Starting phenix.real_space_refine
on Wed Sep 17 17:47:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xek_38292/09_2025/8xek_38292_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xek_38292/09_2025/8xek_38292.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xek_38292/09_2025/8xek_38292.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xek_38292/09_2025/8xek_38292.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xek_38292/09_2025/8xek_38292_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xek_38292/09_2025/8xek_38292_neut.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.007
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      56      5.16       5
     C    5207      2.51       5
     N    1411      2.21       5
     O    1616      1.98       5
     H    1840      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10130
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 592, 5600
          Classifications: {'peptide': 592}
          Link IDs: {'PTRANS': 28, 'TRANS': 563}
    Chain: "B"
      Number of atoms: 4530
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 481, 4530
          Classifications: {'peptide': 481}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 25, 'TRANS': 452}
  Time building chain proxies: 2.44, per 1000 atoms: 0.24
  Number of scatterers: 10130
  At special positions: 0
  Unit cell: (66, 102.3, 132.66, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      56     16.00
     O    1616      8.00
     N    1411      7.00
     C    5207      6.00
     H    1840      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=16, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  89 " - pdb=" SG  CYS A  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 138 " - pdb=" SG  CYS A 158 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 172 " - pdb=" SG  CYS A 185 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 491 " - pdb=" SG  CYS A 502 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 508 " - pdb=" SG  CYS A 565 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  31 " - pdb=" SG  CYS B  49 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  39 " - pdb=" SG  CYS B 461 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  42 " - pdb=" SG  CYS B  64 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  52 " - pdb=" SG  CYS B  75 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 203 " - pdb=" SG  CYS B 210 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 258 " - pdb=" SG  CYS B 299 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 400 " - pdb=" SG  CYS B 412 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 432 " - pdb=" SG  CYS B 459 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 463 " - pdb=" SG  CYS B 483 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 474 " - pdb=" SG  CYS B 486 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 488 " - pdb=" SG  CYS B 497 " distance=2.03

  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: 1.01
  Conformation dependent library (CDL) restraints added in 396.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1970

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 19 sheets defined
      17.1% alpha, 28.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 205 through 210
    Processing helix  chain 'A' and resid 218 through 224
    Processing helix  chain 'A' and resid 244 through 248
    Processing helix  chain 'A' and resid 275 through 280
    Processing helix  chain 'A' and resid 396 through 400
      removed outlier: 3.684A  pdb=" N   LYS A 400 " --> pdb=" O   GLU A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 531 through 534
    Processing helix  chain 'A' and resid 594 through 599
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 4.070A  pdb=" N   ARG B  34 " --> pdb=" O   CYS B  31 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 46
      removed outlier: 4.323A  pdb=" N   ALA B  44 " --> pdb=" O   GLN B  40 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   SER B  46 " --> pdb=" O   CYS B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 73
      removed outlier: 3.748A  pdb=" N   LEU B  71 " --> pdb=" O   LYS B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 149
      No H-bonds generated for 'chain 'B' and resid 147 through 149'
    Processing helix  chain 'B' and resid 150 through 157
    Processing helix  chain 'B' and resid 159 through 169
      removed outlier: 3.829A  pdb=" N   LYS B 163 " --> pdb=" O   ASN B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 200
    Processing helix  chain 'B' and resid 203 through 207
    Processing helix  chain 'B' and resid 225 through 234
      removed outlier: 3.855A  pdb=" N   PHE B 229 " --> pdb=" O   GLN B 225 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ASN B 230 " --> pdb=" O   VAL B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 258
      removed outlier: 3.802A  pdb=" N   ALA B 251 " --> pdb=" O   GLY B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 263
    Processing helix  chain 'B' and resid 285 through 290
    Processing helix  chain 'B' and resid 307 through 312
      removed outlier: 4.265A  pdb=" N   THR B 311 " --> pdb=" O   SER B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 329
    Processing helix  chain 'B' and resid 340 through 350
      removed outlier: 3.857A  pdb=" N   LEU B 350 " --> pdb=" O   ASN B 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 378
    Processing helix  chain 'B' and resid 461 through 467
    Processing helix  chain 'B' and resid 474 through 477
      removed outlier: 3.631A  pdb=" N   GLY B 477 " --> pdb=" O   CYS B 474 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 474 through 477'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 42
      removed outlier: 4.420A  pdb=" N   THR A 442 " --> pdb=" O   ASP A 451 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   ILE A 453 " --> pdb=" O   GLY A 440 " (cutoff:3.500A)
      removed outlier: 5.539A  pdb=" N   GLY A 440 " --> pdb=" O   ILE A 453 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   GLY A 455 " --> pdb=" O   MET A 438 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   MET A 438 " --> pdb=" O   GLY A 455 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56
    Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 111
      removed outlier: 7.192A  pdb=" N   ASP A 114 " --> pdb=" O   TYR A 110 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 118
      removed outlier: 3.683A  pdb=" N   HIS A 143 " --> pdb=" O   PHE A 118 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 131
    Processing sheet with id=AA6, first strand: chain 'A' and resid 190 through 193
      removed outlier: 3.663A  pdb=" N   SER A 190 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 256 through 259
      removed outlier: 6.402A  pdb=" N   VAL A 283 " --> pdb=" O   ASN A 296 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   ASN A 296 " --> pdb=" O   VAL A 283 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   ILE A 285 " --> pdb=" O   LEU A 294 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 310 through 313
    Processing sheet with id=AA9, first strand: chain 'A' and resid 331 through 333
    Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 378
      removed outlier: 6.579A  pdb=" N   ILE A 374 " --> pdb=" O   ALA A 391 " (cutoff:3.500A)
      removed outlier: 7.488A  pdb=" N   ALA A 391 " --> pdb=" O   ILE A 374 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   ALA A 389 " --> pdb=" O   PRO A 376 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLY A 378 " --> pdb=" O   ASP A 387 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 374 through 378
      removed outlier: 6.579A  pdb=" N   ILE A 374 " --> pdb=" O   ALA A 391 " (cutoff:3.500A)
      removed outlier: 7.488A  pdb=" N   ALA A 391 " --> pdb=" O   ILE A 374 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   ALA A 389 " --> pdb=" O   PRO A 376 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLY A 378 " --> pdb=" O   ASP A 387 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   GLN A 419 " --> pdb=" O   ILE A 405 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 541 through 543
      removed outlier: 3.508A  pdb=" N   GLN A 564 " --> pdb=" O   LEU A 509 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 483 through 485
    Processing sheet with id=AB5, first strand: chain 'A' and resid 491 through 492
      removed outlier: 3.651A  pdb=" N   CYS A 491 " --> pdb=" O   VAL A 500 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 49 through 51
    Processing sheet with id=AB7, first strand: chain 'B' and resid 86 through 91
      removed outlier: 6.395A  pdb=" N   ARG B 113 " --> pdb=" O   LEU B  90 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   ILE B 114 " --> pdb=" O   GLN B 454 " (cutoff:3.500A)
      removed outlier: 7.649A  pdb=" N   THR B 456 " --> pdb=" O   ILE B 114 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   LEU B 116 " --> pdb=" O   THR B 456 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 109 through 110
      removed outlier: 4.207A  pdb=" N   SER B 422 " --> pdb=" O   THR B 399 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 216 through 223
      removed outlier: 7.049A  pdb=" N   VAL B 219 " --> pdb=" O   ALA B 181 " (cutoff:3.500A)
      removed outlier: 8.582A  pdb=" N   ALA B 181 " --> pdb=" O   VAL B 219 " (cutoff:3.500A)
      removed outlier: 5.458A  pdb=" N   THR B 221 " --> pdb=" O   PHE B 179 " (cutoff:3.500A)
      removed outlier: 5.830A  pdb=" N   PHE B 179 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 8.859A  pdb=" N   THR B 355 " --> pdb=" O   ILE B 330 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   LEU B 332 " --> pdb=" O   THR B 355 " (cutoff:3.500A)
      removed outlier: 8.176A  pdb=" N   GLY B 357 " --> pdb=" O   LEU B 332 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   PHE B 334 " --> pdb=" O   GLY B 357 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 468 through 471
      removed outlier: 3.638A  pdb=" N   GLU B 468 " --> pdb=" O   PHE B 481 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   ASN B 470 " --> pdb=" O   GLY B 479 " (cutoff:3.500A)
      removed outlier: 5.753A  pdb=" N   GLY B 479 " --> pdb=" O   ASN B 470 " (cutoff:3.500A)

    282 hydrogen bonds defined for protein.
    711 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: 2.04

  Time building geometry restraints manager: 1.32 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 1840
        1.03 -     1.23: 19
        1.23 -     1.42: 3547
        1.42 -     1.62: 4817
        1.62 -     1.81: 79
  Bond restraints: 10302
  Sorted by residual:
  bond pdb=" N   GLY B  27 "
       pdb=" CA  GLY B  27 "
    ideal  model  delta    sigma   weight residual
    1.451  1.491 -0.040 1.60e-02 3.91e+03 6.28e+00
  bond pdb=" N   ASN A  32 "
       pdb=" CA  ASN A  32 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.90e-02 2.77e+03 2.52e+00
  bond pdb=" N   GLY B  27 "
       pdb=" H   GLY B  27 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.29e+00
  bond pdb=" N   ASN A  32 "
       pdb=" H   ASN A  32 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.25e+00
  bond pdb=" C   ALA A 375 "
       pdb=" O   ALA A 375 "
    ideal  model  delta    sigma   weight residual
    1.249  1.236  0.013 8.50e-03 1.38e+04 2.22e+00
  ... (remaining 10297 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 14602
        1.95 -     3.89: 135
        3.89 -     5.84: 16
        5.84 -     7.78: 1
        7.78 -     9.73: 2
  Bond angle restraints: 14756
  Sorted by residual:
  angle pdb=" C   GLU B 502 "
        pdb=" N   ASP B 503 "
        pdb=" CA  ASP B 503 "
      ideal   model   delta    sigma   weight residual
     121.70  131.43   -9.73 1.80e+00 3.09e-01 2.92e+01
  angle pdb=" CG  ARG B 473 "
        pdb=" CD  ARG B 473 "
        pdb=" NE  ARG B 473 "
      ideal   model   delta    sigma   weight residual
     112.00  119.79   -7.79 2.20e+00 2.07e-01 1.25e+01
  angle pdb=" CA  ARG B 473 "
        pdb=" CB  ARG B 473 "
        pdb=" CG  ARG B 473 "
      ideal   model   delta    sigma   weight residual
     114.10  119.91   -5.81 2.00e+00 2.50e-01 8.44e+00
  angle pdb=" CA  GLN B 464 "
        pdb=" CB  GLN B 464 "
        pdb=" CG  GLN B 464 "
      ideal   model   delta    sigma   weight residual
     114.10  119.43   -5.33 2.00e+00 2.50e-01 7.10e+00
  angle pdb=" C   ASN A 485 "
        pdb=" CA  ASN A 485 "
        pdb=" CB  ASN A 485 "
      ideal   model   delta    sigma   weight residual
     109.53  113.90   -4.37 1.65e+00 3.67e-01 7.00e+00
  ... (remaining 14751 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.73: 5998
       16.73 -    33.45: 409
       33.45 -    50.18: 112
       50.18 -    66.90: 42
       66.90 -    83.63: 15
  Dihedral angle restraints: 6576
    sinusoidal: 3473
      harmonic: 3103
  Sorted by residual:
  dihedral pdb=" CB  CYS B 488 "
           pdb=" SG  CYS B 488 "
           pdb=" SG  CYS B 497 "
           pdb=" CB  CYS B 497 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  154.31  -61.31     1      1.00e+01 1.00e-02 4.99e+01
  dihedral pdb=" CB  CYS A 172 "
           pdb=" SG  CYS A 172 "
           pdb=" SG  CYS A 185 "
           pdb=" CB  CYS A 185 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   52.13   40.87     1      1.00e+01 1.00e-02 2.34e+01
  dihedral pdb=" CB  CYS B 474 "
           pdb=" SG  CYS B 474 "
           pdb=" SG  CYS B 486 "
           pdb=" CB  CYS B 486 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -120.47   34.47     1      1.00e+01 1.00e-02 1.69e+01
  ... (remaining 6573 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 879
       0.038 -    0.075: 253
       0.075 -    0.113: 91
       0.113 -    0.150: 28
       0.150 -    0.188: 1
  Chirality restraints: 1252
  Sorted by residual:
  chirality pdb=" CA  SER B 194 "
            pdb=" N   SER B 194 "
            pdb=" C   SER B 194 "
            pdb=" CB  SER B 194 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.84e-01
  chirality pdb=" CA  PRO B  47 "
            pdb=" N   PRO B  47 "
            pdb=" C   PRO B  47 "
            pdb=" CB  PRO B  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.72e-01
  chirality pdb=" CA  ILE B 406 "
            pdb=" N   ILE B 406 "
            pdb=" C   ILE B 406 "
            pdb=" CB  ILE B 406 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.56e-01
  ... (remaining 1249 not shown)

  Planarity restraints: 2535
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 592 "    0.189 9.50e-02 1.11e+02   6.34e-02 4.99e+00
        pdb=" NE  ARG A 592 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 592 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 592 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 592 "    0.000 2.00e-02 2.50e+03
        pdb="HH11 ARG A 592 "   -0.003 2.00e-02 2.50e+03
        pdb="HH12 ARG A 592 "   -0.001 2.00e-02 2.50e+03
        pdb="HH21 ARG A 592 "    0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG A 592 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 194 "    0.028 5.00e-02 4.00e+02   4.13e-02 2.73e+00
        pdb=" N   PRO B 195 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO B 195 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 195 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B  46 "   -0.025 5.00e-02 4.00e+02   3.70e-02 2.19e+00
        pdb=" N   PRO B  47 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO B  47 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B  47 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 2532 not shown)

  Histogram of nonbonded interaction distances:
        1.43 -     2.06: 199
        2.06 -     2.70: 4913
        2.70 -     3.33: 17186
        3.33 -     3.97: 23920
        3.97 -     4.60: 35184
  Nonbonded interactions: 81402
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU B 390 "
            pdb=" H   GLU B 390 "
     model   vdw
     1.427 2.450
  nonbonded pdb=" OE1 GLU B 260 "
            pdb=" H   GLU B 260 "
     model   vdw
     1.499 2.450
  nonbonded pdb=" OD1 ASP A 383 "
            pdb=" H   PHE A 385 "
     model   vdw
     1.530 2.450
  nonbonded pdb=" OE1 GLN B 434 "
            pdb=" H   GLN B 434 "
     model   vdw
     1.545 2.450
  nonbonded pdb=" OD2 ASP B 205 "
            pdb="HH12 ARG B 240 "
     model   vdw
     1.597 2.450
  ... (remaining 81397 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             14.050
  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:             0.110
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.730
  Find NCS groups from input model:        0.040
  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:8.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8796
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8478  Z= 0.162
  Angle     :  0.578   9.729  11495  Z= 0.325
  Chirality :  0.043   0.188   1252
  Planarity :  0.004   0.084   1519
  Dihedral  : 14.007  83.625   3132
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  : 11.42 %
    Favored  : 88.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.26), residues: 1069
  helix:  0.08 (0.54), residues: 102
  sheet:  1.07 (0.29), residues: 338
  loop : -0.13 (0.25), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG B 473 
 TYR   0.012   0.001   TYR B 204 
 PHE   0.008   0.001   PHE A 193 
 TRP   0.006   0.001   TRP B 264 
 HIS   0.005   0.001   HIS B 472 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 8462)
  covalent geometry    : angle       0.57840 (11463)
  SS BOND              : bond        0.00128 (   16)
  SS BOND              : angle       0.46954 (   32)
  hydrogen bonds       : bond        0.19124 (  275)
  hydrogen bonds       : angle       8.93820 (  711)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   33 is missing expected H atoms. Skipping.
