Starting phenix.real_space_refine
on Wed Feb  4 14:46:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ys8_39563/02_2026/8ys8_39563.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ys8_39563/02_2026/8ys8_39563.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ys8_39563/02_2026/8ys8_39563.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ys8_39563/02_2026/8ys8_39563.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ys8_39563/02_2026/8ys8_39563.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ys8_39563/02_2026/8ys8_39563.map"
  }
  resolution = 3.79
  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=   0.018 sd=   0.099
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     Cl      2      4.86       5
     C    7375      2.51       5
     N    1769      2.21       5
     O    1934      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11122
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 693, 5410
          Classifications: {'peptide': 693}
          Link IDs: {'PTRANS': 30, 'TRANS': 662}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 5390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 691, 5390
          Classifications: {'peptide': 691}
          Link IDs: {'PTRANS': 30, 'TRANS': 660}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 161
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 161
          Unusual residues: {'I2U': 1, 'Y01': 4}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "B"
      Number of atoms: 161
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 161
          Unusual residues: {'I2U': 1, 'Y01': 4}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 2.56, per 1000 atoms: 0.23
  Number of scatterers: 11122
  At special positions: 0
  Unit cell: (92.22, 126.14, 103.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      2     17.00
     S      42     16.00
     O    1934      8.00
     N    1769      7.00
     C    7375      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: 0.98
  Conformation dependent library (CDL) restraints added in 541.6 milliseconds
  

