=" O   THR A 306 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   GLY A 320 " --> pdb=" O   PHE A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
    Processing helix  chain 'A' and resid 338 through 372
      removed outlier: 3.617A  pdb=" N   ASP A 342 " --> pdb=" O   ASN A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 380
      removed outlier: 3.932A  pdb=" N   VAL A 379 " --> pdb=" O   ASN A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 389
      removed outlier: 3.722A  pdb=" N   VAL A 387 " --> pdb=" O   GLY A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 398
      removed outlier: 3.684A  pdb=" N   THR A 397 " --> pdb=" O   GLU A 393 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LEU A 398 " --> pdb=" O   ALA A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 435
      removed outlier: 3.707A  pdb=" N   TRP A 404 " --> pdb=" O   GLY A 400 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   SER A 419 " --> pdb=" O   LEU A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 441
      removed outlier: 3.816A  pdb=" N   LYS A 439 " --> pdb=" O   PHE A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 456
    Processing helix  chain 'A' and resid 464 through 494
      removed outlier: 3.864A  pdb=" N   VAL A 468 " --> pdb=" O   GLY A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 509
    Processing helix  chain 'A' and resid 514 through 523
      removed outlier: 3.527A  pdb=" N   ARG A 518 " --> pdb=" O   GLY A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 539
    Processing helix  chain 'A' and resid 551 through 579
      removed outlier: 3.809A  pdb=" N   ASN A 555 " --> pdb=" O   PRO A 551 " (cutoff:3.500A)
      Proline residue:  A 570  - end of helix
    Processing helix  chain 'A' and resid 583 through 589
    Processing helix  chain 'A' and resid 598 through 604
      removed outlier: 3.924A  pdb=" N   ALA A 602 " --> pdb=" O   HIS A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 615
      removed outlier: 4.036A  pdb=" N   TRP A 614 " --> pdb=" O   GLN A 610 " (cutoff:3.500A)

    546 hydrogen bonds defined for protein.
    1617 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: 1.01

  Time building geometry restraints manager: 1.07 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2671
        1.34 -     1.46: 2605
        1.46 -     1.58: 4026
        1.58 -     1.70: 2
        1.70 -     1.81: 62
  Bond restraints: 9366
  Sorted by residual:
  bond pdb=" C01 A1LX5 D 703 "
       pdb=" N02 A1LX5 D 703 "
    ideal  model  delta    sigma   weight residual
    1.444  1.290  0.154 2.00e-02 2.50e+03 5.93e+01
  bond pdb=" C01 A1LX5 A 701 "
       pdb=" N02 A1LX5 A 701 "
    ideal  model  delta    sigma   weight residual
    1.444  1.291  0.153 2.00e-02 2.50e+03 5.84e+01
  bond pdb=" C07 A1LX5 A 701 "
       pdb=" N02 A1LX5 A 701 "
    ideal  model  delta    sigma   weight residual
    1.444  1.375  0.069 2.00e-02 2.50e+03 1.19e+01
  bond pdb=" C07 A1LX5 D 703 "
       pdb=" N02 A1LX5 D 703 "
    ideal  model  delta    sigma   weight residual
    1.444  1.376  0.068 2.00e-02 2.50e+03 1.16e+01
  bond pdb=" C05 A1LX5 D 703 "
       pdb=" C06 A1LX5 D 703 "
    ideal  model  delta    sigma   weight residual
    1.391  1.325  0.066 2.00e-02 2.50e+03 1.10e+01
  ... (remaining 9361 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 12521
        1.64 -     3.27: 222
        3.27 -     4.91: 29
        4.91 -     6.54: 8
        6.54 -     8.18: 2
  Bond angle restraints: 12782
  Sorted by residual:
  angle pdb=" C   GLY D 106 "
        pdb=" N   MET D 107 "
        pdb=" CA  MET D 107 "
      ideal   model   delta    sigma   weight residual
     121.80  113.62    8.18 2.44e+00 1.68e-01 1.12e+01
  angle pdb=" C   GLY A 106 "
        pdb=" N   MET A 107 "
        pdb=" CA  MET A 107 "
      ideal   model   delta    sigma   weight residual
     121.80  113.65    8.15 2.44e+00 1.68e-01 1.12e+01
  angle pdb=" N   ASP D 546 "
        pdb=" CA  ASP D 546 "
        pdb=" C   ASP D 546 "
      ideal   model   delta    sigma   weight residual
     111.11  107.54    3.57 1.20e+00 6.94e-01 8.85e+00
  angle pdb=" N   ASP A 546 "
        pdb=" CA  ASP A 546 "
        pdb=" C   ASP A 546 "
      ideal   model   delta    sigma   weight residual
     111.11  107.59    3.52 1.20e+00 6.94e-01 8.63e+00
  angle pdb=" C   ASP D 546 "
        pdb=" CA  ASP D 546 "
        pdb=" CB  ASP D 546 "
      ideal   model   delta    sigma   weight residual
     110.81  115.42   -4.61 1.60e+00 3.91e-01 8.30e+00
  ... (remaining 12777 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.97: 4884
       14.97 -    29.93: 238
       29.93 -    44.90: 93
       44.90 -    59.86: 19
       59.86 -    74.83: 8
  Dihedral angle restraints: 5242
    sinusoidal: 1978
      harmonic: 3264
  Sorted by residual:
  dihedral pdb=" CA  THR A 179 "
           pdb=" C   THR A 179 "
           pdb=" N   TRP A 180 "
           pdb=" CA  TRP A 180 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -129.07  -50.93     0      5.00e+00 4.00e-02 1.04e+02
  dihedral pdb=" CA  THR D 179 "
           pdb=" C   THR D 179 "
           pdb=" N   TRP D 180 "
           pdb=" CA  TRP D 180 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -129.08  -50.92     0      5.00e+00 4.00e-02 1.04e+02
  dihedral pdb=" CA  HIS A 178 "
           pdb=" C   HIS A 178 "
           pdb=" N   THR A 179 "
           pdb=" CA  THR A 179 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.81   30.19     0      5.00e+00 4.00e-02 3.65e+01