Residue VAL   35 is missing expected H atoms. Skipping.
Residue ALA   39 is missing expected H atoms. Skipping.
Residue ALA   52 is missing expected H atoms. Skipping.
Residue VAL   53 is missing expected H atoms. Skipping.
Residue VAL   57 is missing expected H atoms. Skipping.
Residue ALA   60 is missing expected H atoms. Skipping.
Residue MET   64 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue VAL   68 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue THR   75 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   86 is missing expected H atoms. Skipping.
Residue LEU   87 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ILE  100 is missing expected H atoms. Skipping.
Residue ALA  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue ALA  111 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue ALA  126 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue ALA  137 is missing expected H atoms. Skipping.
Residue ALA  139 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  146 is missing expected H atoms. Skipping.
Residue MET  148 is missing expected H atoms. Skipping.
Residue VAL  155 is missing expected H atoms. Skipping.
Residue THR  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  164 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue VAL  167 is missing expected H atoms. Skipping.
Residue ALA  170 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  179 is missing expected H atoms. Skipping.
Residue ILE  191 is missing expected H atoms. Skipping.
Residue THR  194 is missing expected H atoms. Skipping.
Residue ALA  196 is missing expected H atoms. Skipping.
Residue VAL  199 is missing expected H atoms. Skipping.
Residue LEU  200 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LEU  213 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue ALA  219 is missing expected H atoms. Skipping.
Residue ILE  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Residue VAL  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LEU  238 is missing expected H atoms. Skipping.
Residue ALA  239 is missing expected H atoms. Skipping.
Residue THR  240 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue ALA  243 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue ILE  246 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue VAL  256 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  258 is missing expected H atoms. Skipping.
Residue ILE  266 is missing expected H atoms. Skipping.
Residue VAL  270 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue ALA  276 is missing expected H atoms. Skipping.
Residue ALA  277 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue LEU  280 is missing expected H atoms. Skipping.
Residue MET  282 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  285 is missing expected H atoms. Skipping.
Residue MET  291 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue THR  298 is missing expected H atoms. Skipping.
Residue MET  302 is missing expected H atoms. Skipping.
Residue ALA  303 is missing expected H atoms. Skipping.
Residue ALA  304 is missing expected H atoms. Skipping.
Residue VAL  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue ALA  312 is missing expected H atoms. Skipping.
Residue THR  313 is missing expected H atoms. Skipping.
Residue ILE  315 is missing expected H atoms. Skipping.
Residue ALA  321 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue ILE  325 is missing expected H atoms. Skipping.
Residue ALA  327 is missing expected H atoms. Skipping.
Residue LEU  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU  339 is missing expected H atoms. Skipping.
Residue VAL  342 is missing expected H atoms. Skipping.
Residue VAL  345 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  349 is missing expected H atoms. Skipping.
Residue ALA  352 is missing expected H atoms. Skipping.
Residue THR  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LEU  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue ALA  368 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  374 is missing expected H atoms. Skipping.
Residue ALA  375 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue LEU  380 is missing expected H atoms. Skipping.
Residue ILE  388 is missing expected H atoms. Skipping.
Residue ALA  389 is missing expected H atoms. Skipping.
Residue ILE  390 is missing expected H atoms. Skipping.
Residue ALA  391 is missing expected H atoms. Skipping.
Residue ALA  392 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue VAL  403 is missing expected H atoms. Skipping.
Residue ILE  405 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Residue ALA  415 is missing expected H atoms. Skipping.
Residue VAL  416 is missing expected H atoms. Skipping.
Residue ILE  420 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue ALA  426 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue MET  438 is missing expected H atoms. Skipping.
Residue ALA  441 is missing expected H atoms. Skipping.
Residue THR  442 is missing expected H atoms. Skipping.
Residue ILE  444 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue ILE  453 is missing expected H atoms. Skipping.
Residue VAL  454 is missing expected H atoms. Skipping.
Residue ALA  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue VAL  470 is missing expected H atoms. Skipping.
Residue ILE  471 is missing expected H atoms. Skipping.
Residue THR  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ALA  475 is missing expected H atoms. Skipping.
Residue LEU  477 is missing expected H atoms. Skipping.
Residue VAL  479 is missing expected H atoms. Skipping.
Residue ILE  483 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue THR  490 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue THR  496 is missing expected H atoms. Skipping.
Residue ALA  497 is missing expected H atoms. Skipping.
Residue LEU  498 is missing expected H atoms. Skipping.
Residue VAL  500 is missing expected H atoms. Skipping.
Residue VAL  505 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue ALA  511 is missing expected H atoms. Skipping.
Residue VAL  516 is missing expected H atoms. Skipping.
Residue LEU  517 is missing expected H atoms. Skipping.
Residue LEU  521 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  532 is missing expected H atoms. Skipping.
Residue ALA  537 is missing expected H atoms. Skipping.
Residue ILE  538 is missing expected H atoms. Skipping.
Residue ALA  541 is missing expected H atoms. Skipping.
Residue LEU  542 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue THR  556 is missing expected H atoms. Skipping.
Residue ILE  557 is missing expected H atoms. Skipping.
Residue LEU  562 is missing expected H atoms. Skipping.
Residue MET  563 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue ALA  570 is missing expected H atoms. Skipping.
Residue LEU  572 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue THR  583 is missing expected H atoms. Skipping.
Residue ILE  585 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue ILE  587 is missing expected H atoms. Skipping.
Residue MET  589 is missing expected H atoms. Skipping.
Residue LEU  593 is missing expected H atoms. Skipping.
Residue THR  597 is missing expected H atoms. Skipping.
Residue ALA  598 is missing expected H atoms. Skipping.
Residue ALA  599 is missing expected H atoms. Skipping.
Residue THR  601 is missing expected H atoms. Skipping.
Residue THR  602 is missing expected H atoms. Skipping.
Residue LEU  604 is missing expected H atoms. Skipping.
Residue ILE  607 is missing expected H atoms. Skipping.
Residue LEU  608 is missing expected H atoms. Skipping.
Residue THR  612 is missing expected H atoms. Skipping.
Residue ALA  614 is missing expected H atoms. Skipping.
Residue ILE  616 is missing expected H atoms. Skipping.
Residue ALA  620 is missing expected H atoms. Skipping.
Residue ILE  622 is missing expected H atoms. Skipping.
Residue ILE   30 is missing expected H atoms. Skipping.
Residue THR   32 is missing expected H atoms. Skipping.
Residue THR   33 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LEU   43 is missing expected H atoms. Skipping.
Residue ALA   44 is missing expected H atoms. Skipping.
Residue VAL   45 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue ALA   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue LEU   59 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ALA   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   84 is missing expected H atoms. Skipping.
Residue ALA   87 is missing expected H atoms. Skipping.
Residue VAL   89 is missing expected H atoms. Skipping.
Residue LEU   90 is missing expected H atoms. Skipping.
Residue LEU   95 is missing expected H atoms. Skipping.
Residue VAL  106 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue VAL  109 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue ALA  115 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue VAL  133 is missing expected H atoms. Skipping.
Residue VAL  138 is missing expected H atoms. Skipping.
Residue ILE  140 is missing expected H atoms. Skipping.
Residue LEU  143 is missing expected H atoms. Skipping.
Residue MET  144 is missing expected H atoms. Skipping.
Residue LEU  146 is missing expected H atoms. Skipping.
Residue MET  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue ILE  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  162 is missing expected H atoms. Skipping.
Residue LEU  164 is missing expected H atoms. Skipping.
Residue ALA  165 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue MET  168 is missing expected H atoms. Skipping.
Residue LEU  171 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  181 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue MET  191 is missing expected H atoms. Skipping.
Residue ILE  193 is missing expected H atoms. Skipping.
Residue ALA  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  206 is missing expected H atoms. Skipping.
Residue THR  208 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue MET  213 is missing expected H atoms. Skipping.
Residue VAL  219 is missing expected H atoms. Skipping.
Residue LEU  220 is missing expected H atoms. Skipping.
Residue THR  221 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue THR  223 is missing expected H atoms. Skipping.
Residue VAL  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue ALA  244 is missing expected H atoms. Skipping.
Residue ALA  251 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue MET  253 is missing expected H atoms. Skipping.
Residue ALA  255 is missing expected H atoms. Skipping.
Residue THR  256 is missing expected H atoms. Skipping.
Residue VAL  257 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ALA  268 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue THR  275 is missing expected H atoms. Skipping.
Residue THR  276 is missing expected H atoms. Skipping.
Residue ALA  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue ILE  282 is missing expected H atoms. Skipping.
Residue ALA  283 is missing expected H atoms. Skipping.
Residue LEU  284 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue ALA  289 is missing expected H atoms. Skipping.
Residue ILE  291 is missing expected H atoms. Skipping.
Residue VAL  292 is missing expected H atoms. Skipping.
Residue VAL  301 is missing expected H atoms. Skipping.
Residue ALA  309 is missing expected H atoms. Skipping.
Residue THR  311 is missing expected H atoms. Skipping.
Residue THR  312 is missing expected H atoms. Skipping.
Residue MET  313 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue LEU  320 is missing expected H atoms. Skipping.
Residue MET  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  325 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue ILE  333 is missing expected H atoms. Skipping.
Residue ALA  335 is missing expected H atoms. Skipping.
Residue VAL  336 is missing expected H atoms. Skipping.
Residue THR  337 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue VAL  341 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  350 is missing expected H atoms. Skipping.
Residue ILE  351 is missing expected H atoms. Skipping.
Residue THR  354 is missing expected H atoms. Skipping.
Residue THR  355 is missing expected H atoms. Skipping.
Residue VAL  356 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue LEU  359 is missing expected H atoms. Skipping.
Residue MET  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue LEU  367 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue VAL  371 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  377 is missing expected H atoms. Skipping.
Residue VAL  381 is missing expected H atoms. Skipping.
Residue LEU  383 is missing expected H atoms. Skipping.
Residue VAL  385 is missing expected H atoms. Skipping.
Residue LEU  388 is missing expected H atoms. Skipping.
Residue LEU  392 is missing expected H atoms. Skipping.
Residue LEU  394 is missing expected H atoms. Skipping.
Residue ALA  398 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue LEU  401 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue ILE  406 is missing expected H atoms. Skipping.
Residue LEU  409 is missing expected H atoms. Skipping.
Residue MET  413 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue ILE  417 is missing expected H atoms. Skipping.
Residue THR  420 is missing expected H atoms. Skipping.
Residue VAL  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  441 is missing expected H atoms. Skipping.
Residue ILE  442 is missing expected H atoms. Skipping.
Residue VAL  445 is missing expected H atoms. Skipping.
Residue LEU  451 is missing expected H atoms. Skipping.
Residue ILE  452 is missing expected H atoms. Skipping.
Residue VAL  453 is missing expected H atoms. Skipping.
Residue VAL  455 is missing expected H atoms. Skipping.
Residue THR  456 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ALA  465 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue THR  480 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Evaluate side-chains
  54 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 52
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   51 TRP cc_start: 0.7818 (t-100) cc_final: 0.7074 (t-100)
  outliers start: 2
  outliers final: 2
  residues processed: 54
  average time/residue: 0.8659
  time to fit residues: 49.7820
Evaluate side-chains
  51 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 49
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 TYR
Chi-restraints excluded: chain A residue  529 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    9.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 212 GLN
A 350 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.092587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.059685 restraints weight = 23706.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.2790 rms_B_bonded: 2.65
r_work: 0.2643 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2515 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8831
moved from start:          0.1136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.046   8478  Z= 0.344
  Angle     :  0.602   5.216  11495  Z= 0.319
  Chirality :  0.047   0.173   1252
  Planarity :  0.004   0.038   1519
  Dihedral  :  5.284  53.006   1167
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 10.65 %
    Favored  : 87.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.25), residues: 1069
  helix: -0.45 (0.49), residues: 110
  sheet:  0.80 (0.28), residues: 327
  loop : -0.21 (0.25), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 242 
 TYR   0.015   0.002   TYR B 374 
 PHE   0.015   0.002   PHE A 306 
 TRP   0.011   0.002   TRP A  91 
 HIS   0.005   0.001   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00814 ( 8462)
  covalent geometry    : angle       0.60148 (11463)
  SS BOND              : bond        0.00224 (   16)
  SS BOND              : angle       0.82488 (   32)
  hydrogen bonds       : bond        0.04339 (  275)
  hydrogen bonds       : angle       6.80023 (  711)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   33 is missing expected H atoms. Skipping.
Residue VAL   35 is missing expected H atoms. Skipping.
Residue ALA   39 is missing expected H atoms. Skipping.
Residue ALA   52 is missing expected H atoms. Skipping.
Residue VAL   53 is missing expected H atoms. Skipping.
Residue VAL   57 is missing expected H atoms. Skipping.
Residue ALA   60 is missing expected H atoms. Skipping.
Residue MET   64 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue VAL   68 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue THR   75 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   86 is missing expected H atoms. Skipping.
Residue LEU   87 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ILE  100 is missing expected H atoms. Skipping.
Residue ALA  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue ALA  111 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue ALA  126 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue ALA  137 is missing expected H atoms. Skipping.
Residue ALA  139 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  146 is missing expected H atoms. Skipping.
Residue MET  148 is missing expected H atoms. Skipping.
Residue VAL  155 is missing expected H atoms. Skipping.
Residue THR  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  164 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue VAL  167 is missing expected H atoms. Skipping.
Residue ALA  170 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  179 is missing expected H atoms. Skipping.
Residue ILE  191 is missing expected H atoms. Skipping.
Residue THR  194 is missing expected H atoms. Skipping.
Residue ALA  196 is missing expected H atoms. Skipping.
Residue VAL  199 is missing expected H atoms. Skipping.
Residue LEU  200 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LEU  213 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue ALA  219 is missing expected H atoms. Skipping.
Residue ILE  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Residue VAL  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LEU  238 is missing expected H atoms. Skipping.
Residue ALA  239 is missing expected H atoms. Skipping.
Residue THR  240 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue ALA  243 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue ILE  246 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue VAL  256 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  258 is missing expected H atoms. Skipping.
Residue ILE  266 is missing expected H atoms. Skipping.
Residue VAL  270 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue ALA  276 is missing expected H atoms. Skipping.
Residue ALA  277 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue LEU  280 is missing expected H atoms. Skipping.
Residue MET  282 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  285 is missing expected H atoms. Skipping.
Residue MET  291 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue THR  298 is missing expected H atoms. Skipping.
Residue MET  302 is missing expected H atoms. Skipping.
Residue ALA  303 is missing expected H atoms. Skipping.
Residue ALA  304 is missing expected H atoms. Skipping.
Residue VAL  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue ALA  312 is missing expected H atoms. Skipping.
Residue THR  313 is missing expected H atoms. Skipping.
Residue ILE  315 is missing expected H atoms. Skipping.