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2588

  Finding SS restraints...
    Secondary structure from input PDB file:
      67 helices and 6 sheets defined
      64.2% alpha, 4.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 58
    Processing helix  chain 'A' and resid 59 through 64
      removed outlier: 3.517A  pdb=" N   TRP A  63 " --> pdb=" O   PRO A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 95
      removed outlier: 6.137A  pdb=" N   LEU A  74 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
      removed outlier: 5.611A  pdb=" N   SER A  75 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   LEU A  92 " --> pdb=" O   VAL A  88 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ALA A  93 " --> pdb=" O   LEU A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 108
      removed outlier: 4.053A  pdb=" N   LEU A 106 " --> pdb=" O   PRO A 102 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   TYR A 107 " --> pdb=" O   VAL A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 120
      removed outlier: 3.646A  pdb=" N   PHE A 118 " --> pdb=" O   ILE A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 148
    Processing helix  chain 'A' and resid 169 through 196
      removed outlier: 4.167A  pdb=" N   ARG A 173 " --> pdb=" O   LEU A 169 " (cutoff:3.500A)
      removed outlier: 4.624A  pdb=" N   VAL A 174 " --> pdb=" O   ASP A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 205
      removed outlier: 3.940A  pdb=" N   VAL A 202 " --> pdb=" O   GLY A 199 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ILE A 203 " --> pdb=" O   PHE A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 225
    Processing helix  chain 'A' and resid 225 through 230
    Processing helix  chain 'A' and resid 242 through 252
      removed outlier: 3.787A  pdb=" N   VAL A 246 " --> pdb=" O   SER A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 257
    Processing helix  chain 'A' and resid 258 through 282
    Processing helix  chain 'A' and resid 291 through 308
    Processing helix  chain 'A' and resid 308 through 313
    Processing helix  chain 'A' and resid 333 through 339
      removed outlier: 3.572A  pdb=" N   GLN A 337 " --> pdb=" O   VAL A 333 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ASN A 338 " --> pdb=" O   GLU A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 364
      removed outlier: 3.948A  pdb=" N   PHE A 344 " --> pdb=" O   VAL A 340 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   GLY A 345 " --> pdb=" O   GLY A 341 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   VAL A 360 " --> pdb=" O   SER A 356 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   TYR A 361 " --> pdb=" O   VAL A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 388
    Processing helix  chain 'A' and resid 396 through 406
    Processing helix  chain 'A' and resid 411 through 427
    Processing helix  chain 'A' and resid 438 through 447
    Processing helix  chain 'A' and resid 447 through 453
      removed outlier: 4.082A  pdb=" N   MET A 451 " --> pdb=" O   ASN A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 456
      No H-bonds generated for 'chain 'A' and resid 454 through 456'
    Processing helix  chain 'A' and resid 457 through 463
      removed outlier: 3.668A  pdb=" N   ARG A 463 " --> pdb=" O   GLY A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 482
    Processing helix  chain 'A' and resid 484 through 504
      removed outlier: 3.814A  pdb=" N   ILE A 499 " --> pdb=" O   GLN A 495 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   VAL A 500 " --> pdb=" O   LEU A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 561
    Processing helix  chain 'A' and resid 563 through 585
    Processing helix  chain 'A' and resid 612 through 618
      removed outlier: 3.551A  pdb=" N   GLN A 618 " --> pdb=" O   VAL A 615 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 677
    Processing helix  chain 'A' and resid 687 through 696
      removed outlier: 3.640A  pdb=" N   ARG A 696 " --> pdb=" O   GLU A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 707
      No H-bonds generated for 'chain 'A' and resid 705 through 707'
    Processing helix  chain 'A' and resid 712 through 725
      removed outlier: 3.637A  pdb=" N   ALA A 716 " --> pdb=" O   THR A 712 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 43
      removed outlier: 3.635A  pdb=" N   VAL B  41 " --> pdb=" O   ASP B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 58
    Processing helix  chain 'B' and resid 59 through 64
      removed outlier: 3.542A  pdb=" N   TRP B  63 " --> pdb=" O   PRO B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 95
      removed outlier: 6.141A  pdb=" N   LEU B  74 " --> pdb=" O   LYS B  70 " (cutoff:3.500A)
      removed outlier: 5.690A  pdb=" N   SER B  75 " --> pdb=" O   GLU B  71 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   LEU B  92 " --> pdb=" O   VAL B  88 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   ALA B  93 " --> pdb=" O   LEU B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 109
      removed outlier: 4.119A  pdb=" N   LEU B 106 " --> pdb=" O   PRO B 102 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   TYR B 107 " --> pdb=" O   VAL B 103 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   SER B 109 " --> pdb=" O   GLY B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 120
      removed outlier: 3.653A  pdb=" N   PHE B 118 " --> pdb=" O   ILE B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 148
    Processing helix  chain 'B' and resid 171 through 196
    Processing helix  chain 'B' and resid 199 through 204
      removed outlier: 4.030A  pdb=" N   VAL B 202 " --> pdb=" O   GLY B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 225
    Processing helix  chain 'B' and resid 225 through 230
    Processing helix  chain 'B' and resid 241 through 252
      removed outlier: 3.515A  pdb=" N   LYS B 245 " --> pdb=" O   VAL B 241 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 257
    Processing helix  chain 'B' and resid 258 through 281
    Processing helix  chain 'B' and resid 291 through 308
    Processing helix  chain 'B' and resid 308 through 313
    Processing helix  chain 'B' and resid 333 through 339
      removed outlier: 3.607A  pdb=" N   GLN B 337 " --> pdb=" O   VAL B 333 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ASN B 338 " --> pdb=" O   GLU B 334 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   THR B 339 " --> pdb=" O   THR B 335 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 333 through 339'
    Processing helix  chain 'B' and resid 339 through 364
      removed outlier: 3.955A  pdb=" N   PHE B 344 " --> pdb=" O   VAL B 340 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLY B 345 " --> pdb=" O   GLY B 341 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   VAL B 360 " --> pdb=" O   SER B 356 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   TYR B 361 " --> pdb=" O   VAL B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 388
    Processing helix  chain 'B' and resid 396 through 406
    Processing helix  chain 'B' and resid 411 through 427
    Processing helix  chain 'B' and resid 438 through 447
    Processing helix  chain 'B' and resid 448 through 453
    Processing helix  chain 'B' and resid 454 through 456
      No H-bonds generated for 'chain 'B' and resid 454 through 456'
    Processing helix  chain 'B' and resid 457 through 463
      removed outlier: 3.652A  pdb=" N   ARG B 463 " --> pdb=" O   GLY B 459 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 482
    Processing helix  chain 'B' and resid 485 through 504
      removed outlier: 3.802A  pdb=" N   ALA B 489 " --> pdb=" O   GLY B 485 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ILE B 499 " --> pdb=" O   GLN B 495 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   VAL B 500 " --> pdb=" O   LEU B 496 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 548 through 561
    Processing helix  chain 'B' and resid 563 through 585
    Processing helix  chain 'B' and resid 612 through 618
      removed outlier: 3.534A  pdb=" N   GLN B 618 " --> pdb=" O   VAL B 615 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 660 through 677
    Processing helix  chain 'B' and resid 687 through 696
      removed outlier: 3.623A  pdb=" N   ARG B 696 " --> pdb=" O   GLU B 692 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 705 through 707
      No H-bonds generated for 'chain 'B' and resid 705 through 707'
    Processing helix  chain 'B' and resid 712 through 725
      removed outlier: 3.646A  pdb=" N   ALA B 716 " --> pdb=" O   THR B 712 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13
    Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522
    Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522
      removed outlier: 3.569A  pdb=" N   SER A 509 " --> pdb=" O   ARG A 539 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ARG A 539 " --> pdb=" O   SER A 509 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   ILE A 537 " --> pdb=" O   LEU A 511 " (cutoff:3.500A)
      removed outlier: 8.338A  pdb=" N   ASN A 513 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
      removed outlier: 12.547A  pdb=" N   VAL A 535 " --> pdb=" O   ASN A 513 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   LYS A 536 " --> pdb=" O   ILE A 650 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   ASP A 652 " --> pdb=" O   LYS A 536 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   PHE A 538 " --> pdb=" O   ASP A 652 " (cutoff:3.500A)
      removed outlier: 7.902A  pdb=" N   PHE A 710 " --> pdb=" O   VAL A 681 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   ILE A 683 " --> pdb=" O   PHE A 710 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 520 through 522
    Processing sheet with id=AA5, first strand: chain 'B' and resid 520 through 522
      removed outlier: 3.573A  pdb=" N   SER B 509 " --> pdb=" O   ARG B 539 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ARG B 539 " --> pdb=" O   SER B 509 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   ILE B 537 " --> pdb=" O   LEU B 511 " (cutoff:3.500A)
      removed outlier: 8.222A  pdb=" N   ASN B 513 " --> pdb=" O   VAL B 535 " (cutoff:3.500A)
      removed outlier: 12.515A  pdb=" N   VAL B 535 " --> pdb=" O   ASN B 513 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   LYS B 536 " --> pdb=" O   ILE B 650 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   ASP B 652 " --> pdb=" O   LYS B 536 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   PHE B 538 " --> pdb=" O   ASP B 652 " (cutoff:3.500A)
      removed outlier: 7.865A  pdb=" N   PHE B 710 " --> pdb=" O   VAL B 681 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   ILE B 683 " --> pdb=" O   PHE B 710 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 587 through 588
      removed outlier: 3.729A  pdb=" N   ILE B 595 " --> pdb=" O   GLN B 588 " (cutoff:3.500A)

    608 hydrogen bonds defined for protein.
    1776 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: 1.71