  ... (remaining 5239 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.093: 1392
       0.093 -    0.185: 26
       0.185 -    0.278: 0
       0.278 -    0.371: 0
       0.371 -    0.464: 2
  Chirality restraints: 1420
  Sorted by residual:
  chirality pdb=" C04 A1LX5 D 703 "
            pdb=" C03 A1LX5 D 703 "
            pdb=" C05 A1LX5 D 703 "
            pdb=" C13 A1LX5 D 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.49    2.96   -0.46 2.00e-01 2.50e+01 5.37e+00
  chirality pdb=" C04 A1LX5 A 701 "
            pdb=" C03 A1LX5 A 701 "
            pdb=" C05 A1LX5 A 701 "
            pdb=" C13 A1LX5 A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.49    2.95   -0.46 2.00e-01 2.50e+01 5.30e+00
  chirality pdb=" CA  MET A 107 "
            pdb=" N   MET A 107 "
            pdb=" C   MET A 107 "
            pdb=" CB  MET A 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.88e-01
  ... (remaining 1417 not shown)

  Planarity restraints: 1556
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE D 104 "    0.011 2.00e-02 2.50e+03   2.22e-02 4.94e+00
        pdb=" C   ILE D 104 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   ILE D 104 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ALA D 105 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 104 "   -0.011 2.00e-02 2.50e+03   2.11e-02 4.45e+00
        pdb=" C   ILE A 104 "    0.036 2.00e-02 2.50e+03
        pdb=" O   ILE A 104 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ALA A 105 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 103 "   -0.010 2.00e-02 2.50e+03   1.94e-02 3.77e+00
        pdb=" C   ILE A 103 "    0.034 2.00e-02 2.50e+03
        pdb=" O   ILE A 103 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ILE A 104 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1553 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 44
        2.53 -     3.12: 7168
        3.12 -     3.72: 14844
        3.72 -     4.31: 20964
        4.31 -     4.90: 34263
  Nonbonded interactions: 77283
  Sorted by model distance:
  nonbonded pdb=" O   GLY A  71 "
            pdb="NA    NA A 702 "
     model   vdw
     1.938 3.210
  nonbonded pdb=" O   GLY D  71 "
            pdb="NA    NA D 701 "
     model   vdw
     2.046 3.210
  nonbonded pdb=" O   ALA A 476 "
            pdb=" OG  SER A 480 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" O   ALA D 476 "
            pdb=" OG  SER D 480 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   TRP D 264 "
            pdb=" OG1 THR D 268 "
     model   vdw
     2.267 3.040
  ... (remaining 77278 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' and resid 53 through 617)
  selection = (chain 'D' and resid 53 through 617)
}

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:             2.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.630
  Find NCS groups from input model:        0.160
  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:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6546
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   0.154   9366  Z= 0.199
  Angle     :  0.553   8.181  12782  Z= 0.332
  Chirality :  0.039   0.464   1420
  Planarity :  0.004   0.035   1556
  Dihedral  : 11.479  74.830   3166
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  :  6.93 %
    Favored  : 88.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.65 (0.24), residues: 1126
  helix: -0.80 (0.17), residues: 746
  sheet:  None (None), residues: 0
  loop : -1.42 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 216 
 TYR   0.013   0.001   TYR D  98 
 PHE   0.012   0.001   PHE A 362 
 TRP   0.007   0.001   TRP D 553 
 HIS   0.001   0.000   HIS D 222 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00370 /  0.20 ( 9366)
  covalent geometry    : angle       0.55347 /  0.33 (12782)
  hydrogen bonds       : bond        0.16178 / 10.32 (  546)
  hydrogen bonds       : angle       6.52136 /  4.60 ( 1617)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 278
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  119 TYR cc_start: 0.7341 (t80) cc_final: 0.6938 (t80)
REVERT: D  264 TRP cc_start: 0.5833 (m100) cc_final: 0.5394 (m-10)
REVERT: D  303 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6993 (ptmt)
REVERT: D  341 ARG cc_start: 0.7259 (ttp-110) cc_final: 0.6742 (ttm-80)
REVERT: D  344 LEU cc_start: 0.7082 (mt) cc_final: 0.6835 (mp)
REVERT: D  376 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.7933 (mt)
REVERT: D  507 GLN cc_start: 0.8029 (tt0) cc_final: 0.7709 (tt0)
REVERT: D  544 THR cc_start: 0.7020 (p) cc_final: 0.6751 (t)
REVERT: D  545 TYR cc_start: 0.6371 (t80) cc_final: 0.5415 (t80)
REVERT: A  119 TYR cc_start: 0.7339 (t80) cc_final: 0.6934 (t80)
REVERT: A  264 TRP cc_start: 0.5841 (m100) cc_final: 0.5385 (m-10)
REVERT: A  341 ARG cc_start: 0.7264 (ttp-110) cc_final: 0.6753 (ttm-80)
REVERT: A  344 LEU cc_start: 0.7073 (mt) cc_final: 0.6825 (mp)
REVERT: A  376 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.7951 (mt)
REVERT: A  507 GLN cc_start: 0.8028 (tt0) cc_final: 0.7703 (tt0)
REVERT: A  544 THR cc_start: 0.7022 (p) cc_final: 0.6769 (t)
REVERT: A  545 TYR cc_start: 0.6360 (t80) cc_final: 0.5450 (t80)
  outliers start: 48
  outliers final: 11
  residues processed: 313
  average time/residue: 0.0833
  time to fit residues: 37.4568
Evaluate side-chains
  174 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 160
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  173 TRP
Chi-restraints excluded: chain D residue  227 ILE
Chi-restraints excluded: chain D residue  303 LYS
Chi-restraints excluded: chain D residue  309 ILE