Residue ALA  321 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue ILE  325 is missing expected H atoms. Skipping.
Residue ALA  327 is missing expected H atoms. Skipping.
Residue LEU  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU  339 is missing expected H atoms. Skipping.
Residue VAL  342 is missing expected H atoms. Skipping.
Residue VAL  345 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  349 is missing expected H atoms. Skipping.
Residue ALA  352 is missing expected H atoms. Skipping.
Residue THR  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LEU  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue ALA  368 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  374 is missing expected H atoms. Skipping.
Residue ALA  375 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue LEU  380 is missing expected H atoms. Skipping.
Residue ILE  388 is missing expected H atoms. Skipping.
Residue ALA  389 is missing expected H atoms. Skipping.
Residue ILE  390 is missing expected H atoms. Skipping.
Residue ALA  391 is missing expected H atoms. Skipping.
Residue ALA  392 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue VAL  403 is missing expected H atoms. Skipping.
Residue ILE  405 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Residue ALA  415 is missing expected H atoms. Skipping.
Residue VAL  416 is missing expected H atoms. Skipping.
Residue ILE  420 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue ALA  426 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue MET  438 is missing expected H atoms. Skipping.
Residue ALA  441 is missing expected H atoms. Skipping.
Residue THR  442 is missing expected H atoms. Skipping.
Residue ILE  444 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue ILE  453 is missing expected H atoms. Skipping.
Residue VAL  454 is missing expected H atoms. Skipping.
Residue ALA  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue VAL  470 is missing expected H atoms. Skipping.
Residue ILE  471 is missing expected H atoms. Skipping.
Residue THR  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ALA  475 is missing expected H atoms. Skipping.
Residue LEU  477 is missing expected H atoms. Skipping.
Residue VAL  479 is missing expected H atoms. Skipping.
Residue ILE  483 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue THR  490 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue THR  496 is missing expected H atoms. Skipping.
Residue ALA  497 is missing expected H atoms. Skipping.
Residue LEU  498 is missing expected H atoms. Skipping.
Residue VAL  500 is missing expected H atoms. Skipping.
Residue VAL  505 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue ALA  511 is missing expected H atoms. Skipping.
Residue VAL  516 is missing expected H atoms. Skipping.
Residue LEU  517 is missing expected H atoms. Skipping.
Residue LEU  521 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  532 is missing expected H atoms. Skipping.
Residue ALA  537 is missing expected H atoms. Skipping.
Residue ILE  538 is missing expected H atoms. Skipping.
Residue ALA  541 is missing expected H atoms. Skipping.
Residue LEU  542 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue THR  556 is missing expected H atoms. Skipping.
Residue ILE  557 is missing expected H atoms. Skipping.
Residue LEU  562 is missing expected H atoms. Skipping.
Residue MET  563 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue ALA  570 is missing expected H atoms. Skipping.
Residue LEU  572 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue THR  583 is missing expected H atoms. Skipping.
Residue ILE  585 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue ILE  587 is missing expected H atoms. Skipping.
Residue MET  589 is missing expected H atoms. Skipping.
Residue LEU  593 is missing expected H atoms. Skipping.
Residue THR  597 is missing expected H atoms. Skipping.
Residue ALA  598 is missing expected H atoms. Skipping.
Residue ALA  599 is missing expected H atoms. Skipping.
Residue THR  601 is missing expected H atoms. Skipping.
Residue THR  602 is missing expected H atoms. Skipping.
Residue LEU  604 is missing expected H atoms. Skipping.
Residue ILE  607 is missing expected H atoms. Skipping.
Residue LEU  608 is missing expected H atoms. Skipping.
Residue THR  612 is missing expected H atoms. Skipping.
Residue ALA  614 is missing expected H atoms. Skipping.
Residue ILE  616 is missing expected H atoms. Skipping.
Residue ALA  620 is missing expected H atoms. Skipping.
Residue ILE  622 is missing expected H atoms. Skipping.
Residue ILE   30 is missing expected H atoms. Skipping.
Residue THR   32 is missing expected H atoms. Skipping.
Residue THR   33 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LEU   43 is missing expected H atoms. Skipping.
Residue ALA   44 is missing expected H atoms. Skipping.
Residue VAL   45 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue ALA   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue LEU   59 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ALA   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   84 is missing expected H atoms. Skipping.
Residue ALA   87 is missing expected H atoms. Skipping.
Residue VAL   89 is missing expected H atoms. Skipping.
Residue LEU   90 is missing expected H atoms. Skipping.
Residue LEU   95 is missing expected H atoms. Skipping.
Residue VAL  106 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue VAL  109 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue ALA  115 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue VAL  133 is missing expected H atoms. Skipping.
Residue VAL  138 is missing expected H atoms. Skipping.
Residue ILE  140 is missing expected H atoms. Skipping.
Residue LEU  143 is missing expected H atoms. Skipping.
Residue MET  144 is missing expected H atoms. Skipping.
Residue LEU  146 is missing expected H atoms. Skipping.
Residue MET  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue ILE  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  162 is missing expected H atoms. Skipping.
Residue LEU  164 is missing expected H atoms. Skipping.
Residue ALA  165 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue MET  168 is missing expected H atoms. Skipping.
Residue LEU  171 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  181 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue MET  191 is missing expected H atoms. Skipping.
Residue ILE  193 is missing expected H atoms. Skipping.
Residue ALA  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  206 is missing expected H atoms. Skipping.
Residue THR  208 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue MET  213 is missing expected H atoms. Skipping.
Residue VAL  219 is missing expected H atoms. Skipping.
Residue LEU  220 is missing expected H atoms. Skipping.
Residue THR  221 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue THR  223 is missing expected H atoms. Skipping.
Residue VAL  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue ALA  244 is missing expected H atoms. Skipping.
Residue ALA  251 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue MET  253 is missing expected H atoms. Skipping.
Residue ALA  255 is missing expected H atoms. Skipping.
Residue THR  256 is missing expected H atoms. Skipping.
Residue VAL  257 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ALA  268 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue THR  275 is missing expected H atoms. Skipping.
Residue THR  276 is missing expected H atoms. Skipping.
Residue ALA  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue ILE  282 is missing expected H atoms. Skipping.
Residue ALA  283 is missing expected H atoms. Skipping.
Residue LEU  284 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue ALA  289 is missing expected H atoms. Skipping.
Residue ILE  291 is missing expected H atoms. Skipping.
Residue VAL  292 is missing expected H atoms. Skipping.
Residue VAL  301 is missing expected H atoms. Skipping.
Residue ALA  309 is missing expected H atoms. Skipping.
Residue THR  311 is missing expected H atoms. Skipping.
Residue THR  312 is missing expected H atoms. Skipping.
Residue MET  313 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue LEU  320 is missing expected H atoms. Skipping.
Residue MET  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  325 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue ILE  333 is missing expected H atoms. Skipping.
Residue ALA  335 is missing expected H atoms. Skipping.
Residue VAL  336 is missing expected H atoms. Skipping.
Residue THR  337 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue VAL  341 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  350 is missing expected H atoms. Skipping.
Residue ILE  351 is missing expected H atoms. Skipping.
Residue THR  354 is missing expected H atoms. Skipping.
Residue THR  355 is missing expected H atoms. Skipping.
Residue VAL  356 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue LEU  359 is missing expected H atoms. Skipping.
Residue MET  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue LEU  367 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue VAL  371 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  377 is missing expected H atoms. Skipping.
Residue VAL  381 is missing expected H atoms. Skipping.
Residue LEU  383 is missing expected H atoms. Skipping.
Residue VAL  385 is missing expected H atoms. Skipping.
Residue LEU  388 is missing expected H atoms. Skipping.
Residue LEU  392 is missing expected H atoms. Skipping.
Residue LEU  394 is missing expected H atoms. Skipping.
Residue ALA  398 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue LEU  401 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue ILE  406 is missing expected H atoms. Skipping.
Residue LEU  409 is missing expected H atoms. Skipping.
Residue MET  413 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue ILE  417 is missing expected H atoms. Skipping.
Residue THR  420 is missing expected H atoms. Skipping.
Residue VAL  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  441 is missing expected H atoms. Skipping.
Residue ILE  442 is missing expected H atoms. Skipping.
Residue VAL  445 is missing expected H atoms. Skipping.
Residue LEU  451 is missing expected H atoms. Skipping.
Residue ILE  452 is missing expected H atoms. Skipping.
Residue VAL  453 is missing expected H atoms. Skipping.
Residue VAL  455 is missing expected H atoms. Skipping.
Residue THR  456 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ALA  465 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue THR  480 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Evaluate side-chains
  65 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 49
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 ASP cc_start: 0.7537 (t0) cc_final: 0.7321 (t0)
  outliers start: 16
  outliers final: 6
  residues processed: 58
  average time/residue: 0.8491
  time to fit residues: 52.4697
Evaluate side-chains
  56 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 TYR
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  573 ARG
Chi-restraints excluded: chain B residue  213 MET
Chi-restraints excluded: chain B residue  412 CYS
Chi-restraints excluded: chain B residue  432 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 83 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   chunk 46 optimal weight:    7.9990
   chunk 22 optimal weight:    1.9990
   chunk 63 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   chunk 58 optimal weight:    3.9990
   chunk 100 optimal weight:    0.6980
   chunk 55 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.094930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.062088 restraints weight = 23796.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.2844 rms_B_bonded: 2.68
r_work: 0.2696 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2567 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8783
moved from start:          0.1369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8478  Z= 0.127
  Angle     :  0.474   7.968  11495  Z= 0.252
  Chirality :  0.043   0.199   1252
  Planarity :  0.003   0.033   1519
  Dihedral  :  4.721  51.912   1167
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 11.53 %
    Favored  : 86.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.26), residues: 1069
  helix: -0.00 (0.50), residues: 109
  sheet:  0.93 (0.28), residues: 332
  loop : -0.21 (0.25), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 592 
 TYR   0.011   0.001   TYR A 545 
 PHE   0.008   0.001   PHE B 274 
 TRP   0.007   0.001   TRP A 209 
 HIS   0.002   0.000   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 8462)
  covalent geometry    : angle       0.46944 (11463)
  SS BOND              : bond        0.00240 (   16)
  SS BOND              : angle       1.34313 (   32)
  hydrogen bonds       : bond        0.03043 (  275)
  hydrogen bonds       : angle       6.06040 (  711)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   33 is missing expected H atoms. Skipping.
Residue VAL   35 is missing expected H atoms. Skipping.
Residue ALA   39 is missing expected H atoms. Skipping.
Residue ALA   52 is missing expected H atoms. Skipping.
Residue VAL   53 is missing expected H atoms. Skipping.
Residue VAL   57 is missing expected H atoms. Skipping.
Residue ALA   60 is missing expected H atoms. Skipping.
Residue MET   64 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue VAL   68 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue THR   75 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   86 is missing expected H atoms. Skipping.
Residue LEU   87 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ILE  100 is missing expected H atoms. Skipping.
Residue ALA  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue ALA  111 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue ALA  126 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue ALA  137 is missing expected H atoms. Skipping.
Residue ALA  139 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  146 is missing expected H atoms. Skipping.
Residue MET  148 is missing expected H atoms. Skipping.
Residue VAL  155 is missing expected H atoms. Skipping.
Residue THR  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  164 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue VAL  167 is missing expected H atoms. Skipping.
Residue ALA  170 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  179 is missing expected H atoms. Skipping.
Residue ILE  191 is missing expected H atoms. Skipping.
Residue THR  194 is missing expected H atoms. Skipping.
Residue ALA  196 is missing expected H atoms. Skipping.
Residue VAL  199 is missing expected H atoms. Skipping.
Residue LEU  200 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LEU  213 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue ALA  219 is missing expected H atoms. Skipping.
Residue ILE  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Residue VAL  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LEU  238 is missing expected H atoms. Skipping.
Residue ALA  239 is missing expected H atoms. Skipping.
Residue THR  240 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue ALA  243 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue ILE  246 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue VAL  256 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  258 is missing expected H atoms. Skipping.
Residue ILE  266 is missing expected H atoms. Skipping.
Residue VAL  270 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue ALA  276 is missing expected H atoms. Skipping.
Residue ALA  277 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue LEU  280 is missing expected H atoms. Skipping.
Residue MET  282 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  285 is missing expected H atoms. Skipping.
Residue MET  291 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue THR  298 is missing expected H atoms. Skipping.
Residue MET  302 is missing expected H atoms. Skipping.
Residue ALA  303 is missing expected H atoms. Skipping.
Residue ALA  304 is missing expected H atoms. Skipping.
Residue VAL  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue ALA  312 is missing expected H atoms. Skipping.
Residue THR  313 is missing expected H atoms. Skipping.
Residue ILE  315 is missing expected H atoms. Skipping.
Residue ALA  321 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue ILE  325 is missing expected H atoms. Skipping.
Residue ALA  327 is missing expected H atoms. Skipping.
Residue LEU  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU  339 is missing expected H atoms. Skipping.
Residue VAL  342 is missing expected H atoms. Skipping.
Residue VAL  345 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  349 is missing expected H atoms. Skipping.
Residue ALA  352 is missing expected H atoms. Skipping.
Residue THR  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LEU  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue ALA  368 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  374 is missing expected H atoms. Skipping.
Residue ALA  375 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue LEU  380 is missing expected H atoms. Skipping.
Residue ILE  388 is missing expected H atoms. Skipping.
Residue ALA  389 is missing expected H atoms. Skipping.
Residue ILE  390 is missing expected H atoms. Skipping.
Residue ALA  391 is missing expected H atoms. Skipping.
Residue ALA  392 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue VAL  403 is missing expected H atoms. Skipping.
Residue ILE  405 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Residue ALA  415 is missing expected H atoms. Skipping.
Residue VAL  416 is missing expected H atoms. Skipping.
Residue ILE  420 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue ALA  426 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue MET  438 is missing expected H atoms. Skipping.
Residue ALA  441 is missing expected H atoms. Skipping.
Residue THR  442 is missing expected H atoms. Skipping.
Residue ILE  444 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue ILE  453 is missing expected H atoms. Skipping.
Residue VAL  454 is missing expected H atoms. Skipping.
Residue ALA  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue VAL  470 is missing expected H atoms. Skipping.
Residue ILE  471 is missing expected H atoms. Skipping.
Residue THR  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ALA  475 is missing expected H atoms. Skipping.
Residue LEU  477 is missing expected H atoms. Skipping.
Residue VAL  479 is missing expected H atoms. Skipping.
Residue ILE  483 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue THR  490 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue THR  496 is missing expected H atoms. Skipping.
Residue ALA  497 is missing expected H atoms. Skipping.
Residue LEU  498 is missing expected H atoms. Skipping.
Residue VAL  500 is missing expected H atoms. Skipping.
Residue VAL  505 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue ALA  511 is missing expected H atoms. Skipping.
Residue VAL  516 is missing expected H atoms. Skipping.
Residue LEU  517 is missing expected H atoms. Skipping.
Residue LEU  521 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  532 is missing expected H atoms. Skipping.
Residue ALA  537 is missing expected H atoms. Skipping.
Residue ILE  538 is missing expected H atoms. Skipping.
Residue ALA  541 is missing expected H atoms. Skipping.