  Time building geometry restraints manager: 1.31 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1728
        1.31 -     1.44: 2892
        1.44 -     1.56: 6696
        1.56 -     1.69: 2
        1.69 -     1.82: 62
  Bond restraints: 11380
  Sorted by residual:
  bond pdb=" C19 I2U B 801 "
       pdb=" C20 I2U B 801 "
    ideal  model  delta    sigma   weight residual
    1.413  1.596 -0.183 2.00e-02 2.50e+03 8.34e+01
  bond pdb=" C19 I2U A 801 "
       pdb=" C20 I2U A 801 "
    ideal  model  delta    sigma   weight residual
    1.413  1.595 -0.182 2.00e-02 2.50e+03 8.28e+01
  bond pdb=" C18 I2U A 801 "
       pdb=" S2  I2U A 801 "
    ideal  model  delta    sigma   weight residual
    1.728  1.553  0.175 2.00e-02 2.50e+03 7.68e+01
  bond pdb=" C18 I2U B 801 "
       pdb=" S2  I2U B 801 "
    ideal  model  delta    sigma   weight residual
    1.728  1.555  0.173 2.00e-02 2.50e+03 7.52e+01
  bond pdb=" C21 I2U A 801 "
       pdb=" S2  I2U A 801 "
    ideal  model  delta    sigma   weight residual
    1.705  1.555  0.150 2.00e-02 2.50e+03 5.63e+01
  ... (remaining 11375 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.06: 15422
        4.06 -     8.12: 57
        8.12 -    12.18: 3
       12.18 -    16.23: 3
       16.23 -    20.29: 4
  Bond angle restraints: 15489
  Sorted by residual:
  angle pdb=" N6  I2U A 801 "
        pdb=" C11 I2U A 801 "
        pdb=" O3  I2U A 801 "
      ideal   model   delta    sigma   weight residual
     117.31  137.60  -20.29 3.00e+00 1.11e-01 4.58e+01
  angle pdb=" N6  I2U B 801 "
        pdb=" C11 I2U B 801 "
        pdb=" O3  I2U B 801 "
      ideal   model   delta    sigma   weight residual
     117.31  137.54  -20.23 3.00e+00 1.11e-01 4.55e+01
  angle pdb=" C10 I2U A 801 "
        pdb=" C11 I2U A 801 "
        pdb=" O3  I2U A 801 "
      ideal   model   delta    sigma   weight residual
     132.02  114.08   17.94 3.00e+00 1.11e-01 3.58e+01
  angle pdb=" C10 I2U B 801 "
        pdb=" C11 I2U B 801 "
        pdb=" O3  I2U B 801 "
      ideal   model   delta    sigma   weight residual
     132.02  114.11   17.91 3.00e+00 1.11e-01 3.57e+01
  angle pdb=" C18 I2U A 801 "
        pdb=" S2  I2U A 801 "
        pdb=" C21 I2U A 801 "
      ideal   model   delta    sigma   weight residual
      91.76  107.59  -15.83 3.00e+00 1.11e-01 2.78e+01
  ... (remaining 15484 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 6072
       17.99 -    35.97: 847
       35.97 -    53.96: 184
       53.96 -    71.95: 32
       71.95 -    89.93: 10
  Dihedral angle restraints: 7145
    sinusoidal: 3142
      harmonic: 4003
  Sorted by residual:
  dihedral pdb=" CA  ASP A 239 "
           pdb=" C   ASP A 239 "
           pdb=" N   PRO A 240 "
           pdb=" CA  PRO A 240 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.98  -29.02     0      5.00e+00 4.00e-02 3.37e+01
  dihedral pdb=" CA  ASP B 239 "
           pdb=" C   ASP B 239 "
           pdb=" N   PRO B 240 "
           pdb=" CA  PRO B 240 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.38  -23.62     0      5.00e+00 4.00e-02 2.23e+01
  dihedral pdb=" CA  ASN B  19 "
           pdb=" C   ASN B  19 "
           pdb=" N   ALA B  20 "
           pdb=" CA  ALA B  20 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.67   19.33     0      5.00e+00 4.00e-02 1.49e+01
  ... (remaining 7142 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 1663
       0.069 -    0.138: 182
       0.138 -    0.208: 3
       0.208 -    0.277: 0
       0.277 -    0.346: 1
  Chirality restraints: 1849
  Sorted by residual:
  chirality pdb=" CG  LEU B 270 "
            pdb=" CB  LEU B 270 "
            pdb=" CD1 LEU B 270 "
            pdb=" CD2 LEU B 270 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.24   -0.35 2.00e-01 2.50e+01 2.99e+00
  chirality pdb=" CG  LEU A 270 "
            pdb=" CB  LEU A 270 "
            pdb=" CD1 LEU A 270 "
            pdb=" CD2 LEU A 270 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 6.91e-01
  chirality pdb=" CA  ASP B 239 "
            pdb=" N   ASP B 239 "
            pdb=" C   ASP B 239 "
            pdb=" CB  ASP B 239 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.96e-01
  ... (remaining 1846 not shown)

  Planarity restraints: 1882
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 239 "    0.049 5.00e-02 4.00e+02   7.48e-02 8.95e+00
        pdb=" N   PRO A 240 "   -0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO A 240 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 240 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 239 "   -0.042 5.00e-02 4.00e+02   6.22e-02 6.20e+00
        pdb=" N   PRO B 240 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO B 240 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 240 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 635 "    0.038 5.00e-02 4.00e+02   5.82e-02 5.42e+00
        pdb=" N   PRO B 636 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO B 636 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B 636 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1879 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 521
        2.73 -     3.27: 11557
        3.27 -     3.81: 18807
        3.81 -     4.36: 20959
        4.36 -     4.90: 36188
  Nonbonded interactions: 88032
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 503 "
            pdb=" OH  TYR A 545 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" OG1 THR B 503 "
            pdb=" OH  TYR B 545 "
     model   vdw
     2.183 3.040
  nonbonded pdb=" OG1 THR A 475 "
            pdb=" OG  SER A 491 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" OG1 THR B 475 "
            pdb=" OG  SER B 491 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" OH  TYR A 365 "
            pdb=" OE2 GLU A 404 "
     model   vdw
     2.227 3.040
  ... (remaining 88027 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 8 through 31 or resid 35 through 805))
  selection = (chain 'B' and (resid 8 through 598 or resid 605 through 805))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.020
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.020
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
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      :  0.006   0.183  11380  Z= 0.281
  Angle     :  0.755  20.292  15489  Z= 0.351
  Chirality :  0.042   0.346   1849
  Planarity :  0.004   0.075   1882
  Dihedral  : 16.829  89.935   4557
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  5.20 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 35.71 %
    Favored  : 63.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.24), residues: 1366
  helix:  1.25 (0.19), residues: 813
  sheet:  1.24 (0.97), residues: 30
  loop : -1.11 (0.27), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 312 
 TYR   0.013   0.001   TYR B 107 
 PHE   0.017   0.001   PHE B 294 
 TRP   0.005   0.001   TRP B 631 
 HIS   0.003   0.000   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00569 (11380)
  covalent geometry    : angle       0.75507 (15489)
  hydrogen bonds       : bond        0.11673 (  604)
  hydrogen bonds       : angle       5.01925 ( 1776)