Chi-restraints excluded: chain D residue  315 ILE
Chi-restraints excluded: chain D residue  376 ILE
Chi-restraints excluded: chain D residue  598 HIS
Chi-restraints excluded: chain A residue  173 TRP
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  598 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    0.7980
   chunk 106 optimal weight:    0.8980
   overall best weight:    0.7780

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.190797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.166945 restraints weight = 11253.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.3921 rms_B_bonded: 1.58
r_work: 0.3833 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3716 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.2711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9366  Z= 0.148
  Angle     :  0.586   8.208  12782  Z= 0.296
  Chirality :  0.040   0.161   1420
  Planarity :  0.004   0.046   1556
  Dihedral  :  6.425  49.846   1276
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 14.18 %
    Favored  : 81.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.25), residues: 1126
  helix:  0.28 (0.18), residues: 764
  sheet:  None (None), residues: 0
  loop : -1.01 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  81 
 TYR   0.015   0.002   TYR D 575 
 PHE   0.022   0.002   PHE A  94 
 TRP   0.011   0.001   TRP D 128 
 HIS   0.008   0.001   HIS A 370 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.15 ( 9366)
  covalent geometry    : angle       0.58615 /  0.30 (12782)
  hydrogen bonds       : bond        0.04972 /  3.17 (  546)
  hydrogen bonds       : angle       5.09897 /  3.58 ( 1617)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 194
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  250 PHE cc_start: 0.8286 (m-10) cc_final: 0.7916 (m-80)
REVERT: D  264 TRP cc_start: 0.6489 (m100) cc_final: 0.5746 (m-10)
REVERT: D  376 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7571 (mt)
REVERT: D  585 TRP cc_start: 0.6101 (m100) cc_final: 0.5725 (m100)
REVERT: D  604 ARG cc_start: 0.5471 (tpt170) cc_final: 0.5214 (mtt-85)
REVERT: A  250 PHE cc_start: 0.8285 (m-10) cc_final: 0.7899 (m-80)
REVERT: A  264 TRP cc_start: 0.6539 (m100) cc_final: 0.5786 (m-10)
REVERT: A  376 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7622 (mt)
REVERT: A  545 TYR cc_start: 0.7364 (t80) cc_final: 0.7035 (t80)
REVERT: A  585 TRP cc_start: 0.6103 (m100) cc_final: 0.5741 (m100)
  outliers start: 37
  outliers final: 21
  residues processed: 219
  average time/residue: 0.0780
  time to fit residues: 24.9678
Evaluate side-chains
  189 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 166
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  173 TRP
Chi-restraints excluded: chain D residue  227 ILE
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  309 ILE
Chi-restraints excluded: chain D residue  315 ILE
Chi-restraints excluded: chain D residue  364 ILE
Chi-restraints excluded: chain D residue  376 ILE
Chi-restraints excluded: chain D residue  378 ASP
Chi-restraints excluded: chain D residue  417 LEU
Chi-restraints excluded: chain D residue  437 VAL
Chi-restraints excluded: chain D residue  598 HIS
Chi-restraints excluded: chain A residue  173 TRP
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  598 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 34 optimal weight:    0.4980
   chunk 80 optimal weight:    7.9990
   chunk 99 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   overall best weight:    1.0182

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.181966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.156663 restraints weight = 11241.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3800 rms_B_bonded: 1.61
r_work: 0.3700 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3573 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.3586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9366  Z= 0.159
  Angle     :  0.605   9.286  12782  Z= 0.305
  Chirality :  0.041   0.152   1420
  Planarity :  0.004   0.047   1556
  Dihedral  :  6.315  46.376   1272
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 14.92 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.25), residues: 1126
  helix:  0.59 (0.19), residues: 762
  sheet:  None (None), residues: 0
  loop : -0.78 (0.35), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 301 
 TYR   0.016   0.002   TYR A 152 
 PHE   0.021   0.002   PHE A 540 
 TRP   0.014   0.001   TRP A  80 
 HIS   0.005   0.001   HIS D 370 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00358 /  0.16 ( 9366)
  covalent geometry    : angle       0.60485 /  0.31 (12782)
  hydrogen bonds       : bond        0.05295 /  3.41 (  546)
  hydrogen bonds       : angle       5.23717 /  3.66 ( 1617)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 178
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   87 TYR cc_start: 0.8243 (t80) cc_final: 0.7968 (t80)
REVERT: D  264 TRP cc_start: 0.6535 (m100) cc_final: 0.5711 (m-10)
REVERT: D  298 ASP cc_start: 0.7350 (t70) cc_final: 0.6837 (t0)
REVERT: D  309 ILE cc_start: 0.7473 (OUTLIER) cc_final: 0.7142 (mp)
REVERT: D  376 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7589 (mt)
REVERT: D  585 TRP cc_start: 0.6116 (m100) cc_final: 0.5706 (m100)
REVERT: D  604 ARG cc_start: 0.5612 (tpt170) cc_final: 0.5247 (mtt-85)
REVERT: A  264 TRP cc_start: 0.6524 (m100) cc_final: 0.5698 (m-10)
REVERT: A  298 ASP cc_start: 0.7377 (t70) cc_final: 0.6846 (t0)
REVERT: A  376 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7593 (mt)