Residue LEU  542 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue THR  556 is missing expected H atoms. Skipping.
Residue ILE  557 is missing expected H atoms. Skipping.
Residue LEU  562 is missing expected H atoms. Skipping.
Residue MET  563 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue ALA  570 is missing expected H atoms. Skipping.
Residue LEU  572 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue THR  583 is missing expected H atoms. Skipping.
Residue ILE  585 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue ILE  587 is missing expected H atoms. Skipping.
Residue MET  589 is missing expected H atoms. Skipping.
Residue LEU  593 is missing expected H atoms. Skipping.
Residue THR  597 is missing expected H atoms. Skipping.
Residue ALA  598 is missing expected H atoms. Skipping.
Residue ALA  599 is missing expected H atoms. Skipping.
Residue THR  601 is missing expected H atoms. Skipping.
Residue THR  602 is missing expected H atoms. Skipping.
Residue LEU  604 is missing expected H atoms. Skipping.
Residue ILE  607 is missing expected H atoms. Skipping.
Residue LEU  608 is missing expected H atoms. Skipping.
Residue THR  612 is missing expected H atoms. Skipping.
Residue ALA  614 is missing expected H atoms. Skipping.
Residue ILE  616 is missing expected H atoms. Skipping.
Residue ALA  620 is missing expected H atoms. Skipping.
Residue ILE  622 is missing expected H atoms. Skipping.
Residue ILE   30 is missing expected H atoms. Skipping.
Residue THR   32 is missing expected H atoms. Skipping.
Residue THR   33 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LEU   43 is missing expected H atoms. Skipping.
Residue ALA   44 is missing expected H atoms. Skipping.
Residue VAL   45 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue ALA   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue LEU   59 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ALA   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   84 is missing expected H atoms. Skipping.
Residue ALA   87 is missing expected H atoms. Skipping.
Residue VAL   89 is missing expected H atoms. Skipping.
Residue LEU   90 is missing expected H atoms. Skipping.
Residue LEU   95 is missing expected H atoms. Skipping.
Residue VAL  106 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue VAL  109 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue ALA  115 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue VAL  133 is missing expected H atoms. Skipping.
Residue VAL  138 is missing expected H atoms. Skipping.
Residue ILE  140 is missing expected H atoms. Skipping.
Residue LEU  143 is missing expected H atoms. Skipping.
Residue MET  144 is missing expected H atoms. Skipping.
Residue LEU  146 is missing expected H atoms. Skipping.
Residue MET  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue ILE  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  162 is missing expected H atoms. Skipping.
Residue LEU  164 is missing expected H atoms. Skipping.
Residue ALA  165 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue MET  168 is missing expected H atoms. Skipping.
Residue LEU  171 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  181 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue MET  191 is missing expected H atoms. Skipping.
Residue ILE  193 is missing expected H atoms. Skipping.
Residue ALA  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  206 is missing expected H atoms. Skipping.
Residue THR  208 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue MET  213 is missing expected H atoms. Skipping.
Residue VAL  219 is missing expected H atoms. Skipping.
Residue LEU  220 is missing expected H atoms. Skipping.
Residue THR  221 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue THR  223 is missing expected H atoms. Skipping.
Residue VAL  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue ALA  244 is missing expected H atoms. Skipping.
Residue ALA  251 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue MET  253 is missing expected H atoms. Skipping.
Residue ALA  255 is missing expected H atoms. Skipping.
Residue THR  256 is missing expected H atoms. Skipping.
Residue VAL  257 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ALA  268 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue THR  275 is missing expected H atoms. Skipping.
Residue THR  276 is missing expected H atoms. Skipping.
Residue ALA  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue ILE  282 is missing expected H atoms. Skipping.
Residue ALA  283 is missing expected H atoms. Skipping.
Residue LEU  284 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue ALA  289 is missing expected H atoms. Skipping.
Residue ILE  291 is missing expected H atoms. Skipping.
Residue VAL  292 is missing expected H atoms. Skipping.
Residue VAL  301 is missing expected H atoms. Skipping.
Residue ALA  309 is missing expected H atoms. Skipping.
Residue THR  311 is missing expected H atoms. Skipping.
Residue THR  312 is missing expected H atoms. Skipping.
Residue MET  313 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue LEU  320 is missing expected H atoms. Skipping.
Residue MET  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  325 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue ILE  333 is missing expected H atoms. Skipping.
Residue ALA  335 is missing expected H atoms. Skipping.
Residue VAL  336 is missing expected H atoms. Skipping.
Residue THR  337 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue VAL  341 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  350 is missing expected H atoms. Skipping.
Residue ILE  351 is missing expected H atoms. Skipping.
Residue THR  354 is missing expected H atoms. Skipping.
Residue THR  355 is missing expected H atoms. Skipping.
Residue VAL  356 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue LEU  359 is missing expected H atoms. Skipping.
Residue MET  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue LEU  367 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue VAL  371 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  377 is missing expected H atoms. Skipping.
Residue VAL  381 is missing expected H atoms. Skipping.
Residue LEU  383 is missing expected H atoms. Skipping.
Residue VAL  385 is missing expected H atoms. Skipping.
Residue LEU  388 is missing expected H atoms. Skipping.
Residue LEU  392 is missing expected H atoms. Skipping.
Residue LEU  394 is missing expected H atoms. Skipping.
Residue ALA  398 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue LEU  401 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue ILE  406 is missing expected H atoms. Skipping.
Residue LEU  409 is missing expected H atoms. Skipping.
Residue MET  413 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue ILE  417 is missing expected H atoms. Skipping.
Residue THR  420 is missing expected H atoms. Skipping.
Residue VAL  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  441 is missing expected H atoms. Skipping.
Residue ILE  442 is missing expected H atoms. Skipping.
Residue VAL  445 is missing expected H atoms. Skipping.
Residue LEU  451 is missing expected H atoms. Skipping.
Residue ILE  452 is missing expected H atoms. Skipping.
Residue VAL  453 is missing expected H atoms. Skipping.
Residue VAL  455 is missing expected H atoms. Skipping.
Residue THR  456 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ALA  465 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue THR  480 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Evaluate side-chains
  70 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 54
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  520 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8473 (pptt)
REVERT: A  528 LEU cc_start: 0.8632 (pt) cc_final: 0.8308 (mt)
REVERT: A  563 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8568 (tpt)
REVERT: B   51 TRP cc_start: 0.7576 (t-100) cc_final: 0.7219 (t-100)
  outliers start: 16
  outliers final: 5
  residues processed: 65
  average time/residue: 0.7825
  time to fit residues: 54.4780
Evaluate side-chains
  55 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 TYR
Chi-restraints excluded: chain A residue  520 LYS
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  401 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 94 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 89 optimal weight:    0.5980
   chunk 49 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0040
   chunk 46 optimal weight:    0.0060
   overall best weight:    0.4610

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.096040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.063338 restraints weight = 23776.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.2867 rms_B_bonded: 2.66
r_work: 0.2737 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2606 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8762
moved from start:          0.1647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   8478  Z= 0.101
  Angle     :  0.452   7.043  11495  Z= 0.238
  Chirality :  0.042   0.134   1252
  Planarity :  0.003   0.031   1519
  Dihedral  :  4.460  49.923   1167
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 12.29 %
    Favored  : 86.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.34 (0.26), residues: 1069
  helix:  0.37 (0.51), residues: 111
  sheet:  0.90 (0.28), residues: 335
  loop : -0.11 (0.25), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 592 
 TYR   0.009   0.001   TYR B 344 
 PHE   0.007   0.001   PHE B 274 
 TRP   0.006   0.001   TRP A 209 
 HIS   0.002   0.000   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 8462)
  covalent geometry    : angle       0.44493 (11463)
  SS BOND              : bond        0.00459 (   16)
  SS BOND              : angle       1.56325 (   32)
  hydrogen bonds       : bond        0.02626 (  275)
  hydrogen bonds       : angle       5.60852 (  711)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   33 is missing expected H atoms. Skipping.
Residue VAL   35 is missing expected H atoms. Skipping.
Residue ALA   39 is missing expected H atoms. Skipping.
Residue ALA   52 is missing expected H atoms. Skipping.
Residue VAL   53 is missing expected H atoms. Skipping.
Residue VAL   57 is missing expected H atoms. Skipping.
Residue ALA   60 is missing expected H atoms. Skipping.
Residue MET   64 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue VAL   68 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue THR   75 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   86 is missing expected H atoms. Skipping.
Residue LEU   87 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ILE  100 is missing expected H atoms. Skipping.
Residue ALA  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue ALA  111 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue ALA  126 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue ALA  137 is missing expected H atoms. Skipping.
Residue ALA  139 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  146 is missing expected H atoms. Skipping.
Residue MET  148 is missing expected H atoms. Skipping.
Residue VAL  155 is missing expected H atoms. Skipping.
Residue THR  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  164 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue VAL  167 is missing expected H atoms. Skipping.
Residue ALA  170 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  179 is missing expected H atoms. Skipping.
Residue ILE  191 is missing expected H atoms. Skipping.
Residue THR  194 is missing expected H atoms. Skipping.
Residue ALA  196 is missing expected H atoms. Skipping.
Residue VAL  199 is missing expected H atoms. Skipping.
Residue LEU  200 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LEU  213 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue ALA  219 is missing expected H atoms. Skipping.
Residue ILE  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Residue VAL  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LEU  238 is missing expected H atoms. Skipping.
Residue ALA  239 is missing expected H atoms. Skipping.
Residue THR  240 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue ALA  243 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue ILE  246 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue VAL  256 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  258 is missing expected H atoms. Skipping.
Residue ILE  266 is missing expected H atoms. Skipping.
Residue VAL  270 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue ALA  276 is missing expected H atoms. Skipping.
Residue ALA  277 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue LEU  280 is missing expected H atoms. Skipping.
Residue MET  282 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  285 is missing expected H atoms. Skipping.
Residue MET  291 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue THR  298 is missing expected H atoms. Skipping.
Residue MET  302 is missing expected H atoms. Skipping.
Residue ALA  303 is missing expected H atoms. Skipping.
Residue ALA  304 is missing expected H atoms. Skipping.
Residue VAL  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue ALA  312 is missing expected H atoms. Skipping.
Residue THR  313 is missing expected H atoms. Skipping.
Residue ILE  315 is missing expected H atoms. Skipping.
Residue ALA  321 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue ILE  325 is missing expected H atoms. Skipping.
Residue ALA  327 is missing expected H atoms. Skipping.
Residue LEU  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU  339 is missing expected H atoms. Skipping.
Residue VAL  342 is missing expected H atoms. Skipping.
Residue VAL  345 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  349 is missing expected H atoms. Skipping.
Residue ALA  352 is missing expected H atoms. Skipping.
Residue THR  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LEU  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue ALA  368 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  374 is missing expected H atoms. Skipping.
Residue ALA  375 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue LEU  380 is missing expected H atoms. Skipping.
Residue ILE  388 is missing expected H atoms. Skipping.
Residue ALA  389 is missing expected H atoms. Skipping.
Residue ILE  390 is missing expected H atoms. Skipping.
Residue ALA  391 is missing expected H atoms. Skipping.
Residue ALA  392 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue VAL  403 is missing expected H atoms. Skipping.
Residue ILE  405 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Residue ALA  415 is missing expected H atoms. Skipping.
Residue VAL  416 is missing expected H atoms. Skipping.
Residue ILE  420 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue ALA  426 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue MET  438 is missing expected H atoms. Skipping.
Residue ALA  441 is missing expected H atoms. Skipping.
Residue THR  442 is missing expected H atoms. Skipping.
Residue ILE  444 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue ILE  453 is missing expected H atoms. Skipping.
Residue VAL  454 is missing expected H atoms. Skipping.
Residue ALA  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue VAL  470 is missing expected H atoms. Skipping.
Residue ILE  471 is missing expected H atoms. Skipping.
Residue THR  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ALA  475 is missing expected H atoms. Skipping.
Residue LEU  477 is missing expected H atoms. Skipping.
Residue VAL  479 is missing expected H atoms. Skipping.
Residue ILE  483 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue THR  490 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue THR  496 is missing expected H atoms. Skipping.
Residue ALA  497 is missing expected H atoms. Skipping.
Residue LEU  498 is missing expected H atoms. Skipping.
Residue VAL  500 is missing expected H atoms. Skipping.
Residue VAL  505 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue ALA  511 is missing expected H atoms. Skipping.
Residue VAL  516 is missing expected H atoms. Skipping.
Residue LEU  517 is missing expected H atoms. Skipping.
Residue LEU  521 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  532 is missing expected H atoms. Skipping.
Residue ALA  537 is missing expected H atoms. Skipping.
Residue ILE  538 is missing expected H atoms. Skipping.
Residue ALA  541 is missing expected H atoms. Skipping.
Residue LEU  542 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue THR  556 is missing expected H atoms. Skipping.
Residue ILE  557 is missing expected H atoms. Skipping.
Residue LEU  562 is missing expected H atoms. Skipping.
Residue MET  563 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue ALA  570 is missing expected H atoms. Skipping.
Residue LEU  572 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue THR  583 is missing expected H atoms. Skipping.
Residue ILE  585 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue ILE  587 is missing expected H atoms. Skipping.
Residue MET  589 is missing expected H atoms. Skipping.
Residue LEU  593 is missing expected H atoms. Skipping.
Residue THR  597 is missing expected H atoms. Skipping.
Residue ALA  598 is missing expected H atoms. Skipping.
Residue ALA  599 is missing expected H atoms. Skipping.
Residue THR  601 is missing expected H atoms. Skipping.
Residue THR  602 is missing expected H atoms. Skipping.
Residue LEU  604 is missing expected H atoms. Skipping.
Residue ILE  607 is missing expected H atoms. Skipping.
Residue LEU  608 is missing expected H atoms. Skipping.
Residue THR  612 is missing expected H atoms. Skipping.
Residue ALA  614 is missing expected H atoms. Skipping.
Residue ILE  616 is missing expected H atoms. Skipping.
Residue ALA  620 is missing expected H atoms. Skipping.
Residue ILE  622 is missing expected H atoms. Skipping.
Residue ILE   30 is missing expected H atoms. Skipping.
Residue THR   32 is missing expected H atoms. Skipping.
Residue THR   33 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LEU   43 is missing expected H atoms. Skipping.
Residue ALA   44 is missing expected H atoms. Skipping.
Residue VAL   45 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue ALA   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue LEU   59 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ALA   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   84 is missing expected H atoms. Skipping.
Residue ALA   87 is missing expected H atoms. Skipping.
Residue VAL   89 is missing expected H atoms. Skipping.
Residue LEU   90 is missing expected H atoms. Skipping.
Residue LEU   95 is missing expected H atoms. Skipping.
Residue VAL  106 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue VAL  109 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue ALA  115 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue VAL  133 is missing expected H atoms. Skipping.
Residue VAL  138 is missing expected H atoms. Skipping.
Residue ILE  140 is missing expected H atoms. Skipping.
Residue LEU  143 is missing expected H atoms. Skipping.
Residue MET  144 is missing expected H atoms. Skipping.
Residue LEU  146 is missing expected H atoms. Skipping.
Residue MET  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue ILE  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  162 is missing expected H atoms. Skipping.
Residue LEU  164 is missing expected H atoms. Skipping.