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

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

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 197
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A  270 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7868 (mm)
REVERT: B  451 MET cc_start: 0.7518 (tpp) cc_final: 0.6962 (tpt)
  outliers start: 7
  outliers final: 5
  residues processed: 198
  average time/residue: 0.0746
  time to fit residues: 23.2385
Evaluate side-chains
  194 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 188
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 HIS
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  644 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    0.7980
   chunk 124 optimal weight:   10.0000
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    6.9990
   chunk 55 optimal weight:   10.0000
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.149071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.111205 restraints weight = 17051.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.115140 restraints weight = 8531.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.117625 restraints weight = 5795.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.118713 restraints weight = 4720.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.119623 restraints weight = 4295.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.0566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11380  Z= 0.137
  Angle     :  0.587   8.065  15489  Z= 0.293
  Chirality :  0.041   0.273   1849
  Planarity :  0.004   0.075   1882
  Dihedral  :  7.459  54.429   2065
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  5.56 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 30.84 %
    Favored  : 64.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.24), residues: 1366
  helix:  1.30 (0.19), residues: 818
  sheet:  1.96 (0.99), residues: 34
  loop : -1.09 (0.28), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 389 
 TYR   0.011   0.001   TYR B 367 
 PHE   0.020   0.001   PHE B 309 
 TRP   0.006   0.001   TRP A  63 
 HIS   0.003   0.001   HIS B 714 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (11380)
  covalent geometry    : angle       0.58688 (15489)
  hydrogen bonds       : bond        0.03542 (  604)
  hydrogen bonds       : angle       4.35549 ( 1776)

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

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

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 215
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.7794 (pt) cc_final: 0.7495 (mm)
REVERT: A   90 GLN cc_start: 0.8651 (mt0) cc_final: 0.8391 (mt0)
REVERT: A  248 TYR cc_start: 0.8048 (t80) cc_final: 0.7693 (t80)
REVERT: A  343 CYS cc_start: 0.8575 (m) cc_final: 0.8054 (m)
REVERT: A  529 MET cc_start: 0.8177 (mmm) cc_final: 0.7879 (mmm)
REVERT: A  673 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7590 (pm20)
REVERT: B  270 LEU cc_start: 0.8095 (mm) cc_final: 0.7860 (mm)
REVERT: B  451 MET cc_start: 0.7652 (tpp) cc_final: 0.7264 (tpt)
REVERT: B  529 MET cc_start: 0.8322 (mmm) cc_final: 0.8095 (mmm)
REVERT: B  589 VAL cc_start: 0.6021 (OUTLIER) cc_final: 0.5741 (p)
  outliers start: 50
  outliers final: 26
  residues processed: 239
  average time/residue: 0.0866
  time to fit residues: 32.1076
Evaluate side-chains
  219 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 191
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 HIS
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  359 SER
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  455 PHE
Chi-restraints excluded: chain A residue  542 SER
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  613 ILE
Chi-restraints excluded: chain A residue  662 SER
Chi-restraints excluded: chain A residue  673 GLU
Chi-restraints excluded: chain A residue  687 ASP
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue  181 SER
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  486 LEU
Chi-restraints excluded: chain B residue  568 LEU
Chi-restraints excluded: chain B residue  589 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 99 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   chunk 35 optimal weight:    7.9990
   chunk 26 optimal weight:    0.0770
   chunk 19 optimal weight:    0.9980
   chunk 114 optimal weight:    2.9990
   chunk 94 optimal weight:   10.0000
   chunk 55 optimal weight:    9.9990
   chunk 42 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   overall best weight:    1.0140

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

Flipped N/Q/H residues before XYZ refinement:
** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.149502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.111855 restraints weight = 17091.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.115772 restraints weight = 8513.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.118226 restraints weight = 5779.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.119364 restraints weight = 4706.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.120305 restraints weight = 4269.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.0714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  11380  Z= 0.125
  Angle     :  0.566   9.091  15489  Z= 0.281
  Chirality :  0.041   0.149   1849
  Planarity :  0.004   0.072   1882
  Dihedral  :  7.085  51.980   2057
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  5.12 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 29.50 %
    Favored  : 65.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.24), residues: 1366
  helix:  1.29 (0.19), residues: 820
  sheet:  2.57 (1.00), residues: 34
  loop : -1.10 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 312 
 TYR   0.011   0.001   TYR B 367 
 PHE   0.013   0.001   PHE B 130 
 TRP   0.006   0.001   TRP B  63 
 HIS   0.003   0.001   HIS A 714 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (11380)
  covalent geometry    : angle       0.56613 (15489)
  hydrogen bonds       : bond        0.03372 (  604)
  hydrogen bonds       : angle       4.18398 ( 1776)

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

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

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 211
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 GLN cc_start: 0.8559 (mt0) cc_final: 0.8268 (mt0)
REVERT: A  248 TYR cc_start: 0.8068 (t80) cc_final: 0.7635 (t80)
REVERT: A  343 CYS cc_start: 0.8621 (m) cc_final: 0.8130 (m)
REVERT: A  529 MET cc_start: 0.8143 (mmm) cc_final: 0.7865 (mmm)
REVERT: A  673 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7586 (pm20)
REVERT: B  185 LEU cc_start: 0.9170 (tp) cc_final: 0.8858 (tp)
REVERT: B  529 MET cc_start: 0.8220 (mmm) cc_final: 0.7965 (mmm)
REVERT: B  673 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7689 (pm20)
  outliers start: 62
  outliers final: 35
  residues processed: 245
  average time/residue: 0.0849
  time to fit residues: 32.2725
Evaluate side-chains
  230 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 193
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  359 SER
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  455 PHE
Chi-restraints excluded: chain A residue  542 SER
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  613 ILE
Chi-restraints excluded: chain A residue  662 SER
Chi-restraints excluded: chain A residue  673 GLU
Chi-restraints excluded: chain A residue  687 ASP
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  486 LEU
Chi-restraints excluded: chain B residue  542 SER
Chi-restraints excluded: chain B residue  568 LEU
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  613 ILE
Chi-restraints excluded: chain B residue  673 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 100 optimal weight:    6.9990
   chunk 101 optimal weight:    2.9990
   chunk 136 optimal weight:    4.9990
   chunk 124 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9990
   chunk 14 optimal weight:    6.9990
   chunk 6 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9990
   chunk 108 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 102 optimal weight:    0.7980
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A  38 HIS
** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.147031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.108752 restraints weight = 17249.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.112669 restraints weight = 8691.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.114977 restraints weight = 5904.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.116388 restraints weight = 4864.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.116932 restraints weight = 4359.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.0927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11380  Z= 0.181
  Angle     :  0.612   8.088  15489  Z= 0.301
  Chirality :  0.042   0.154   1849
  Planarity :  0.004   0.069   1882
  Dihedral  :  6.838  53.807   2055
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  6.15 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 29.33 %
    Favored  : 64.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.24), residues: 1366
  helix:  1.28 (0.19), residues: 824
  sheet:  2.30 (0.99), residues: 36
  loop : -0.98 (0.28), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 579 
 TYR   0.014   0.001   TYR B 367 
 PHE   0.014   0.001   PHE B 130 
 TRP   0.006   0.001   TRP B  63 
 HIS   0.005   0.001   HIS A 714 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 (11380)
  covalent geometry    : angle       0.61159 (15489)
  hydrogen bonds       : bond        0.03471 (  604)
  hydrogen bonds       : angle       4.18797 ( 1776)