REVERT: A  585 TRP cc_start: 0.6026 (m100) cc_final: 0.5728 (m100)
  outliers start: 38
  outliers final: 20
  residues processed: 204
  average time/residue: 0.0724
  time to fit residues: 21.9585
Evaluate side-chains
  176 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 153
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  173 TRP
Chi-restraints excluded: chain D residue  227 ILE
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain D residue  309 ILE
Chi-restraints excluded: chain D residue  364 ILE
Chi-restraints excluded: chain D residue  376 ILE
Chi-restraints excluded: chain D residue  437 VAL
Chi-restraints excluded: chain D residue  481 ILE
Chi-restraints excluded: chain D residue  598 HIS
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  173 TRP
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  598 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 82 optimal weight:    0.5980
   chunk 95 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 96 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 17 optimal weight:    0.1980
   chunk 91 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 90 optimal weight:    0.0000
   overall best weight:    0.4784

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.185986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.161228 restraints weight = 11381.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3850 rms_B_bonded: 1.60
r_work: 0.3755 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3635 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.3790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9366  Z= 0.122
  Angle     :  0.552   9.784  12782  Z= 0.276
  Chirality :  0.038   0.138   1420
  Planarity :  0.004   0.034   1556
  Dihedral  :  5.930  44.831   1268
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 15.02 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.44 (0.26), residues: 1126
  helix:  0.85 (0.19), residues: 764
  sheet:  None (None), residues: 0
  loop : -0.77 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  81 
 TYR   0.015   0.001   TYR A 152 
 PHE   0.016   0.001   PHE D 316 
 TRP   0.011   0.001   TRP D  80 
 HIS   0.007   0.001   HIS A 372 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.12 ( 9366)
  covalent geometry    : angle       0.55185 /  0.28 (12782)
  hydrogen bonds       : bond        0.04634 /  3.04 (  546)
  hydrogen bonds       : angle       5.05475 /  3.54 ( 1617)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 177
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: D   87 TYR cc_start: 0.8230 (t80) cc_final: 0.7946 (t80)
REVERT: D  250 PHE cc_start: 0.8430 (m-10) cc_final: 0.8089 (m-80)
REVERT: D  264 TRP cc_start: 0.6484 (m100) cc_final: 0.5648 (m-10)
REVERT: D  309 ILE cc_start: 0.7473 (OUTLIER) cc_final: 0.7166 (mp)
REVERT: D  367 TYR cc_start: 0.8453 (t80) cc_final: 0.8214 (t80)
REVERT: D  376 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7468 (mt)
REVERT: D  585 TRP cc_start: 0.6116 (m100) cc_final: 0.5702 (m100)
REVERT: A  250 PHE cc_start: 0.8427 (m-10) cc_final: 0.8085 (m-80)
REVERT: A  264 TRP cc_start: 0.6443 (m100) cc_final: 0.5637 (m-10)
REVERT: A  309 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7052 (mp)
REVERT: A  376 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7519 (mt)
REVERT: A  585 TRP cc_start: 0.6050 (m100) cc_final: 0.5726 (m100)
  outliers start: 38
  outliers final: 26
  residues processed: 204
  average time/residue: 0.0840
  time to fit residues: 24.3864
Evaluate side-chains
  185 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 155
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   57 GLU
Chi-restraints excluded: chain D residue  126 THR
Chi-restraints excluded: chain D residue  173 TRP
Chi-restraints excluded: chain D residue  199 HIS
Chi-restraints excluded: chain D residue  227 ILE
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain D residue  309 ILE
Chi-restraints excluded: chain D residue  364 ILE
Chi-restraints excluded: chain D residue  376 ILE
Chi-restraints excluded: chain D residue  381 THR
Chi-restraints excluded: chain D residue  386 LEU
Chi-restraints excluded: chain D residue  437 VAL
Chi-restraints excluded: chain D residue  481 ILE
Chi-restraints excluded: chain D residue  529 LEU
Chi-restraints excluded: chain D residue  531 PHE
Chi-restraints excluded: chain D residue  598 HIS
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  173 TRP
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  598 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 51 optimal weight:    0.4980
   chunk 99 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 97 optimal weight:    0.6980
   chunk 79 optimal weight:    0.2980
   chunk 34 optimal weight:    0.0970
   chunk 67 optimal weight:    0.4980
   chunk 104 optimal weight:    0.8980
   chunk 24 optimal weight:   10.0000
   chunk 98 optimal weight:    0.5980
   overall best weight:    0.3978

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.187516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.163127 restraints weight = 11323.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3862 rms_B_bonded: 1.60
r_work: 0.3766 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3647 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.3939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9366  Z= 0.118
  Angle     :  0.540   8.181  12782  Z= 0.268
  Chirality :  0.038   0.143   1420
  Planarity :  0.004   0.033   1556
  Dihedral  :  5.816  44.504   1268