Residue ALA  165 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue MET  168 is missing expected H atoms. Skipping.
Residue LEU  171 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  181 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue MET  191 is missing expected H atoms. Skipping.
Residue ILE  193 is missing expected H atoms. Skipping.
Residue ALA  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  206 is missing expected H atoms. Skipping.
Residue THR  208 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue MET  213 is missing expected H atoms. Skipping.
Residue VAL  219 is missing expected H atoms. Skipping.
Residue LEU  220 is missing expected H atoms. Skipping.
Residue THR  221 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue THR  223 is missing expected H atoms. Skipping.
Residue VAL  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue ALA  244 is missing expected H atoms. Skipping.
Residue ALA  251 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue MET  253 is missing expected H atoms. Skipping.
Residue ALA  255 is missing expected H atoms. Skipping.
Residue THR  256 is missing expected H atoms. Skipping.
Residue VAL  257 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ALA  268 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue THR  275 is missing expected H atoms. Skipping.
Residue THR  276 is missing expected H atoms. Skipping.
Residue ALA  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue ILE  282 is missing expected H atoms. Skipping.
Residue ALA  283 is missing expected H atoms. Skipping.
Residue LEU  284 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue ALA  289 is missing expected H atoms. Skipping.
Residue ILE  291 is missing expected H atoms. Skipping.
Residue VAL  292 is missing expected H atoms. Skipping.
Residue VAL  301 is missing expected H atoms. Skipping.
Residue ALA  309 is missing expected H atoms. Skipping.
Residue THR  311 is missing expected H atoms. Skipping.
Residue THR  312 is missing expected H atoms. Skipping.
Residue MET  313 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue LEU  320 is missing expected H atoms. Skipping.
Residue MET  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  325 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue ILE  333 is missing expected H atoms. Skipping.
Residue ALA  335 is missing expected H atoms. Skipping.
Residue VAL  336 is missing expected H atoms. Skipping.
Residue THR  337 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue VAL  341 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  350 is missing expected H atoms. Skipping.
Residue ILE  351 is missing expected H atoms. Skipping.
Residue THR  354 is missing expected H atoms. Skipping.
Residue THR  355 is missing expected H atoms. Skipping.
Residue VAL  356 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue LEU  359 is missing expected H atoms. Skipping.
Residue MET  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue LEU  367 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue VAL  371 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  377 is missing expected H atoms. Skipping.
Residue VAL  381 is missing expected H atoms. Skipping.
Residue LEU  383 is missing expected H atoms. Skipping.
Residue VAL  385 is missing expected H atoms. Skipping.
Residue LEU  388 is missing expected H atoms. Skipping.
Residue LEU  392 is missing expected H atoms. Skipping.
Residue LEU  394 is missing expected H atoms. Skipping.
Residue ALA  398 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue LEU  401 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue ILE  406 is missing expected H atoms. Skipping.
Residue LEU  409 is missing expected H atoms. Skipping.
Residue MET  413 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue ILE  417 is missing expected H atoms. Skipping.
Residue THR  420 is missing expected H atoms. Skipping.
Residue VAL  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  441 is missing expected H atoms. Skipping.
Residue ILE  442 is missing expected H atoms. Skipping.
Residue VAL  445 is missing expected H atoms. Skipping.
Residue LEU  451 is missing expected H atoms. Skipping.
Residue ILE  452 is missing expected H atoms. Skipping.
Residue VAL  453 is missing expected H atoms. Skipping.
Residue VAL  455 is missing expected H atoms. Skipping.
Residue THR  456 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ALA  465 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue THR  480 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Evaluate side-chains
  63 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  520 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8467 (pptt)
  outliers start: 14
  outliers final: 6
  residues processed: 59
  average time/residue: 0.7255
  time to fit residues: 46.2251
Evaluate side-chains
  56 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 49
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  520 LYS
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain B residue   97 ASP
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  413 MET
Chi-restraints excluded: chain B residue  432 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 94 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 98 optimal weight:    5.9990
   chunk 90 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 63 optimal weight:    6.9990
   chunk 74 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.3584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.093632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.060861 restraints weight = 23484.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.2807 rms_B_bonded: 2.65
r_work: 0.2664 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2536 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8801
moved from start:          0.1678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8478  Z= 0.222
  Angle     :  0.512   8.247  11495  Z= 0.268
  Chirality :  0.044   0.173   1252
  Planarity :  0.003   0.030   1519
  Dihedral  :  4.552  47.517   1165
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 14.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 12.73 %
    Favored  : 85.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.25), residues: 1069
  helix:  0.13 (0.50), residues: 111
  sheet:  0.82 (0.29), residues: 332
  loop : -0.21 (0.25), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 242 
 TYR   0.011   0.001   TYR A 394 
 PHE   0.013   0.001   PHE A 306 
 TRP   0.010   0.002   TRP B 264 
 HIS   0.003   0.001   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00521 ( 8462)
  covalent geometry    : angle       0.50638 (11463)
  SS BOND              : bond        0.00173 (   16)
  SS BOND              : angle       1.49681 (   32)
  hydrogen bonds       : bond        0.03203 (  275)
  hydrogen bonds       : angle       5.85933 (  711)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   33 is missing expected H atoms. Skipping.
Residue VAL   35 is missing expected H atoms. Skipping.
Residue ALA   39 is missing expected H atoms. Skipping.
Residue ALA   52 is missing expected H atoms. Skipping.
Residue VAL   53 is missing expected H atoms. Skipping.
Residue VAL   57 is missing expected H atoms. Skipping.
Residue ALA   60 is missing expected H atoms. Skipping.
Residue MET   64 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue VAL   68 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue THR   75 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   86 is missing expected H atoms. Skipping.
Residue LEU   87 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ILE  100 is missing expected H atoms. Skipping.
Residue ALA  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue ALA  111 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue ALA  126 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue ALA  137 is missing expected H atoms. Skipping.
Residue ALA  139 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  146 is missing expected H atoms. Skipping.
Residue MET  148 is missing expected H atoms. Skipping.
Residue VAL  155 is missing expected H atoms. Skipping.
Residue THR  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  164 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue VAL  167 is missing expected H atoms. Skipping.
Residue ALA  170 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  179 is missing expected H atoms. Skipping.
Residue ILE  191 is missing expected H atoms. Skipping.
Residue THR  194 is missing expected H atoms. Skipping.
Residue ALA  196 is missing expected H atoms. Skipping.
Residue VAL  199 is missing expected H atoms. Skipping.
Residue LEU  200 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LEU  213 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue ALA  219 is missing expected H atoms. Skipping.
Residue ILE  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Residue VAL  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LEU  238 is missing expected H atoms. Skipping.
Residue ALA  239 is missing expected H atoms. Skipping.
Residue THR  240 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue ALA  243 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue ILE  246 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue VAL  256 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  258 is missing expected H atoms. Skipping.
Residue ILE  266 is missing expected H atoms. Skipping.
Residue VAL  270 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue ALA  276 is missing expected H atoms. Skipping.
Residue ALA  277 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue LEU  280 is missing expected H atoms. Skipping.
Residue MET  282 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  285 is missing expected H atoms. Skipping.
Residue MET  291 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue THR  298 is missing expected H atoms. Skipping.
Residue MET  302 is missing expected H atoms. Skipping.
Residue ALA  303 is missing expected H atoms. Skipping.
Residue ALA  304 is missing expected H atoms. Skipping.
Residue VAL  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue ALA  312 is missing expected H atoms. Skipping.
Residue THR  313 is missing expected H atoms. Skipping.
Residue ILE  315 is missing expected H atoms. Skipping.
Residue ALA  321 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue ILE  325 is missing expected H atoms. Skipping.
Residue ALA  327 is missing expected H atoms. Skipping.
Residue LEU  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU  339 is missing expected H atoms. Skipping.
Residue VAL  342 is missing expected H atoms. Skipping.
Residue VAL  345 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  349 is missing expected H atoms. Skipping.
Residue ALA  352 is missing expected H atoms. Skipping.
Residue THR  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LEU  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue ALA  368 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  374 is missing expected H atoms. Skipping.
Residue ALA  375 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue LEU  380 is missing expected H atoms. Skipping.
Residue ILE  388 is missing expected H atoms. Skipping.
Residue ALA  389 is missing expected H atoms. Skipping.
Residue ILE  390 is missing expected H atoms. Skipping.
Residue ALA  391 is missing expected H atoms. Skipping.
Residue ALA  392 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue VAL  403 is missing expected H atoms. Skipping.
Residue ILE  405 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Residue ALA  415 is missing expected H atoms. Skipping.
Residue VAL  416 is missing expected H atoms. Skipping.
Residue ILE  420 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue ALA  426 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue MET  438 is missing expected H atoms. Skipping.
Residue ALA  441 is missing expected H atoms. Skipping.
Residue THR  442 is missing expected H atoms. Skipping.
Residue ILE  444 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue ILE  453 is missing expected H atoms. Skipping.
Residue VAL  454 is missing expected H atoms. Skipping.
Residue ALA  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue VAL  470 is missing expected H atoms. Skipping.
Residue ILE  471 is missing expected H atoms. Skipping.
Residue THR  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ALA  475 is missing expected H atoms. Skipping.
Residue LEU  477 is missing expected H atoms. Skipping.
Residue VAL  479 is missing expected H atoms. Skipping.
Residue ILE  483 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue THR  490 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue THR  496 is missing expected H atoms. Skipping.
Residue ALA  497 is missing expected H atoms. Skipping.
Residue LEU  498 is missing expected H atoms. Skipping.
Residue VAL  500 is missing expected H atoms. Skipping.
Residue VAL  505 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue ALA  511 is missing expected H atoms. Skipping.
Residue VAL  516 is missing expected H atoms. Skipping.
Residue LEU  517 is missing expected H atoms. Skipping.
Residue LEU  521 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  532 is missing expected H atoms. Skipping.
Residue ALA  537 is missing expected H atoms. Skipping.
Residue ILE  538 is missing expected H atoms. Skipping.
Residue ALA  541 is missing expected H atoms. Skipping.
Residue LEU  542 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue THR  556 is missing expected H atoms. Skipping.
Residue ILE  557 is missing expected H atoms. Skipping.
Residue LEU  562 is missing expected H atoms. Skipping.
Residue MET  563 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue ALA  570 is missing expected H atoms. Skipping.
Residue LEU  572 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue THR  583 is missing expected H atoms. Skipping.
Residue ILE  585 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue ILE  587 is missing expected H atoms. Skipping.
Residue MET  589 is missing expected H atoms. Skipping.
Residue LEU  593 is missing expected H atoms. Skipping.
Residue THR  597 is missing expected H atoms. Skipping.
Residue ALA  598 is missing expected H atoms. Skipping.
Residue ALA  599 is missing expected H atoms. Skipping.
Residue THR  601 is missing expected H atoms. Skipping.
Residue THR  602 is missing expected H atoms. Skipping.
Residue LEU  604 is missing expected H atoms. Skipping.
Residue ILE  607 is missing expected H atoms. Skipping.
Residue LEU  608 is missing expected H atoms. Skipping.
Residue THR  612 is missing expected H atoms. Skipping.
Residue ALA  614 is missing expected H atoms. Skipping.
Residue ILE  616 is missing expected H atoms. Skipping.
Residue ALA  620 is missing expected H atoms. Skipping.
Residue ILE  622 is missing expected H atoms. Skipping.
Residue ILE   30 is missing expected H atoms. Skipping.
Residue THR   32 is missing expected H atoms. Skipping.
Residue THR   33 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LEU   43 is missing expected H atoms. Skipping.
Residue ALA   44 is missing expected H atoms. Skipping.
Residue VAL   45 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue ALA   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue LEU   59 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ALA   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   84 is missing expected H atoms. Skipping.
Residue ALA   87 is missing expected H atoms. Skipping.
Residue VAL   89 is missing expected H atoms. Skipping.
Residue LEU   90 is missing expected H atoms. Skipping.
Residue LEU   95 is missing expected H atoms. Skipping.
Residue VAL  106 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue VAL  109 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue ALA  115 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue VAL  133 is missing expected H atoms. Skipping.
Residue VAL  138 is missing expected H atoms. Skipping.
Residue ILE  140 is missing expected H atoms. Skipping.
Residue LEU  143 is missing expected H atoms. Skipping.
Residue MET  144 is missing expected H atoms. Skipping.
Residue LEU  146 is missing expected H atoms. Skipping.
Residue MET  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue ILE  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  162 is missing expected H atoms. Skipping.
Residue LEU  164 is missing expected H atoms. Skipping.
Residue ALA  165 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue MET  168 is missing expected H atoms. Skipping.
Residue LEU  171 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  181 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue MET  191 is missing expected H atoms. Skipping.
Residue ILE  193 is missing expected H atoms. Skipping.
Residue ALA  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  206 is missing expected H atoms. Skipping.
Residue THR  208 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue MET  213 is missing expected H atoms. Skipping.
Residue VAL  219 is missing expected H atoms. Skipping.
Residue LEU  220 is missing expected H atoms. Skipping.
Residue THR  221 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue THR  223 is missing expected H atoms. Skipping.
Residue VAL  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue ALA  244 is missing expected H atoms. Skipping.
Residue ALA  251 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue MET  253 is missing expected H atoms. Skipping.
Residue ALA  255 is missing expected H atoms. Skipping.
Residue THR  256 is missing expected H atoms. Skipping.
Residue VAL  257 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ALA  268 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue THR  275 is missing expected H atoms. Skipping.
Residue THR  276 is missing expected H atoms. Skipping.
Residue ALA  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue ILE  282 is missing expected H atoms. Skipping.
Residue ALA  283 is missing expected H atoms. Skipping.
Residue LEU  284 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue ALA  289 is missing expected H atoms. Skipping.
Residue ILE  291 is missing expected H atoms. Skipping.
Residue VAL  292 is missing expected H atoms. Skipping.
Residue VAL  301 is missing expected H atoms. Skipping.
Residue ALA  309 is missing expected H atoms. Skipping.
Residue THR  311 is missing expected H atoms. Skipping.
Residue THR  312 is missing expected H atoms. Skipping.
Residue MET  313 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue LEU  320 is missing expected H atoms. Skipping.
Residue MET  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  325 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue ILE  333 is missing expected H atoms. Skipping.
Residue ALA  335 is missing expected H atoms. Skipping.
Residue VAL  336 is missing expected H atoms. Skipping.
Residue THR  337 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue VAL  341 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  350 is missing expected H atoms. Skipping.
Residue ILE  351 is missing expected H atoms. Skipping.
Residue THR  354 is missing expected H atoms. Skipping.
Residue THR  355 is missing expected H atoms. Skipping.
Residue VAL  356 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue LEU  359 is missing expected H atoms. Skipping.
Residue MET  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue LEU  367 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue VAL  371 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  377 is missing expected H atoms. Skipping.
Residue VAL  381 is missing expected H atoms. Skipping.
Residue LEU  383 is missing expected H atoms. Skipping.
Residue VAL  385 is missing expected H atoms. Skipping.
Residue LEU  388 is missing expected H atoms. Skipping.
Residue LEU  392 is missing expected H atoms. Skipping.
Residue LEU  394 is missing expected H atoms. Skipping.