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

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

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 208
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 LEU cc_start: 0.5483 (OUTLIER) cc_final: 0.5280 (pp)
REVERT: A   39 LEU cc_start: 0.7839 (pt) cc_final: 0.7515 (mm)
REVERT: A  248 TYR cc_start: 0.8133 (t80) cc_final: 0.7688 (t80)
REVERT: A  270 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7855 (mm)
REVERT: A  343 CYS cc_start: 0.8666 (m) cc_final: 0.8182 (m)
REVERT: A  529 MET cc_start: 0.8172 (mmm) cc_final: 0.7913 (mmm)
REVERT: A  673 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7631 (pm20)
REVERT: B  107 TYR cc_start: 0.8536 (m-10) cc_final: 0.8312 (m-10)
REVERT: B  185 LEU cc_start: 0.9261 (tp) cc_final: 0.8930 (tp)
REVERT: B  529 MET cc_start: 0.8324 (mmm) cc_final: 0.8019 (mmm)
REVERT: B  589 VAL cc_start: 0.6241 (OUTLIER) cc_final: 0.5916 (p)
REVERT: B  673 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7693 (pm20)
  outliers start: 68
  outliers final: 42
  residues processed: 246
  average time/residue: 0.0824
  time to fit residues: 31.8663
Evaluate side-chains
  237 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 190
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   38 HIS
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  455 PHE
Chi-restraints excluded: chain A residue  542 SER
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  613 ILE
Chi-restraints excluded: chain A residue  662 SER
Chi-restraints excluded: chain A residue  673 GLU
Chi-restraints excluded: chain A residue  687 ASP
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   42 CYS
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  542 SER
Chi-restraints excluded: chain B residue  568 LEU
Chi-restraints excluded: chain B residue  589 VAL
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  613 ILE
Chi-restraints excluded: chain B residue  673 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 89 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9980
   chunk 110 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 104 optimal weight:    3.9990
   chunk 98 optimal weight:    0.6980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 447 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.149187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.111241 restraints weight = 16906.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.115188 restraints weight = 8474.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.117675 restraints weight = 5736.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.118796 restraints weight = 4667.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.119712 restraints weight = 4242.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.0948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11380  Z= 0.120
  Angle     :  0.586   8.750  15489  Z= 0.287
  Chirality :  0.041   0.149   1849
  Planarity :  0.004   0.067   1882
  Dihedral  :  6.738  51.233   2055
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  5.27 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 30.00 %
    Favored  : 64.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.69 (0.24), residues: 1366
  helix:  1.31 (0.19), residues: 817
  sheet:  2.62 (0.98), residues: 36
  loop : -1.11 (0.28), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 312 
 TYR   0.010   0.001   TYR B 367 
 PHE   0.015   0.001   PHE B 111 
 TRP   0.006   0.001   TRP B  63 
 HIS   0.007   0.001   HIS A  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (11380)
  covalent geometry    : angle       0.58629 (15489)
  hydrogen bonds       : bond        0.03303 (  604)
  hydrogen bonds       : angle       4.12687 ( 1776)

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

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

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 209
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.7932 (pt) cc_final: 0.7592 (mm)
REVERT: A  248 TYR cc_start: 0.8120 (t80) cc_final: 0.7641 (t80)
REVERT: A  270 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7904 (mm)
REVERT: A  343 CYS cc_start: 0.8679 (m) cc_final: 0.8259 (m)
REVERT: A  529 MET cc_start: 0.8074 (mmm) cc_final: 0.7769 (mmm)
REVERT: A  673 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7586 (pm20)
REVERT: B  185 LEU cc_start: 0.9185 (tp) cc_final: 0.8901 (tp)
REVERT: B  529 MET cc_start: 0.8128 (mmm) cc_final: 0.7894 (mmm)
REVERT: B  589 VAL cc_start: 0.6246 (OUTLIER) cc_final: 0.5946 (p)
REVERT: B  673 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7662 (pm20)
  outliers start: 65
  outliers final: 39
  residues processed: 247
  average time/residue: 0.0825
  time to fit residues: 31.9618
Evaluate side-chains
  232 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 189
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  455 PHE
Chi-restraints excluded: chain A residue  542 SER
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  613 ILE
Chi-restraints excluded: chain A residue  662 SER
Chi-restraints excluded: chain A residue  673 GLU
Chi-restraints excluded: chain A residue  687 ASP
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   42 CYS
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  486 LEU
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  542 SER
Chi-restraints excluded: chain B residue  568 LEU
Chi-restraints excluded: chain B residue  589 VAL
Chi-restraints excluded: chain B residue  613 ILE
Chi-restraints excluded: chain B residue  672 GLN
Chi-restraints excluded: chain B residue  673 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 99 optimal weight:    0.9990
   chunk 125 optimal weight:   10.0000
   chunk 13 optimal weight:    5.9990
   chunk 39 optimal weight:    5.9990
   chunk 56 optimal weight:    0.5980
   chunk 106 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 98 optimal weight:    0.0970
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.127591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.088536 restraints weight = 17193.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.091405 restraints weight = 10044.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.093288 restraints weight = 7356.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.094297 restraints weight = 6118.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.094956 restraints weight = 5567.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.1057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11380  Z= 0.115
  Angle     :  0.587   9.226  15489  Z= 0.287
  Chirality :  0.041   0.150   1849
  Planarity :  0.004   0.065   1882
  Dihedral  :  6.635  50.844   2055
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  5.34 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 30.00 %
    Favored  : 64.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.24), residues: 1366
  helix:  1.30 (0.19), residues: 815
  sheet:  3.05 (0.94), residues: 37
  loop : -1.04 (0.28), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 312 
 TYR   0.011   0.001   TYR B 107 
 PHE   0.014   0.001   PHE B 130 
 TRP   0.006   0.001   TRP B  63 
 HIS   0.005   0.001   HIS A  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (11380)
  covalent geometry    : angle       0.58680 (15489)
  hydrogen bonds       : bond        0.03200 (  604)
  hydrogen bonds       : angle       4.05279 ( 1776)