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 15.86 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.26), residues: 1126
  helix:  1.21 (0.19), residues: 748
  sheet:  None (None), residues: 0
  loop : -0.78 (0.34), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  81 
 TYR   0.015   0.001   TYR D 152 
 PHE   0.015   0.001   PHE A 511 
 TRP   0.007   0.001   TRP D 404 
 HIS   0.003   0.001   HIS D 220 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.12 ( 9366)
  covalent geometry    : angle       0.53968 /  0.27 (12782)
  hydrogen bonds       : bond        0.04515 /  2.98 (  546)
  hydrogen bonds       : angle       4.95991 /  3.47 ( 1617)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 170
  time to evaluate  : 0.221 
Fit side-chains
REVERT: D   87 TYR cc_start: 0.8187 (t80) cc_final: 0.7906 (t80)
REVERT: D  190 LEU cc_start: 0.7667 (tt) cc_final: 0.7401 (pp)
REVERT: D  250 PHE cc_start: 0.8372 (m-10) cc_final: 0.8033 (m-80)
REVERT: D  264 TRP cc_start: 0.6449 (m100) cc_final: 0.5592 (m-10)
REVERT: D  298 ASP cc_start: 0.7243 (t70) cc_final: 0.6673 (t0)
REVERT: D  309 ILE cc_start: 0.7440 (OUTLIER) cc_final: 0.7111 (mp)
REVERT: D  376 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7547 (mt)
REVERT: D  585 TRP cc_start: 0.6013 (m100) cc_final: 0.5706 (m100)
REVERT: A  250 PHE cc_start: 0.8397 (m-10) cc_final: 0.8038 (m-80)
REVERT: A  264 TRP cc_start: 0.6448 (m100) cc_final: 0.5601 (m-10)
REVERT: A  298 ASP cc_start: 0.7133 (t70) cc_final: 0.6523 (t0)
REVERT: A  309 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.7017 (mp)
REVERT: A  376 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7398 (mt)
REVERT: A  585 TRP cc_start: 0.6066 (m100) cc_final: 0.5716 (m100)
  outliers start: 37
  outliers final: 24
  residues processed: 189
  average time/residue: 0.0791
  time to fit residues: 21.5472
Evaluate side-chains
  188 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 160
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  126 THR
Chi-restraints excluded: chain D residue  173 TRP
Chi-restraints excluded: chain D residue  199 HIS
Chi-restraints excluded: chain D residue  227 ILE
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain D residue  309 ILE
Chi-restraints excluded: chain D residue  376 ILE
Chi-restraints excluded: chain D residue  381 THR
Chi-restraints excluded: chain D residue  437 VAL
Chi-restraints excluded: chain D residue  479 THR
Chi-restraints excluded: chain D residue  481 ILE
Chi-restraints excluded: chain D residue  598 HIS
Chi-restraints excluded: chain A residue  173 TRP
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain A residue  598 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 92 optimal weight:    0.9990
   chunk 72 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 47 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0980
   chunk 39 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 56 optimal weight:   10.0000
   chunk 97 optimal weight:    4.9990
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.6584

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.184603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.159955 restraints weight = 11291.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3832 rms_B_bonded: 1.59
r_work: 0.3734 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3615 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.4157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9366  Z= 0.131
  Angle     :  0.559  10.534  12782  Z= 0.276
  Chirality :  0.039   0.144   1420
  Planarity :  0.004   0.036   1556
  Dihedral  :  5.687  39.935   1266
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 16.18 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.26), residues: 1126
  helix:  1.22 (0.19), residues: 750
  sheet:  None (None), residues: 0
  loop : -0.81 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  81 
 TYR   0.020   0.001   TYR D 111 
 PHE   0.022   0.001   PHE D 540 
 TRP   0.008   0.001   TRP D  80 
 HIS   0.004   0.001   HIS A 220 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.13 ( 9366)
  covalent geometry    : angle       0.55905 /  0.28 (12782)
  hydrogen bonds       : bond        0.04810 /  3.16 (  546)
  hydrogen bonds       : angle       5.04780 /  3.53 ( 1617)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 164
  time to evaluate  : 0.257 
Fit side-chains
REVERT: D   87 TYR cc_start: 0.8196 (t80) cc_final: 0.7900 (t80)
REVERT: D  173 TRP cc_start: 0.6790 (OUTLIER) cc_final: 0.6482 (m-90)
REVERT: D  250 PHE cc_start: 0.8448 (m-10) cc_final: 0.8132 (m-80)
REVERT: D  264 TRP cc_start: 0.6487 (m100) cc_final: 0.5628 (m-10)
REVERT: D  298 ASP cc_start: 0.7301 (t70) cc_final: 0.6736 (t0)
REVERT: D  309 ILE cc_start: 0.7442 (OUTLIER) cc_final: 0.7165 (mp)
REVERT: D  376 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7412 (mt)
REVERT: D  585 TRP cc_start: 0.6069 (m100) cc_final: 0.5727 (m100)
REVERT: A  190 LEU cc_start: 0.7717 (tt) cc_final: 0.7065 (pp)
REVERT: A  250 PHE cc_start: 0.8470 (m-10) cc_final: 0.8144 (m-80)
REVERT: A  264 TRP cc_start: 0.6525 (m100) cc_final: 0.6254 (t60)
REVERT: A  298 ASP cc_start: 0.7226 (t70) cc_final: 0.6636 (t0)
REVERT: A  309 ILE cc_start: 0.7484 (OUTLIER) cc_final: 0.7167 (mp)
REVERT: A  376 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7556 (mt)
REVERT: A  433 ASP cc_start: 0.7310 (m-30) cc_final: 0.7041 (m-30)
  outliers start: 38
  outliers final: 27
  residues processed: 185
  average time/residue: 0.0794
  time to fit residues: 21.3312
Evaluate side-chains
  180 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 148