Residue ALA  398 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue LEU  401 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue ILE  406 is missing expected H atoms. Skipping.
Residue LEU  409 is missing expected H atoms. Skipping.
Residue MET  413 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue ILE  417 is missing expected H atoms. Skipping.
Residue THR  420 is missing expected H atoms. Skipping.
Residue VAL  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  441 is missing expected H atoms. Skipping.
Residue ILE  442 is missing expected H atoms. Skipping.
Residue VAL  445 is missing expected H atoms. Skipping.
Residue LEU  451 is missing expected H atoms. Skipping.
Residue ILE  452 is missing expected H atoms. Skipping.
Residue VAL  453 is missing expected H atoms. Skipping.
Residue VAL  455 is missing expected H atoms. Skipping.
Residue THR  456 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ALA  465 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue THR  480 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Evaluate side-chains
  66 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 51
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   51 TRP cc_start: 0.7502 (t-100) cc_final: 0.7251 (t-100)
  outliers start: 15
  outliers final: 11
  residues processed: 63
  average time/residue: 0.7878
  time to fit residues: 53.2319
Evaluate side-chains
  58 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  305 TYR
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain B residue   97 ASP
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  213 MET
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  432 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 63 optimal weight:    7.9990
   chunk 50 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9980
   chunk 67 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 212 GLN
B 475 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.092741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.060010 restraints weight = 24053.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.2800 rms_B_bonded: 2.64
r_work: 0.2666 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2538 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8840
moved from start:          0.1845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.033   8478  Z= 0.256
  Angle     :  0.567  11.948  11495  Z= 0.294
  Chirality :  0.045   0.231   1252
  Planarity :  0.003   0.029   1519
  Dihedral  :  4.714  49.823   1165
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 15.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 12.73 %
    Favored  : 84.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.05 (0.25), residues: 1069
  helix: -0.03 (0.50), residues: 110
  sheet:  0.71 (0.28), residues: 334
  loop : -0.28 (0.24), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 242 
 TYR   0.013   0.001   TYR B 204 
 PHE   0.014   0.001   PHE A 306 
 TRP   0.011   0.002   TRP B 264 
 HIS   0.004   0.001   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00601 ( 8462)
  covalent geometry    : angle       0.54508 (11463)
  SS BOND              : bond        0.00186 (   16)
  SS BOND              : angle       3.02131 (   32)
  hydrogen bonds       : bond        0.03324 (  275)
  hydrogen bonds       : angle       5.94021 (  711)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   33 is missing expected H atoms. Skipping.
Residue VAL   35 is missing expected H atoms. Skipping.
Residue ALA   39 is missing expected H atoms. Skipping.
Residue ALA   52 is missing expected H atoms. Skipping.
Residue VAL   53 is missing expected H atoms. Skipping.
Residue VAL   57 is missing expected H atoms. Skipping.
Residue ALA   60 is missing expected H atoms. Skipping.
Residue MET   64 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue VAL   68 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue THR   75 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   86 is missing expected H atoms. Skipping.
Residue LEU   87 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ILE  100 is missing expected H atoms. Skipping.
Residue ALA  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue ALA  111 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue ALA  126 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue ALA  137 is missing expected H atoms. Skipping.
Residue ALA  139 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  146 is missing expected H atoms. Skipping.
Residue MET  148 is missing expected H atoms. Skipping.
Residue VAL  155 is missing expected H atoms. Skipping.
Residue THR  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  164 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue VAL  167 is missing expected H atoms. Skipping.
Residue ALA  170 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  179 is missing expected H atoms. Skipping.
Residue ILE  191 is missing expected H atoms. Skipping.
Residue THR  194 is missing expected H atoms. Skipping.
Residue ALA  196 is missing expected H atoms. Skipping.
Residue VAL  199 is missing expected H atoms. Skipping.
Residue LEU  200 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LEU  213 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue ALA  219 is missing expected H atoms. Skipping.
Residue ILE  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Residue VAL  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LEU  238 is missing expected H atoms. Skipping.
Residue ALA  239 is missing expected H atoms. Skipping.
Residue THR  240 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue ALA  243 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue ILE  246 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue VAL  256 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  258 is missing expected H atoms. Skipping.
Residue ILE  266 is missing expected H atoms. Skipping.
Residue VAL  270 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue ALA  276 is missing expected H atoms. Skipping.
Residue ALA  277 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue LEU  280 is missing expected H atoms. Skipping.
Residue MET  282 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  285 is missing expected H atoms. Skipping.
Residue MET  291 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue THR  298 is missing expected H atoms. Skipping.
Residue MET  302 is missing expected H atoms. Skipping.
Residue ALA  303 is missing expected H atoms. Skipping.
Residue ALA  304 is missing expected H atoms. Skipping.
Residue VAL  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue ALA  312 is missing expected H atoms. Skipping.
Residue THR  313 is missing expected H atoms. Skipping.
Residue ILE  315 is missing expected H atoms. Skipping.
Residue ALA  321 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue ILE  325 is missing expected H atoms. Skipping.
Residue ALA  327 is missing expected H atoms. Skipping.
Residue LEU  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU  339 is missing expected H atoms. Skipping.
Residue VAL  342 is missing expected H atoms. Skipping.
Residue VAL  345 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  349 is missing expected H atoms. Skipping.
Residue ALA  352 is missing expected H atoms. Skipping.
Residue THR  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LEU  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue ALA  368 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  374 is missing expected H atoms. Skipping.
Residue ALA  375 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue LEU  380 is missing expected H atoms. Skipping.
Residue ILE  388 is missing expected H atoms. Skipping.
Residue ALA  389 is missing expected H atoms. Skipping.
Residue ILE  390 is missing expected H atoms. Skipping.
Residue ALA  391 is missing expected H atoms. Skipping.
Residue ALA  392 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue VAL  403 is missing expected H atoms. Skipping.
Residue ILE  405 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Residue ALA  415 is missing expected H atoms. Skipping.
Residue VAL  416 is missing expected H atoms. Skipping.
Residue ILE  420 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue ALA  426 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue MET  438 is missing expected H atoms. Skipping.
Residue ALA  441 is missing expected H atoms. Skipping.
Residue THR  442 is missing expected H atoms. Skipping.
Residue ILE  444 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue ILE  453 is missing expected H atoms. Skipping.
Residue VAL  454 is missing expected H atoms. Skipping.
Residue ALA  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue VAL  470 is missing expected H atoms. Skipping.
Residue ILE  471 is missing expected H atoms. Skipping.
Residue THR  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ALA  475 is missing expected H atoms. Skipping.
Residue LEU  477 is missing expected H atoms. Skipping.
Residue VAL  479 is missing expected H atoms. Skipping.
Residue ILE  483 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue THR  490 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue THR  496 is missing expected H atoms. Skipping.
Residue ALA  497 is missing expected H atoms. Skipping.
Residue LEU  498 is missing expected H atoms. Skipping.
Residue VAL  500 is missing expected H atoms. Skipping.
Residue VAL  505 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue ALA  511 is missing expected H atoms. Skipping.
Residue VAL  516 is missing expected H atoms. Skipping.
Residue LEU  517 is missing expected H atoms. Skipping.
Residue LEU  521 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  532 is missing expected H atoms. Skipping.
Residue ALA  537 is missing expected H atoms. Skipping.
Residue ILE  538 is missing expected H atoms. Skipping.
Residue ALA  541 is missing expected H atoms. Skipping.
Residue LEU  542 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue THR  556 is missing expected H atoms. Skipping.
Residue ILE  557 is missing expected H atoms. Skipping.
Residue LEU  562 is missing expected H atoms. Skipping.
Residue MET  563 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue ALA  570 is missing expected H atoms. Skipping.
Residue LEU  572 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue THR  583 is missing expected H atoms. Skipping.
Residue ILE  585 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue ILE  587 is missing expected H atoms. Skipping.
Residue MET  589 is missing expected H atoms. Skipping.
Residue LEU  593 is missing expected H atoms. Skipping.
Residue THR  597 is missing expected H atoms. Skipping.
Residue ALA  598 is missing expected H atoms. Skipping.
Residue ALA  599 is missing expected H atoms. Skipping.
Residue THR  601 is missing expected H atoms. Skipping.
Residue THR  602 is missing expected H atoms. Skipping.
Residue LEU  604 is missing expected H atoms. Skipping.
Residue ILE  607 is missing expected H atoms. Skipping.
Residue LEU  608 is missing expected H atoms. Skipping.
Residue THR  612 is missing expected H atoms. Skipping.
Residue ALA  614 is missing expected H atoms. Skipping.
Residue ILE  616 is missing expected H atoms. Skipping.
Residue ALA  620 is missing expected H atoms. Skipping.
Residue ILE  622 is missing expected H atoms. Skipping.
Residue ILE   30 is missing expected H atoms. Skipping.
Residue THR   32 is missing expected H atoms. Skipping.
Residue THR   33 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LEU   43 is missing expected H atoms. Skipping.
Residue ALA   44 is missing expected H atoms. Skipping.
Residue VAL   45 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue ALA   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue LEU   59 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ALA   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   84 is missing expected H atoms. Skipping.
Residue ALA   87 is missing expected H atoms. Skipping.
Residue VAL   89 is missing expected H atoms. Skipping.
Residue LEU   90 is missing expected H atoms. Skipping.
Residue LEU   95 is missing expected H atoms. Skipping.
Residue VAL  106 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue VAL  109 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue ALA  115 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue VAL  133 is missing expected H atoms. Skipping.
Residue VAL  138 is missing expected H atoms. Skipping.
Residue ILE  140 is missing expected H atoms. Skipping.
Residue LEU  143 is missing expected H atoms. Skipping.
Residue MET  144 is missing expected H atoms. Skipping.
Residue LEU  146 is missing expected H atoms. Skipping.
Residue MET  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue ILE  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  162 is missing expected H atoms. Skipping.
Residue LEU  164 is missing expected H atoms. Skipping.
Residue ALA  165 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue MET  168 is missing expected H atoms. Skipping.
Residue LEU  171 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  181 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue MET  191 is missing expected H atoms. Skipping.
Residue ILE  193 is missing expected H atoms. Skipping.
Residue ALA  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  206 is missing expected H atoms. Skipping.
Residue THR  208 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue MET  213 is missing expected H atoms. Skipping.
Residue VAL  219 is missing expected H atoms. Skipping.
Residue LEU  220 is missing expected H atoms. Skipping.
Residue THR  221 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue THR  223 is missing expected H atoms. Skipping.
Residue VAL  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue ALA  244 is missing expected H atoms. Skipping.
Residue ALA  251 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue MET  253 is missing expected H atoms. Skipping.
Residue ALA  255 is missing expected H atoms. Skipping.
Residue THR  256 is missing expected H atoms. Skipping.
Residue VAL  257 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ALA  268 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue THR  275 is missing expected H atoms. Skipping.
Residue THR  276 is missing expected H atoms. Skipping.
Residue ALA  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue ILE  282 is missing expected H atoms. Skipping.
Residue ALA  283 is missing expected H atoms. Skipping.
Residue LEU  284 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue ALA  289 is missing expected H atoms. Skipping.
Residue ILE  291 is missing expected H atoms. Skipping.
Residue VAL  292 is missing expected H atoms. Skipping.
Residue VAL  301 is missing expected H atoms. Skipping.
Residue ALA  309 is missing expected H atoms. Skipping.
Residue THR  311 is missing expected H atoms. Skipping.
Residue THR  312 is missing expected H atoms. Skipping.
Residue MET  313 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue LEU  320 is missing expected H atoms. Skipping.
Residue MET  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  325 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue ILE  333 is missing expected H atoms. Skipping.
Residue ALA  335 is missing expected H atoms. Skipping.
Residue VAL  336 is missing expected H atoms. Skipping.
Residue THR  337 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue VAL  341 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  350 is missing expected H atoms. Skipping.
Residue ILE  351 is missing expected H atoms. Skipping.
Residue THR  354 is missing expected H atoms. Skipping.
Residue THR  355 is missing expected H atoms. Skipping.
Residue VAL  356 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue LEU  359 is missing expected H atoms. Skipping.
Residue MET  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue LEU  367 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue VAL  371 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  377 is missing expected H atoms. Skipping.
Residue VAL  381 is missing expected H atoms. Skipping.
Residue LEU  383 is missing expected H atoms. Skipping.
Residue VAL  385 is missing expected H atoms. Skipping.
Residue LEU  388 is missing expected H atoms. Skipping.
Residue LEU  392 is missing expected H atoms. Skipping.
Residue LEU  394 is missing expected H atoms. Skipping.
Residue ALA  398 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue LEU  401 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue ILE  406 is missing expected H atoms. Skipping.
Residue LEU  409 is missing expected H atoms. Skipping.
Residue MET  413 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue ILE  417 is missing expected H atoms. Skipping.
Residue THR  420 is missing expected H atoms. Skipping.
Residue VAL  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  441 is missing expected H atoms. Skipping.
Residue ILE  442 is missing expected H atoms. Skipping.
Residue VAL  445 is missing expected H atoms. Skipping.
Residue LEU  451 is missing expected H atoms. Skipping.
Residue ILE  452 is missing expected H atoms. Skipping.
Residue VAL  453 is missing expected H atoms. Skipping.
Residue VAL  455 is missing expected H atoms. Skipping.
Residue THR  456 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ALA  465 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue THR  480 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Evaluate side-chains
  69 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 48
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 21
  outliers final: 11
  residues processed: 63
  average time/residue: 0.7924
  time to fit residues: 53.4839
Evaluate side-chains
  59 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  305 TYR
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  547 ARG
Chi-restraints excluded: chain B residue   97 ASP
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  432 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 104 optimal weight:    0.2980
   chunk 6 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 8 optimal weight:    0.0970
   chunk 83 optimal weight:    1.9990
   chunk 59 optimal weight:    7.9990
   chunk 19 optimal weight:    0.4980
   chunk 23 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
A 182 GLN
A 212 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.094751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.062070 restraints weight = 23549.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.2851 rms_B_bonded: 2.66
r_work: 0.2706 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2576 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8772
moved from start:          0.1971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8478  Z= 0.103
  Angle     :  0.500  12.756  11495  Z= 0.258
  Chirality :  0.042   0.221   1252
  Planarity :  0.003   0.026   1519
  Dihedral  :  4.249  49.287   1165
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 16.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 13.72 %
    Favored  : 84.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.28 (0.26), residues: 1069
  helix:  0.48 (0.52), residues: 111
  sheet:  0.76 (0.29), residues: 337
  loop : -0.14 (0.25), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 242 
 TYR   0.012   0.001   TYR B 204 
 PHE   0.008   0.001   PHE B 274 
 TRP   0.006   0.001   TRP A 209 
 HIS   0.001   0.000   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 8462)
  covalent geometry    : angle       0.47125 (11463)
  SS BOND              : bond        0.00190 (   16)
  SS BOND              : angle       3.20482 (   32)
  hydrogen bonds       : bond        0.02567 (  275)
  hydrogen bonds       : angle       5.48060 (  711)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   33 is missing expected H atoms. Skipping.
Residue VAL   35 is missing expected H atoms. Skipping.
Residue ALA   39 is missing expected H atoms. Skipping.
Residue ALA   52 is missing expected H atoms. Skipping.
Residue VAL   53 is missing expected H atoms. Skipping.