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

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

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 206
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 TYR cc_start: 0.8109 (t80) cc_final: 0.7656 (t80)
REVERT: A  270 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7959 (mm)
REVERT: A  343 CYS cc_start: 0.8654 (m) cc_final: 0.8251 (m)
REVERT: A  410 THR cc_start: 0.9508 (t) cc_final: 0.9255 (m)
REVERT: A  529 MET cc_start: 0.8071 (mmm) cc_final: 0.7834 (mmm)
REVERT: A  673 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7561 (pm20)
REVERT: B  185 LEU cc_start: 0.9224 (tp) cc_final: 0.8934 (tp)
REVERT: B  248 TYR cc_start: 0.7950 (t80) cc_final: 0.7493 (t80)
REVERT: B  270 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7610 (mm)
REVERT: B  309 PHE cc_start: 0.8388 (m-80) cc_final: 0.8083 (m-80)
REVERT: B  410 THR cc_start: 0.9500 (t) cc_final: 0.9263 (m)
REVERT: B  529 MET cc_start: 0.8096 (mmm) cc_final: 0.7786 (mmm)
REVERT: B  589 VAL cc_start: 0.6153 (OUTLIER) cc_final: 0.5869 (p)
REVERT: B  673 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7598 (pm20)
  outliers start: 64
  outliers final: 43
  residues processed: 245
  average time/residue: 0.0798
  time to fit residues: 30.7843
Evaluate side-chains
  241 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 193
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  304 SER
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  359 SER
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  455 PHE
Chi-restraints excluded: chain A residue  542 SER
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  613 ILE
Chi-restraints excluded: chain A residue  662 SER
Chi-restraints excluded: chain A residue  673 GLU
Chi-restraints excluded: chain A residue  687 ASP
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   42 CYS
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  181 SER
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  486 LEU
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  542 SER
Chi-restraints excluded: chain B residue  568 LEU
Chi-restraints excluded: chain B residue  589 VAL
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  613 ILE
Chi-restraints excluded: chain B residue  672 GLN
Chi-restraints excluded: chain B residue  673 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 70 optimal weight:    6.9990
   chunk 19 optimal weight:    0.8980
   chunk 99 optimal weight:    0.4980
   chunk 100 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9990
   chunk 132 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9980
   chunk 83 optimal weight:    0.7980
   chunk 133 optimal weight:    2.9990
   chunk 130 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  38 HIS
A 504 GLN
** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.138048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.100762 restraints weight = 16704.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.104010 restraints weight = 9176.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.106159 restraints weight = 6470.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.107116 restraints weight = 5307.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.108017 restraints weight = 4808.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.1107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11380  Z= 0.120
  Angle     :  0.595   8.586  15489  Z= 0.292
  Chirality :  0.041   0.150   1849
  Planarity :  0.004   0.063   1882
  Dihedral  :  6.553  50.660   2055
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  5.49 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  5.55 %
    Allowed  : 30.84 %
    Favored  : 63.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.24), residues: 1366
  helix:  1.29 (0.19), residues: 816
  sheet:  3.17 (0.94), residues: 36
  loop : -1.02 (0.28), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 312 
 TYR   0.010   0.001   TYR B 367 
 PHE   0.019   0.001   PHE B 282 
 TRP   0.005   0.001   TRP A  63 
 HIS   0.002   0.000   HIS B 714 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (11380)
  covalent geometry    : angle       0.59507 (15489)
  hydrogen bonds       : bond        0.03188 (  604)
  hydrogen bonds       : angle       4.02478 ( 1776)

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

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

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 209
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 GLN cc_start: 0.8559 (mt0) cc_final: 0.8306 (mt0)
REVERT: A  248 TYR cc_start: 0.8065 (t80) cc_final: 0.7644 (t80)
REVERT: A  332 ASP cc_start: 0.8018 (m-30) cc_final: 0.7720 (m-30)
REVERT: A  343 CYS cc_start: 0.8624 (m) cc_final: 0.8254 (m)
REVERT: A  410 THR cc_start: 0.9512 (t) cc_final: 0.9259 (m)
REVERT: A  529 MET cc_start: 0.7925 (mmm) cc_final: 0.7674 (mmm)
REVERT: A  673 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7541 (pm20)
REVERT: B  185 LEU cc_start: 0.9217 (tp) cc_final: 0.8914 (tp)
REVERT: B  248 TYR cc_start: 0.7982 (t80) cc_final: 0.7525 (t80)
REVERT: B  270 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7547 (mm)
REVERT: B  309 PHE cc_start: 0.8274 (m-80) cc_final: 0.7982 (m-80)
REVERT: B  529 MET cc_start: 0.8120 (mmm) cc_final: 0.7730 (mmm)
REVERT: B  589 VAL cc_start: 0.6117 (OUTLIER) cc_final: 0.5851 (p)
REVERT: B  673 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7637 (pm20)
  outliers start: 66
  outliers final: 48
  residues processed: 247
  average time/residue: 0.0758
  time to fit residues: 29.2668
Evaluate side-chains
  246 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 194
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  304 SER
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  359 SER
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  455 PHE
Chi-restraints excluded: chain A residue  542 SER
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  613 ILE
Chi-restraints excluded: chain A residue  673 GLU
Chi-restraints excluded: chain A residue  687 ASP
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   42 CYS
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  181 SER
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  486 LEU
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  542 SER
Chi-restraints excluded: chain B residue  568 LEU
Chi-restraints excluded: chain B residue  589 VAL
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  613 ILE
Chi-restraints excluded: chain B residue  672 GLN
Chi-restraints excluded: chain B residue  673 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 132 optimal weight:    3.9990
   chunk 124 optimal weight:    8.9990
   chunk 110 optimal weight:    3.9990
   chunk 128 optimal weight:    9.9990
   chunk 25 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 91 optimal weight:    1.9990
   chunk 109 optimal weight:    3.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.125892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.086614 restraints weight = 17328.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.089436 restraints weight = 10280.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.091224 restraints weight = 7569.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.092018 restraints weight = 6365.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.092018 restraints weight = 5839.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.1196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  11380  Z= 0.151
  Angle     :  0.614   8.529  15489  Z= 0.301
  Chirality :  0.042   0.154   1849
  Planarity :  0.004   0.062   1882
  Dihedral  :  6.478  50.814   2053
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  5.93 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 30.59 %
    Favored  : 63.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.24), residues: 1366
  helix:  1.28 (0.19), residues: 816
  sheet:  3.19 (0.94), residues: 36
  loop : -1.04 (0.28), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 312 
 TYR   0.012   0.001   TYR B 367 
 PHE   0.014   0.001   PHE B 130 
 TRP   0.006   0.001   TRP A  63 
 HIS   0.004   0.001   HIS B 714 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 (11380)
  covalent geometry    : angle       0.61426 (15489)
  hydrogen bonds       : bond        0.03259 (  604)
  hydrogen bonds       : angle       4.03900 ( 1776)