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  126 THR
Chi-restraints excluded: chain D residue  173 TRP
Chi-restraints excluded: chain D residue  199 HIS
Chi-restraints excluded: chain D residue  227 ILE
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain D residue  309 ILE
Chi-restraints excluded: chain D residue  364 ILE
Chi-restraints excluded: chain D residue  376 ILE
Chi-restraints excluded: chain D residue  381 THR
Chi-restraints excluded: chain D residue  386 LEU
Chi-restraints excluded: chain D residue  437 VAL
Chi-restraints excluded: chain D residue  479 THR
Chi-restraints excluded: chain D residue  481 ILE
Chi-restraints excluded: chain D residue  598 HIS
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  173 TRP
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain A residue  598 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 106 optimal weight:    0.7980
   chunk 26 optimal weight:    0.4980
   chunk 103 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 109 optimal weight:    0.8980
   chunk 46 optimal weight:    4.9990
   overall best weight:    0.7180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.183688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.158690 restraints weight = 11364.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3818 rms_B_bonded: 1.61
r_work: 0.3721 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3600 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.4271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9366  Z= 0.135
  Angle     :  0.565   9.615  12782  Z= 0.282
  Chirality :  0.039   0.139   1420
  Planarity :  0.004   0.036   1556
  Dihedral  :  5.734  39.541   1266
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 17.12 %
    Favored  : 79.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.26), residues: 1126
  helix:  1.27 (0.19), residues: 748
  sheet:  None (None), residues: 0
  loop : -0.75 (0.34), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  81 
 TYR   0.021   0.001   TYR A 111 
 PHE   0.023   0.002   PHE A 213 
 TRP   0.009   0.001   TRP D  80 
 HIS   0.005   0.001   HIS A 220 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.14 ( 9366)
  covalent geometry    : angle       0.56531 /  0.28 (12782)
  hydrogen bonds       : bond        0.04956 /  3.27 (  546)
  hydrogen bonds       : angle       5.10294 /  3.57 ( 1617)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 156
  time to evaluate  : 0.320 
Fit side-chains
REVERT: D  118 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.8021 (tt0)
REVERT: D  264 TRP cc_start: 0.6494 (m100) cc_final: 0.5640 (m-10)
REVERT: D  309 ILE cc_start: 0.7443 (OUTLIER) cc_final: 0.7183 (mp)
REVERT: D  376 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7516 (mt)
REVERT: A  173 TRP cc_start: 0.6876 (OUTLIER) cc_final: 0.6262 (m-90)
REVERT: A  190 LEU cc_start: 0.7884 (tt) cc_final: 0.7655 (pp)
REVERT: A  264 TRP cc_start: 0.6500 (m100) cc_final: 0.6250 (t60)
REVERT: A  298 ASP cc_start: 0.7200 (t70) cc_final: 0.6623 (t0)
REVERT: A  309 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7233 (mp)
REVERT: A  376 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7487 (mt)
  outliers start: 35
  outliers final: 26
  residues processed: 176
  average time/residue: 0.0832
  time to fit residues: 21.3698
Evaluate side-chains
  176 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 144
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  118 GLN
Chi-restraints excluded: chain D residue  126 THR
Chi-restraints excluded: chain D residue  190 LEU
Chi-restraints excluded: chain D residue  199 HIS
Chi-restraints excluded: chain D residue  227 ILE
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain D residue  309 ILE
Chi-restraints excluded: chain D residue  364 ILE
Chi-restraints excluded: chain D residue  376 ILE
Chi-restraints excluded: chain D residue  381 THR
Chi-restraints excluded: chain D residue  386 LEU
Chi-restraints excluded: chain D residue  437 VAL
Chi-restraints excluded: chain D residue  479 THR
Chi-restraints excluded: chain D residue  481 ILE
Chi-restraints excluded: chain D residue  598 HIS
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  173 TRP
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain A residue  598 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 85 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 7 optimal weight:    0.5980
   chunk 83 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 70 optimal weight:    0.0770
   chunk 56 optimal weight:    9.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.6338

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.183601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.158774 restraints weight = 11262.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3817 rms_B_bonded: 1.58
r_work: 0.3716 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3596 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.4350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9366  Z= 0.131
  Angle     :  0.573  12.634  12782  Z= 0.283
  Chirality :  0.039   0.140   1420
  Planarity :  0.004   0.034   1556
  Dihedral  :  5.592  39.665   1264
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 17.12 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.94 (0.26), residues: 1126
  helix:  1.28 (0.19), residues: 752
  sheet:  None (None), residues: 0
  loop : -0.65 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  81 
 TYR   0.019   0.001   TYR D 111 
 PHE   0.020   0.001   PHE A 213 
 TRP   0.009   0.001   TRP D  80 