Residue VAL   57 is missing expected H atoms. Skipping.
Residue ALA   60 is missing expected H atoms. Skipping.
Residue MET   64 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue VAL   68 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue THR   75 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   86 is missing expected H atoms. Skipping.
Residue LEU   87 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ILE  100 is missing expected H atoms. Skipping.
Residue ALA  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue ALA  111 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue ALA  126 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue ALA  137 is missing expected H atoms. Skipping.
Residue ALA  139 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  146 is missing expected H atoms. Skipping.
Residue MET  148 is missing expected H atoms. Skipping.
Residue VAL  155 is missing expected H atoms. Skipping.
Residue THR  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  164 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue VAL  167 is missing expected H atoms. Skipping.
Residue ALA  170 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  179 is missing expected H atoms. Skipping.
Residue ILE  191 is missing expected H atoms. Skipping.
Residue THR  194 is missing expected H atoms. Skipping.
Residue ALA  196 is missing expected H atoms. Skipping.
Residue VAL  199 is missing expected H atoms. Skipping.
Residue LEU  200 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LEU  213 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue ALA  219 is missing expected H atoms. Skipping.
Residue ILE  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Residue VAL  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LEU  238 is missing expected H atoms. Skipping.
Residue ALA  239 is missing expected H atoms. Skipping.
Residue THR  240 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue ALA  243 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue ILE  246 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue VAL  256 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  258 is missing expected H atoms. Skipping.
Residue ILE  266 is missing expected H atoms. Skipping.
Residue VAL  270 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue ALA  276 is missing expected H atoms. Skipping.
Residue ALA  277 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue LEU  280 is missing expected H atoms. Skipping.
Residue MET  282 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  285 is missing expected H atoms. Skipping.
Residue MET  291 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue THR  298 is missing expected H atoms. Skipping.
Residue MET  302 is missing expected H atoms. Skipping.
Residue ALA  303 is missing expected H atoms. Skipping.
Residue ALA  304 is missing expected H atoms. Skipping.
Residue VAL  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue ALA  312 is missing expected H atoms. Skipping.
Residue THR  313 is missing expected H atoms. Skipping.
Residue ILE  315 is missing expected H atoms. Skipping.
Residue ALA  321 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue ILE  325 is missing expected H atoms. Skipping.
Residue ALA  327 is missing expected H atoms. Skipping.
Residue LEU  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU  339 is missing expected H atoms. Skipping.
Residue VAL  342 is missing expected H atoms. Skipping.
Residue VAL  345 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  349 is missing expected H atoms. Skipping.
Residue ALA  352 is missing expected H atoms. Skipping.
Residue THR  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LEU  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue ALA  368 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  374 is missing expected H atoms. Skipping.
Residue ALA  375 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue LEU  380 is missing expected H atoms. Skipping.
Residue ILE  388 is missing expected H atoms. Skipping.
Residue ALA  389 is missing expected H atoms. Skipping.
Residue ILE  390 is missing expected H atoms. Skipping.
Residue ALA  391 is missing expected H atoms. Skipping.
Residue ALA  392 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue VAL  403 is missing expected H atoms. Skipping.
Residue ILE  405 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Residue ALA  415 is missing expected H atoms. Skipping.
Residue VAL  416 is missing expected H atoms. Skipping.
Residue ILE  420 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue ALA  426 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue MET  438 is missing expected H atoms. Skipping.
Residue ALA  441 is missing expected H atoms. Skipping.
Residue THR  442 is missing expected H atoms. Skipping.
Residue ILE  444 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue ILE  453 is missing expected H atoms. Skipping.
Residue VAL  454 is missing expected H atoms. Skipping.
Residue ALA  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue VAL  470 is missing expected H atoms. Skipping.
Residue ILE  471 is missing expected H atoms. Skipping.
Residue THR  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ALA  475 is missing expected H atoms. Skipping.
Residue LEU  477 is missing expected H atoms. Skipping.
Residue VAL  479 is missing expected H atoms. Skipping.
Residue ILE  483 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue THR  490 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue THR  496 is missing expected H atoms. Skipping.
Residue ALA  497 is missing expected H atoms. Skipping.
Residue LEU  498 is missing expected H atoms. Skipping.
Residue VAL  500 is missing expected H atoms. Skipping.
Residue VAL  505 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue ALA  511 is missing expected H atoms. Skipping.
Residue VAL  516 is missing expected H atoms. Skipping.
Residue LEU  517 is missing expected H atoms. Skipping.
Residue LEU  521 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  532 is missing expected H atoms. Skipping.
Residue ALA  537 is missing expected H atoms. Skipping.
Residue ILE  538 is missing expected H atoms. Skipping.
Residue ALA  541 is missing expected H atoms. Skipping.
Residue LEU  542 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue THR  556 is missing expected H atoms. Skipping.
Residue ILE  557 is missing expected H atoms. Skipping.
Residue LEU  562 is missing expected H atoms. Skipping.
Residue MET  563 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue ALA  570 is missing expected H atoms. Skipping.
Residue LEU  572 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue THR  583 is missing expected H atoms. Skipping.
Residue ILE  585 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue ILE  587 is missing expected H atoms. Skipping.
Residue MET  589 is missing expected H atoms. Skipping.
Residue LEU  593 is missing expected H atoms. Skipping.
Residue THR  597 is missing expected H atoms. Skipping.
Residue ALA  598 is missing expected H atoms. Skipping.
Residue ALA  599 is missing expected H atoms. Skipping.
Residue THR  601 is missing expected H atoms. Skipping.
Residue THR  602 is missing expected H atoms. Skipping.
Residue LEU  604 is missing expected H atoms. Skipping.
Residue ILE  607 is missing expected H atoms. Skipping.
Residue LEU  608 is missing expected H atoms. Skipping.
Residue THR  612 is missing expected H atoms. Skipping.
Residue ALA  614 is missing expected H atoms. Skipping.
Residue ILE  616 is missing expected H atoms. Skipping.
Residue ALA  620 is missing expected H atoms. Skipping.
Residue ILE  622 is missing expected H atoms. Skipping.
Residue ILE   30 is missing expected H atoms. Skipping.
Residue THR   32 is missing expected H atoms. Skipping.
Residue THR   33 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LEU   43 is missing expected H atoms. Skipping.
Residue ALA   44 is missing expected H atoms. Skipping.
Residue VAL   45 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue ALA   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue LEU   59 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ALA   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   84 is missing expected H atoms. Skipping.
Residue ALA   87 is missing expected H atoms. Skipping.
Residue VAL   89 is missing expected H atoms. Skipping.
Residue LEU   90 is missing expected H atoms. Skipping.
Residue LEU   95 is missing expected H atoms. Skipping.
Residue VAL  106 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue VAL  109 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue ALA  115 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue VAL  133 is missing expected H atoms. Skipping.
Residue VAL  138 is missing expected H atoms. Skipping.
Residue ILE  140 is missing expected H atoms. Skipping.
Residue LEU  143 is missing expected H atoms. Skipping.
Residue MET  144 is missing expected H atoms. Skipping.
Residue LEU  146 is missing expected H atoms. Skipping.
Residue MET  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue ILE  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  162 is missing expected H atoms. Skipping.
Residue LEU  164 is missing expected H atoms. Skipping.
Residue ALA  165 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue MET  168 is missing expected H atoms. Skipping.
Residue LEU  171 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  181 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue MET  191 is missing expected H atoms. Skipping.
Residue ILE  193 is missing expected H atoms. Skipping.
Residue ALA  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  206 is missing expected H atoms. Skipping.
Residue THR  208 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue MET  213 is missing expected H atoms. Skipping.
Residue VAL  219 is missing expected H atoms. Skipping.
Residue LEU  220 is missing expected H atoms. Skipping.
Residue THR  221 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue THR  223 is missing expected H atoms. Skipping.
Residue VAL  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue ALA  244 is missing expected H atoms. Skipping.
Residue ALA  251 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue MET  253 is missing expected H atoms. Skipping.
Residue ALA  255 is missing expected H atoms. Skipping.
Residue THR  256 is missing expected H atoms. Skipping.
Residue VAL  257 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ALA  268 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue THR  275 is missing expected H atoms. Skipping.
Residue THR  276 is missing expected H atoms. Skipping.
Residue ALA  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue ILE  282 is missing expected H atoms. Skipping.
Residue ALA  283 is missing expected H atoms. Skipping.
Residue LEU  284 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue ALA  289 is missing expected H atoms. Skipping.
Residue ILE  291 is missing expected H atoms. Skipping.
Residue VAL  292 is missing expected H atoms. Skipping.
Residue VAL  301 is missing expected H atoms. Skipping.
Residue ALA  309 is missing expected H atoms. Skipping.
Residue THR  311 is missing expected H atoms. Skipping.
Residue THR  312 is missing expected H atoms. Skipping.
Residue MET  313 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue LEU  320 is missing expected H atoms. Skipping.
Residue MET  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  325 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue ILE  333 is missing expected H atoms. Skipping.
Residue ALA  335 is missing expected H atoms. Skipping.
Residue VAL  336 is missing expected H atoms. Skipping.
Residue THR  337 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue VAL  341 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  350 is missing expected H atoms. Skipping.
Residue ILE  351 is missing expected H atoms. Skipping.
Residue THR  354 is missing expected H atoms. Skipping.
Residue THR  355 is missing expected H atoms. Skipping.
Residue VAL  356 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue LEU  359 is missing expected H atoms. Skipping.
Residue MET  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue LEU  367 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue VAL  371 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  377 is missing expected H atoms. Skipping.
Residue VAL  381 is missing expected H atoms. Skipping.
Residue LEU  383 is missing expected H atoms. Skipping.
Residue VAL  385 is missing expected H atoms. Skipping.
Residue LEU  388 is missing expected H atoms. Skipping.
Residue LEU  392 is missing expected H atoms. Skipping.
Residue LEU  394 is missing expected H atoms. Skipping.
Residue ALA  398 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue LEU  401 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue ILE  406 is missing expected H atoms. Skipping.
Residue LEU  409 is missing expected H atoms. Skipping.
Residue MET  413 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue ILE  417 is missing expected H atoms. Skipping.
Residue THR  420 is missing expected H atoms. Skipping.
Residue VAL  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  441 is missing expected H atoms. Skipping.
Residue ILE  442 is missing expected H atoms. Skipping.
Residue VAL  445 is missing expected H atoms. Skipping.
Residue LEU  451 is missing expected H atoms. Skipping.
Residue ILE  452 is missing expected H atoms. Skipping.
Residue VAL  453 is missing expected H atoms. Skipping.
Residue VAL  455 is missing expected H atoms. Skipping.
Residue THR  456 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ALA  465 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue THR  480 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Evaluate side-chains
  70 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 53
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  451 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8393 (m-30)
  outliers start: 17
  outliers final: 10
  residues processed: 65
  average time/residue: 0.7953
  time to fit residues: 55.1717
Evaluate side-chains
  59 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  451 ASP
Chi-restraints excluded: chain A residue  508 CYS
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  547 ARG
Chi-restraints excluded: chain B residue   97 ASP
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  429 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 104 optimal weight:    9.9990
   chunk 69 optimal weight:    1.9990
   chunk 103 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    1.7988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.092440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.059706 restraints weight = 23914.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.2787 rms_B_bonded: 2.65
r_work: 0.2644 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2517 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8816
moved from start:          0.1982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.036   8478  Z= 0.286
  Angle     :  0.594  12.807  11495  Z= 0.306
  Chirality :  0.046   0.219   1252
  Planarity :  0.003   0.028   1519
  Dihedral  :  4.724  52.264   1165
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 16.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 13.61 %
    Favored  : 84.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.04 (0.25), residues: 1069
  helix:  0.02 (0.50), residues: 110
  sheet:  0.64 (0.28), residues: 334
  loop : -0.26 (0.25), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 242 
 TYR   0.015   0.001   TYR B 204 
 PHE   0.015   0.002   PHE A 306 
 TRP   0.029   0.003   TRP B  51 
 HIS   0.004   0.001   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00674 ( 8462)
  covalent geometry    : angle       0.56983 (11463)
  SS BOND              : bond        0.00234 (   16)
  SS BOND              : angle       3.23349 (   32)
  hydrogen bonds       : bond        0.03327 (  275)
  hydrogen bonds       : angle       5.90027 (  711)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   33 is missing expected H atoms. Skipping.
Residue VAL   35 is missing expected H atoms. Skipping.
Residue ALA   39 is missing expected H atoms. Skipping.
Residue ALA   52 is missing expected H atoms. Skipping.
Residue VAL   53 is missing expected H atoms. Skipping.
Residue VAL   57 is missing expected H atoms. Skipping.
Residue ALA   60 is missing expected H atoms. Skipping.
Residue MET   64 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue VAL   68 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue THR   75 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   86 is missing expected H atoms. Skipping.
Residue LEU   87 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ILE  100 is missing expected H atoms. Skipping.
Residue ALA  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue ALA  111 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue ALA  126 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue ALA  137 is missing expected H atoms. Skipping.
Residue ALA  139 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  146 is missing expected H atoms. Skipping.
Residue MET  148 is missing expected H atoms. Skipping.
Residue VAL  155 is missing expected H atoms. Skipping.
Residue THR  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  164 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue VAL  167 is missing expected H atoms. Skipping.
Residue ALA  170 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  179 is missing expected H atoms. Skipping.
Residue ILE  191 is missing expected H atoms. Skipping.
Residue THR  194 is missing expected H atoms. Skipping.
Residue ALA  196 is missing expected H atoms. Skipping.
Residue VAL  199 is missing expected H atoms. Skipping.
Residue LEU  200 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LEU  213 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue ALA  219 is missing expected H atoms. Skipping.
Residue ILE  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Residue VAL  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LEU  238 is missing expected H atoms. Skipping.
Residue ALA  239 is missing expected H atoms. Skipping.
Residue THR  240 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue ALA  243 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue ILE  246 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue VAL  256 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  258 is missing expected H atoms. Skipping.
Residue ILE  266 is missing expected H atoms. Skipping.
Residue VAL  270 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue ALA  276 is missing expected H atoms. Skipping.
Residue ALA  277 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue LEU  280 is missing expected H atoms. Skipping.
Residue MET  282 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  285 is missing expected H atoms. Skipping.
Residue MET  291 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue THR  298 is missing expected H atoms. Skipping.
Residue MET  302 is missing expected H atoms. Skipping.
Residue ALA  303 is missing expected H atoms. Skipping.
Residue ALA  304 is missing expected H atoms. Skipping.
Residue VAL  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue ALA  312 is missing expected H atoms. Skipping.
Residue THR  313 is missing expected H atoms. Skipping.
Residue ILE  315 is missing expected H atoms. Skipping.
Residue ALA  321 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue ILE  325 is missing expected H atoms. Skipping.
Residue ALA  327 is missing expected H atoms. Skipping.
Residue LEU  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU  339 is missing expected H atoms. Skipping.
Residue VAL  342 is missing expected H atoms. Skipping.
Residue VAL  345 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  349 is missing expected H atoms. Skipping.
Residue ALA  352 is missing expected H atoms. Skipping.
Residue THR  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LEU  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue ALA  368 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  374 is missing expected H atoms. Skipping.