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

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

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 197
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 TYR cc_start: 0.8062 (t80) cc_final: 0.7663 (t80)
REVERT: A  332 ASP cc_start: 0.8086 (m-30) cc_final: 0.7774 (m-30)
REVERT: A  343 CYS cc_start: 0.8750 (m) cc_final: 0.8282 (m)
REVERT: A  529 MET cc_start: 0.7975 (mmm) cc_final: 0.7627 (mmm)
REVERT: A  673 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7581 (pm20)
REVERT: B  185 LEU cc_start: 0.9273 (tp) cc_final: 0.8984 (tp)
REVERT: B  248 TYR cc_start: 0.7994 (t80) cc_final: 0.7522 (t80)
REVERT: B  270 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7534 (mm)
REVERT: B  309 PHE cc_start: 0.8401 (m-80) cc_final: 0.7994 (m-80)
REVERT: B  516 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7443 (mmm160)
REVERT: B  589 VAL cc_start: 0.6273 (OUTLIER) cc_final: 0.6003 (p)
REVERT: B  673 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7663 (pm20)
  outliers start: 65
  outliers final: 49
  residues processed: 236
  average time/residue: 0.0791
  time to fit residues: 28.7410
Evaluate side-chains
  246 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 192
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  304 SER
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  359 SER
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  455 PHE
Chi-restraints excluded: chain A residue  495 GLN
Chi-restraints excluded: chain A residue  542 SER
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  613 ILE
Chi-restraints excluded: chain A residue  664 VAL
Chi-restraints excluded: chain A residue  673 GLU
Chi-restraints excluded: chain A residue  687 ASP
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   42 CYS
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  181 SER
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  486 LEU
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  516 ARG
Chi-restraints excluded: chain B residue  542 SER
Chi-restraints excluded: chain B residue  568 LEU
Chi-restraints excluded: chain B residue  589 VAL
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  613 ILE
Chi-restraints excluded: chain B residue  664 VAL
Chi-restraints excluded: chain B residue  673 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 131 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 84 optimal weight:    0.7980
   chunk 110 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 133 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 52 optimal weight:    0.5980
   chunk 69 optimal weight:    3.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.128149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.088842 restraints weight = 17003.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.091851 restraints weight = 9829.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.093771 restraints weight = 7115.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.094837 restraints weight = 5934.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.095295 restraints weight = 5379.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.1255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11380  Z= 0.121
  Angle     :  0.609   8.788  15489  Z= 0.297
  Chirality :  0.041   0.151   1849
  Planarity :  0.004   0.063   1882
  Dihedral  :  6.409  50.525   2053
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  5.71 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 30.84 %
    Favored  : 64.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.68 (0.24), residues: 1366
  helix:  1.25 (0.19), residues: 816
  sheet:  3.35 (0.97), residues: 35
  loop : -1.05 (0.28), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 312 
 TYR   0.010   0.001   TYR B 367 
 PHE   0.015   0.001   PHE B 282 
 TRP   0.005   0.001   TRP A  63 
 HIS   0.003   0.001   HIS A  25 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (11380)
  covalent geometry    : angle       0.60876 (15489)
  hydrogen bonds       : bond        0.03201 (  604)
  hydrogen bonds       : angle       3.99931 ( 1776)