 HIS   0.004   0.001   HIS A 220 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.13 ( 9366)
  covalent geometry    : angle       0.57269 /  0.28 (12782)
  hydrogen bonds       : bond        0.04882 /  3.23 (  546)
  hydrogen bonds       : angle       5.10173 /  3.58 ( 1617)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 146
  time to evaluate  : 0.356 
Fit side-chains
REVERT: D  118 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.8012 (tt0)
REVERT: D  173 TRP cc_start: 0.6740 (OUTLIER) cc_final: 0.6225 (m-90)
REVERT: D  264 TRP cc_start: 0.6447 (m100) cc_final: 0.6232 (t60)
REVERT: D  298 ASP cc_start: 0.7260 (t70) cc_final: 0.6601 (t0)
REVERT: D  309 ILE cc_start: 0.7437 (OUTLIER) cc_final: 0.7175 (mp)
REVERT: D  376 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7509 (mt)
REVERT: D  566 MET cc_start: 0.6853 (mpp) cc_final: 0.6593 (mpp)
REVERT: A  173 TRP cc_start: 0.6884 (OUTLIER) cc_final: 0.6205 (m-90)
REVERT: A  189 LYS cc_start: 0.7058 (pptt) cc_final: 0.6674 (pptt)
REVERT: A  190 LEU cc_start: 0.7849 (tt) cc_final: 0.7601 (pp)
REVERT: A  264 TRP cc_start: 0.6506 (m100) cc_final: 0.6287 (t60)
REVERT: A  309 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.7253 (mp)
REVERT: A  376 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7481 (mt)
  outliers start: 39
  outliers final: 27
  residues processed: 167
  average time/residue: 0.0821
  time to fit residues: 20.0857
Evaluate side-chains
  177 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 143
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  118 GLN
Chi-restraints excluded: chain D residue  126 THR
Chi-restraints excluded: chain D residue  173 TRP
Chi-restraints excluded: chain D residue  190 LEU
Chi-restraints excluded: chain D residue  199 HIS
Chi-restraints excluded: chain D residue  227 ILE
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain D residue  309 ILE
Chi-restraints excluded: chain D residue  364 ILE
Chi-restraints excluded: chain D residue  376 ILE
Chi-restraints excluded: chain D residue  379 VAL
Chi-restraints excluded: chain D residue  381 THR
Chi-restraints excluded: chain D residue  386 LEU
Chi-restraints excluded: chain D residue  437 VAL
Chi-restraints excluded: chain D residue  479 THR
Chi-restraints excluded: chain D residue  481 ILE
Chi-restraints excluded: chain D residue  598 HIS
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  173 TRP
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain A residue  598 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 14 optimal weight:    0.0170
   chunk 105 optimal weight:    0.0060
   chunk 62 optimal weight:    0.7980
   chunk 27 optimal weight:    0.5980
   chunk 44 optimal weight:    0.7980
   chunk 50 optimal weight:    0.4980
   chunk 10 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 95 optimal weight:    3.9990
   overall best weight:    0.3834

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.186784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.162406 restraints weight = 11291.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3858 rms_B_bonded: 1.58
r_work: 0.3762 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3646 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.4317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9366  Z= 0.117
  Angle     :  0.559  11.993  12782  Z= 0.274
  Chirality :  0.038   0.136   1420
  Planarity :  0.004   0.031   1556
  Dihedral  :  5.436  40.175   1264
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 17.65 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.26), residues: 1126
  helix:  1.41 (0.19), residues: 752
  sheet:  None (None), residues: 0
  loop : -0.65 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  81 
 TYR   0.017   0.001   TYR D 111 
 PHE   0.020   0.001   PHE A 213 
 TRP   0.007   0.001   TRP A 404 
 HIS   0.003   0.001   HIS A 220 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00249 /  0.12 ( 9366)
  covalent geometry    : angle       0.55899 /  0.27 (12782)
  hydrogen bonds       : bond        0.04504 /  3.00 (  546)
  hydrogen bonds       : angle       4.99125 /  3.50 ( 1617)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 163
  time to evaluate  : 0.209 
Fit side-chains
REVERT: D   87 TYR cc_start: 0.8193 (t80) cc_final: 0.7880 (t80)
REVERT: D  250 PHE cc_start: 0.8432 (m-10) cc_final: 0.8112 (m-80)
REVERT: D  264 TRP cc_start: 0.6452 (m100) cc_final: 0.6237 (t60)
REVERT: D  298 ASP cc_start: 0.7228 (t70) cc_final: 0.6586 (t0)
REVERT: D  309 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7179 (mp)
REVERT: D  376 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7568 (mt)
REVERT: D  566 MET cc_start: 0.6749 (mpp) cc_final: 0.6491 (mpp)
REVERT: A  107 MET cc_start: 0.7168 (mmt) cc_final: 0.6343 (mmt)
REVERT: A  173 TRP cc_start: 0.6798 (OUTLIER) cc_final: 0.6064 (m-90)
REVERT: A  250 PHE cc_start: 0.8456 (m-10) cc_final: 0.8125 (m-80)
REVERT: A  298 ASP cc_start: 0.7030 (t70) cc_final: 0.6386 (t0)
REVERT: A  309 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.7216 (mp)
REVERT: A  376 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7479 (mt)
  outliers start: 33
  outliers final: 24
  residues processed: 179
  average time/residue: 0.0827
  time to fit residues: 21.4690
Evaluate side-chains
  174 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 145
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  190 LEU
Chi-restraints excluded: chain D residue  199 HIS
Chi-restraints excluded: chain D residue  227 ILE
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain D residue  309 ILE
Chi-restraints excluded: chain D residue  364 ILE
Chi-restraints excluded: chain D residue  376 ILE
Chi-restraints excluded: chain D residue  379 VAL
Chi-restraints excluded: chain D residue  381 THR
Chi-restraints excluded: chain D residue  386 LEU
Chi-restraints excluded: chain D residue  437 VAL
Chi-restraints excluded: chain D residue  479 THR
Chi-restraints excluded: chain D residue  481 ILE
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  173 TRP
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  544 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 79 optimal weight:    5.9990
   chunk 36 optimal weight:    0.7980
   chunk 76 optimal weight:    6.9990
   chunk 37 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 105 optimal weight:    0.4980
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.8582

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.181781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.156523 restraints weight = 11304.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3794 rms_B_bonded: 1.60
r_work: 0.3692 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3573 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.4561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9366  Z= 0.146
  Angle     :  0.603  12.598  12782  Z= 0.296
  Chirality :  0.040   0.169   1420
  Planarity :  0.004   0.035   1556
  Dihedral  :  5.495  39.211   1260
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 17.96 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.26), residues: 1126
  helix:  1.20 (0.19), residues: 766
  sheet:  None (None), residues: 0
  loop : -0.69 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  81 
 TYR   0.021   0.001   TYR D 111 
 PHE   0.018   0.002   PHE A 213 
 TRP   0.012   0.001   TRP D  80 
 HIS   0.006   0.001   HIS A 220 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.15 ( 9366)
  covalent geometry    : angle       0.60282 /  0.30 (12782)
  hydrogen bonds       : bond        0.05156 /  3.38 (  546)
  hydrogen bonds       : angle       5.14601 /  3.60 ( 1617)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 145
  time to evaluate  : 0.350 
Fit side-chains
REVERT: D   87 TYR cc_start: 0.8242 (t80) cc_final: 0.7879 (t80)
REVERT: D  173 TRP cc_start: 0.6913 (OUTLIER) cc_final: 0.6387 (m-90)
REVERT: D  264 TRP cc_start: 0.6513 (m100) cc_final: 0.6281 (t60)
REVERT: D  298 ASP cc_start: 0.7322 (t70) cc_final: 0.6668 (t0)
REVERT: D  309 ILE cc_start: 0.7402 (OUTLIER) cc_final: 0.7130 (mp)
REVERT: D  376 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7582 (mt)
REVERT: A  298 ASP cc_start: 0.7289 (t70) cc_final: 0.6595 (t0)
REVERT: A  309 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.7259 (mp)
REVERT: A  376 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7557 (mt)
  outliers start: 33
  outliers final: 25
  residues processed: 163
  average time/residue: 0.0825
  time to fit residues: 19.8926
Evaluate side-chains
  173 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 143
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  173 TRP
Chi-restraints excluded: chain D residue  190 LEU
Chi-restraints excluded: chain D residue  199 HIS
Chi-restraints excluded: chain D residue  227 ILE
Chi-restraints excluded: chain D residue  230 ILE
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain D residue  309 ILE
Chi-restraints excluded: chain D residue  364 ILE
Chi-restraints excluded: chain D residue  376 ILE
Chi-restraints excluded: chain D residue  379 VAL
Chi-restraints excluded: chain D residue  381 THR
Chi-restraints excluded: chain D residue  386 LEU
Chi-restraints excluded: chain D residue  437 VAL
Chi-restraints excluded: chain D residue  479 THR
Chi-restraints excluded: chain D residue  481 ILE
Chi-restraints excluded: chain D residue  598 HIS
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  544 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   chunk 14 optimal weight:    0.2980
   chunk 76 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 111 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.1784

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.178059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.152129 restraints weight = 11224.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 1.62
r_work: 0.3635 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3512 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.4754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9366  Z= 0.170
  Angle     :  0.631  11.741  12782  Z= 0.315
  Chirality :  0.041   0.145   1420
  Planarity :  0.005   0.037   1556
  Dihedral  :  5.626  40.179   1258
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 18.17 %
    Favored  : 78.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.25), residues: 1126
  helix:  1.05 (0.19), residues: 764
  sheet:  None (None), residues: 0
  loop : -0.70 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  81 
 TYR   0.025   0.002   TYR D 111 
 PHE   0.020   0.002   PHE A 409 
 TRP   0.012   0.001   TRP D  80 
 HIS   0.006   0.001   HIS A 220 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00391 /  0.17 ( 9366)
  covalent geometry    : angle       0.63059 /  0.31 (12782)
  hydrogen bonds       : bond        0.05643 /  3.69 (  546)
  hydrogen bonds       : angle       5.27641 /  3.69 ( 1617)
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

===============================================================================
Job complete
usr+sys time: 2160.67 seconds
wall clock time: 37 minutes 26.74 seconds (2246.74 seconds total)