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

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

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 206
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 GLN cc_start: 0.8540 (mt0) cc_final: 0.8269 (mt0)
REVERT: A  248 TYR cc_start: 0.8057 (t80) cc_final: 0.7665 (t80)
REVERT: A  332 ASP cc_start: 0.8098 (m-30) cc_final: 0.7798 (m-30)
REVERT: A  343 CYS cc_start: 0.8702 (m) cc_final: 0.8296 (m)
REVERT: A  410 THR cc_start: 0.9516 (t) cc_final: 0.9288 (m)
REVERT: A  516 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7442 (mmm160)
REVERT: A  529 MET cc_start: 0.7941 (mmm) cc_final: 0.7617 (mmm)
REVERT: A  673 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7557 (pm20)
REVERT: B  185 LEU cc_start: 0.9225 (tp) cc_final: 0.8908 (tp)
REVERT: B  248 TYR cc_start: 0.7988 (t80) cc_final: 0.7547 (t80)
REVERT: B  270 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7499 (mm)
REVERT: B  309 PHE cc_start: 0.8342 (m-80) cc_final: 0.7946 (m-80)
REVERT: B  410 THR cc_start: 0.9506 (t) cc_final: 0.9293 (m)
REVERT: B  430 PHE cc_start: 0.8376 (p90) cc_final: 0.8174 (p90)
REVERT: B  516 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7405 (mmm160)
REVERT: B  589 VAL cc_start: 0.6303 (OUTLIER) cc_final: 0.6030 (p)
REVERT: B  673 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7681 (pm20)
  outliers start: 56
  outliers final: 45
  residues processed: 239
  average time/residue: 0.0873
  time to fit residues: 32.0846
Evaluate side-chains
  246 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 195
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  304 SER
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  359 SER
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  455 PHE
Chi-restraints excluded: chain A residue  516 ARG
Chi-restraints excluded: chain A residue  542 SER
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  613 ILE
Chi-restraints excluded: chain A residue  673 GLU
Chi-restraints excluded: chain A residue  687 ASP
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   42 CYS
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue  181 SER
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  486 LEU
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  516 ARG
Chi-restraints excluded: chain B residue  542 SER
Chi-restraints excluded: chain B residue  568 LEU
Chi-restraints excluded: chain B residue  589 VAL
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  613 ILE
Chi-restraints excluded: chain B residue  644 ILE
Chi-restraints excluded: chain B residue  673 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 80 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 60 optimal weight:    0.0980
   chunk 11 optimal weight:    7.9990
   chunk 4 optimal weight:   10.0000
   chunk 18 optimal weight:    0.7980
   chunk 116 optimal weight:    0.7980
   chunk 119 optimal weight:    0.0670
   chunk 27 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.128838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.089676 restraints weight = 17129.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.092687 restraints weight = 9926.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.094490 restraints weight = 7187.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.095764 restraints weight = 5997.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.096168 restraints weight = 5406.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.1342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11380  Z= 0.115
  Angle     :  0.618   9.534  15489  Z= 0.300
  Chirality :  0.041   0.151   1849
  Planarity :  0.004   0.062   1882
  Dihedral  :  6.367  50.586   2053
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  5.34 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 31.43 %
    Favored  : 64.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.69 (0.24), residues: 1366
  helix:  1.25 (0.19), residues: 816
  sheet:  3.47 (0.97), residues: 35
  loop : -1.04 (0.28), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 312 
 TYR   0.009   0.001   TYR B 367 
 PHE   0.016   0.001   PHE B 282 
 TRP   0.005   0.001   TRP A  63 
 HIS   0.003   0.001   HIS A  25 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (11380)
  covalent geometry    : angle       0.61818 (15489)
  hydrogen bonds       : bond        0.03138 (  604)
  hydrogen bonds       : angle       3.95025 ( 1776)

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

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

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 205
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 PHE cc_start: 0.3554 (OUTLIER) cc_final: 0.2757 (m-80)
REVERT: A  248 TYR cc_start: 0.7928 (t80) cc_final: 0.7566 (t80)
REVERT: A  332 ASP cc_start: 0.8100 (m-30) cc_final: 0.7816 (m-30)
REVERT: A  343 CYS cc_start: 0.8650 (m) cc_final: 0.8255 (m)
REVERT: A  410 THR cc_start: 0.9497 (t) cc_final: 0.9255 (m)
REVERT: A  516 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7395 (mmm160)
REVERT: A  529 MET cc_start: 0.7906 (mmm) cc_final: 0.7572 (mmm)
REVERT: A  673 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7510 (pm20)
REVERT: A  691 ILE cc_start: 0.8741 (tp) cc_final: 0.8508 (tp)
REVERT: B  185 LEU cc_start: 0.9253 (tp) cc_final: 0.8935 (tp)
REVERT: B  248 TYR cc_start: 0.7916 (t80) cc_final: 0.7485 (t80)
REVERT: B  270 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7524 (mm)
REVERT: B  309 PHE cc_start: 0.8285 (m-80) cc_final: 0.7922 (m-80)
REVERT: B  343 CYS cc_start: 0.8601 (m) cc_final: 0.7899 (m)
REVERT: B  410 THR cc_start: 0.9484 (t) cc_final: 0.9256 (m)
REVERT: B  516 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7702 (mmm160)
REVERT: B  589 VAL cc_start: 0.6261 (OUTLIER) cc_final: 0.5991 (p)
REVERT: B  673 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7480 (pm20)
REVERT: B  691 ILE cc_start: 0.8732 (tp) cc_final: 0.8522 (tp)
  outliers start: 54
  outliers final: 44
  residues processed: 239
  average time/residue: 0.0840
  time to fit residues: 30.7942
Evaluate side-chains
  248 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 197
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   35 PHE
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  304 SER
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  359 SER
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  455 PHE
Chi-restraints excluded: chain A residue  495 GLN
Chi-restraints excluded: chain A residue  516 ARG
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  613 ILE
Chi-restraints excluded: chain A residue  673 GLU
Chi-restraints excluded: chain A residue  687 ASP
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   42 CYS
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  181 SER
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  486 LEU
Chi-restraints excluded: chain B residue  516 ARG
Chi-restraints excluded: chain B residue  542 SER
Chi-restraints excluded: chain B residue  568 LEU
Chi-restraints excluded: chain B residue  589 VAL
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  613 ILE
Chi-restraints excluded: chain B residue  644 ILE
Chi-restraints excluded: chain B residue  673 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 95 optimal weight:    8.9990
   chunk 67 optimal weight:    2.9990
   chunk 120 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 124 optimal weight:    9.9990
   chunk 27 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 130 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 35 optimal weight:    8.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.125701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.086357 restraints weight = 17365.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.089249 restraints weight = 10182.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.091059 restraints weight = 7427.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.092088 restraints weight = 6234.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.092430 restraints weight = 5654.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.1387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  11380  Z= 0.200
  Angle     :  0.659   9.186  15489  Z= 0.325
  Chirality :  0.044   0.159   1849
  Planarity :  0.004   0.062   1882
  Dihedral  :  6.448  51.092   2053
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.15 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 31.68 %
    Favored  : 63.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.24), residues: 1366
  helix:  1.21 (0.19), residues: 824
  sheet:  3.69 (0.95), residues: 37
  loop : -0.90 (0.28), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 312 
 TYR   0.014   0.001   TYR B 367 
 PHE   0.016   0.001   PHE A 313 
 TRP   0.006   0.001   TRP A  63 
 HIS   0.005   0.001   HIS A  25 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 (11380)
  covalent geometry    : angle       0.65945 (15489)
  hydrogen bonds       : bond        0.03375 (  604)
  hydrogen bonds       : angle       4.02498 ( 1776)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1744.60 seconds
wall clock time: 31 minutes 6.17 seconds (1866.17 seconds total)