Residue ALA  375 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue LEU  380 is missing expected H atoms. Skipping.
Residue ILE  388 is missing expected H atoms. Skipping.
Residue ALA  389 is missing expected H atoms. Skipping.
Residue ILE  390 is missing expected H atoms. Skipping.
Residue ALA  391 is missing expected H atoms. Skipping.
Residue ALA  392 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue VAL  403 is missing expected H atoms. Skipping.
Residue ILE  405 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Residue ALA  415 is missing expected H atoms. Skipping.
Residue VAL  416 is missing expected H atoms. Skipping.
Residue ILE  420 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue ALA  426 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue MET  438 is missing expected H atoms. Skipping.
Residue ALA  441 is missing expected H atoms. Skipping.
Residue THR  442 is missing expected H atoms. Skipping.
Residue ILE  444 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue ILE  453 is missing expected H atoms. Skipping.
Residue VAL  454 is missing expected H atoms. Skipping.
Residue ALA  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue VAL  470 is missing expected H atoms. Skipping.
Residue ILE  471 is missing expected H atoms. Skipping.
Residue THR  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ALA  475 is missing expected H atoms. Skipping.
Residue LEU  477 is missing expected H atoms. Skipping.
Residue VAL  479 is missing expected H atoms. Skipping.
Residue ILE  483 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue THR  490 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue THR  496 is missing expected H atoms. Skipping.
Residue ALA  497 is missing expected H atoms. Skipping.
Residue LEU  498 is missing expected H atoms. Skipping.
Residue VAL  500 is missing expected H atoms. Skipping.
Residue VAL  505 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue ALA  511 is missing expected H atoms. Skipping.
Residue VAL  516 is missing expected H atoms. Skipping.
Residue LEU  517 is missing expected H atoms. Skipping.
Residue LEU  521 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  532 is missing expected H atoms. Skipping.
Residue ALA  537 is missing expected H atoms. Skipping.
Residue ILE  538 is missing expected H atoms. Skipping.
Residue ALA  541 is missing expected H atoms. Skipping.
Residue LEU  542 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue THR  556 is missing expected H atoms. Skipping.
Residue ILE  557 is missing expected H atoms. Skipping.
Residue LEU  562 is missing expected H atoms. Skipping.
Residue MET  563 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue ALA  570 is missing expected H atoms. Skipping.
Residue LEU  572 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue THR  583 is missing expected H atoms. Skipping.
Residue ILE  585 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue ILE  587 is missing expected H atoms. Skipping.
Residue MET  589 is missing expected H atoms. Skipping.
Residue LEU  593 is missing expected H atoms. Skipping.
Residue THR  597 is missing expected H atoms. Skipping.
Residue ALA  598 is missing expected H atoms. Skipping.
Residue ALA  599 is missing expected H atoms. Skipping.
Residue THR  601 is missing expected H atoms. Skipping.
Residue THR  602 is missing expected H atoms. Skipping.
Residue LEU  604 is missing expected H atoms. Skipping.
Residue ILE  607 is missing expected H atoms. Skipping.
Residue LEU  608 is missing expected H atoms. Skipping.
Residue THR  612 is missing expected H atoms. Skipping.
Residue ALA  614 is missing expected H atoms. Skipping.
Residue ILE  616 is missing expected H atoms. Skipping.
Residue ALA  620 is missing expected H atoms. Skipping.
Residue ILE  622 is missing expected H atoms. Skipping.
Residue ILE   30 is missing expected H atoms. Skipping.
Residue THR   32 is missing expected H atoms. Skipping.
Residue THR   33 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LEU   43 is missing expected H atoms. Skipping.
Residue ALA   44 is missing expected H atoms. Skipping.
Residue VAL   45 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue ALA   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue LEU   59 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ALA   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   84 is missing expected H atoms. Skipping.
Residue ALA   87 is missing expected H atoms. Skipping.
Residue VAL   89 is missing expected H atoms. Skipping.
Residue LEU   90 is missing expected H atoms. Skipping.
Residue LEU   95 is missing expected H atoms. Skipping.
Residue VAL  106 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue VAL  109 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue ALA  115 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue VAL  133 is missing expected H atoms. Skipping.
Residue VAL  138 is missing expected H atoms. Skipping.
Residue ILE  140 is missing expected H atoms. Skipping.
Residue LEU  143 is missing expected H atoms. Skipping.
Residue MET  144 is missing expected H atoms. Skipping.
Residue LEU  146 is missing expected H atoms. Skipping.
Residue MET  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue ILE  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  162 is missing expected H atoms. Skipping.
Residue LEU  164 is missing expected H atoms. Skipping.
Residue ALA  165 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue MET  168 is missing expected H atoms. Skipping.
Residue LEU  171 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  181 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue MET  191 is missing expected H atoms. Skipping.
Residue ILE  193 is missing expected H atoms. Skipping.
Residue ALA  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  206 is missing expected H atoms. Skipping.
Residue THR  208 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue MET  213 is missing expected H atoms. Skipping.
Residue VAL  219 is missing expected H atoms. Skipping.
Residue LEU  220 is missing expected H atoms. Skipping.
Residue THR  221 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue THR  223 is missing expected H atoms. Skipping.
Residue VAL  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue ALA  244 is missing expected H atoms. Skipping.
Residue ALA  251 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue MET  253 is missing expected H atoms. Skipping.
Residue ALA  255 is missing expected H atoms. Skipping.
Residue THR  256 is missing expected H atoms. Skipping.
Residue VAL  257 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ALA  268 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue THR  275 is missing expected H atoms. Skipping.
Residue THR  276 is missing expected H atoms. Skipping.
Residue ALA  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue ILE  282 is missing expected H atoms. Skipping.
Residue ALA  283 is missing expected H atoms. Skipping.
Residue LEU  284 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue ALA  289 is missing expected H atoms. Skipping.
Residue ILE  291 is missing expected H atoms. Skipping.
Residue VAL  292 is missing expected H atoms. Skipping.
Residue VAL  301 is missing expected H atoms. Skipping.
Residue ALA  309 is missing expected H atoms. Skipping.
Residue THR  311 is missing expected H atoms. Skipping.
Residue THR  312 is missing expected H atoms. Skipping.
Residue MET  313 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue LEU  320 is missing expected H atoms. Skipping.
Residue MET  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  325 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue ILE  333 is missing expected H atoms. Skipping.
Residue ALA  335 is missing expected H atoms. Skipping.
Residue VAL  336 is missing expected H atoms. Skipping.
Residue THR  337 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue VAL  341 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  350 is missing expected H atoms. Skipping.
Residue ILE  351 is missing expected H atoms. Skipping.
Residue THR  354 is missing expected H atoms. Skipping.
Residue THR  355 is missing expected H atoms. Skipping.
Residue VAL  356 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue LEU  359 is missing expected H atoms. Skipping.
Residue MET  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue LEU  367 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue VAL  371 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  377 is missing expected H atoms. Skipping.
Residue VAL  381 is missing expected H atoms. Skipping.
Residue LEU  383 is missing expected H atoms. Skipping.
Residue VAL  385 is missing expected H atoms. Skipping.
Residue LEU  388 is missing expected H atoms. Skipping.
Residue LEU  392 is missing expected H atoms. Skipping.
Residue LEU  394 is missing expected H atoms. Skipping.
Residue ALA  398 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue LEU  401 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue ILE  406 is missing expected H atoms. Skipping.
Residue LEU  409 is missing expected H atoms. Skipping.
Residue MET  413 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue ILE  417 is missing expected H atoms. Skipping.
Residue THR  420 is missing expected H atoms. Skipping.
Residue VAL  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  441 is missing expected H atoms. Skipping.
Residue ILE  442 is missing expected H atoms. Skipping.
Residue VAL  445 is missing expected H atoms. Skipping.
Residue LEU  451 is missing expected H atoms. Skipping.
Residue ILE  452 is missing expected H atoms. Skipping.
Residue VAL  453 is missing expected H atoms. Skipping.
Residue VAL  455 is missing expected H atoms. Skipping.
Residue THR  456 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ALA  465 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue THR  480 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Evaluate side-chains
  70 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 50
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8075 (tmt90)
REVERT: A  547 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8546 (tpt170)
REVERT: A  563 MET cc_start: 0.8775 (tpp) cc_final: 0.8560 (ttt)
  outliers start: 20
  outliers final: 13
  residues processed: 66
  average time/residue: 0.8324
  time to fit residues: 58.6709
Evaluate side-chains
  63 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 48
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  145 ARG
Chi-restraints excluded: chain A residue  305 TYR
Chi-restraints excluded: chain A residue  451 ASP
Chi-restraints excluded: chain A residue  508 CYS
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  547 ARG
Chi-restraints excluded: chain A residue  555 MET
Chi-restraints excluded: chain B residue   97 ASP
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  432 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 102 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.094049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.061589 restraints weight = 23688.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.2840 rms_B_bonded: 2.63
r_work: 0.2702 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2574 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8811
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8478  Z= 0.138
  Angle     :  0.522  12.384  11495  Z= 0.269
  Chirality :  0.043   0.198   1252
  Planarity :  0.003   0.025   1519
  Dihedral  :  4.358  52.250   1165
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 17.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 14.16 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.21 (0.26), residues: 1069
  helix:  0.36 (0.51), residues: 111
  sheet:  0.74 (0.29), residues: 333
  loop : -0.17 (0.25), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 242 
 TYR   0.014   0.001   TYR B 204 
 PHE   0.009   0.001   PHE B 274 
 TRP   0.035   0.002   TRP B  51 
 HIS   0.002   0.000   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8462)
  covalent geometry    : angle       0.49639 (11463)
  SS BOND              : bond        0.00214 (   16)
  SS BOND              : angle       3.11155 (   32)
  hydrogen bonds       : bond        0.02643 (  275)
  hydrogen bonds       : angle       5.53896 (  711)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   33 is missing expected H atoms. Skipping.
Residue VAL   35 is missing expected H atoms. Skipping.
Residue ALA   39 is missing expected H atoms. Skipping.
Residue ALA   52 is missing expected H atoms. Skipping.
Residue VAL   53 is missing expected H atoms. Skipping.
Residue VAL   57 is missing expected H atoms. Skipping.
Residue ALA   60 is missing expected H atoms. Skipping.
Residue MET   64 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue VAL   68 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue THR   75 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   86 is missing expected H atoms. Skipping.
Residue LEU   87 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ILE  100 is missing expected H atoms. Skipping.
Residue ALA  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue ALA  111 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue ALA  126 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue ALA  137 is missing expected H atoms. Skipping.
Residue ALA  139 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  146 is missing expected H atoms. Skipping.
Residue MET  148 is missing expected H atoms. Skipping.
Residue VAL  155 is missing expected H atoms. Skipping.
Residue THR  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  164 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue VAL  167 is missing expected H atoms. Skipping.
Residue ALA  170 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  179 is missing expected H atoms. Skipping.
Residue ILE  191 is missing expected H atoms. Skipping.
Residue THR  194 is missing expected H atoms. Skipping.
Residue ALA  196 is missing expected H atoms. Skipping.
Residue VAL  199 is missing expected H atoms. Skipping.
Residue LEU  200 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LEU  213 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue ALA  219 is missing expected H atoms. Skipping.
Residue ILE  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Residue VAL  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LEU  238 is missing expected H atoms. Skipping.
Residue ALA  239 is missing expected H atoms. Skipping.
Residue THR  240 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue ALA  243 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue ILE  246 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue VAL  256 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  258 is missing expected H atoms. Skipping.
Residue ILE  266 is missing expected H atoms. Skipping.
Residue VAL  270 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue ALA  276 is missing expected H atoms. Skipping.
Residue ALA  277 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue LEU  280 is missing expected H atoms. Skipping.
Residue MET  282 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  285 is missing expected H atoms. Skipping.
Residue MET  291 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue THR  298 is missing expected H atoms. Skipping.
Residue MET  302 is missing expected H atoms. Skipping.
Residue ALA  303 is missing expected H atoms. Skipping.
Residue ALA  304 is missing expected H atoms. Skipping.
Residue VAL  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue ALA  312 is missing expected H atoms. Skipping.
Residue THR  313 is missing expected H atoms. Skipping.
Residue ILE  315 is missing expected H atoms. Skipping.
Residue ALA  321 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue ILE  325 is missing expected H atoms. Skipping.
Residue ALA  327 is missing expected H atoms. Skipping.
Residue LEU  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU  339 is missing expected H atoms. Skipping.
Residue VAL  342 is missing expected H atoms. Skipping.
Residue VAL  345 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  349 is missing expected H atoms. Skipping.
Residue ALA  352 is missing expected H atoms. Skipping.
Residue THR  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LEU  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue ALA  368 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  374 is missing expected H atoms. Skipping.
Residue ALA  375 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue LEU  380 is missing expected H atoms. Skipping.
Residue ILE  388 is missing expected H atoms. Skipping.
Residue ALA  389 is missing expected H atoms. Skipping.
Residue ILE  390 is missing expected H atoms. Skipping.
Residue ALA  391 is missing expected H atoms. Skipping.
Residue ALA  392 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue VAL  403 is missing expected H atoms. Skipping.
Residue ILE  405 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Residue ALA  415 is missing expected H atoms. Skipping.
Residue VAL  416 is missing expected H atoms. Skipping.
Residue ILE  420 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue ALA  426 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue MET  438 is missing expected H atoms. Skipping.
Residue ALA  441 is missing expected H atoms. Skipping.
Residue THR  442 is missing expected H atoms. Skipping.
Residue ILE  444 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue ILE  453 is missing expected H atoms. Skipping.
Residue VAL  454 is missing expected H atoms. Skipping.
Residue ALA  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue VAL  470 is missing expected H atoms. Skipping.
Residue ILE  471 is missing expected H atoms. Skipping.
Residue THR  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ALA  475 is missing expected H atoms. Skipping.
Residue LEU  477 is missing expected H atoms. Skipping.
Residue VAL  479 is missing expected H atoms. Skipping.
Residue ILE  483 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue THR  490 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue THR  496 is missing expected H atoms. Skipping.
Residue ALA  497 is missing expected H atoms. Skipping.
Residue LEU  498 is missing expected H atoms. Skipping.
Residue VAL  500 is missing expected H atoms. Skipping.
Residue VAL  505 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue ALA  511 is missing expected H atoms. Skipping.
Residue VAL  516 is missing expected H atoms. Skipping.
Residue LEU  517 is missing expected H atoms. Skipping.
Residue LEU  521 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  532 is missing expected H atoms. Skipping.
Residue ALA  537 is missing expected H atoms. Skipping.
Residue ILE  538 is missing expected H atoms. Skipping.
Residue ALA  541 is missing expected H atoms. Skipping.
Residue LEU  542 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue THR  556 is missing expected H atoms. Skipping.
Residue ILE  557 is missing expected H atoms. Skipping.
Residue LEU  562 is missing expected H atoms. Skipping.
Residue MET  563 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue ALA  570 is missing expected H atoms. Skipping.
Residue LEU  572 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue THR  583 is missing expected H atoms. Skipping.
Residue ILE  585 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue ILE  587 is missing expected H atoms. Skipping.
Residue MET  589 is missing expected H atoms. Skipping.
Residue LEU  593 is missing expected H atoms. Skipping.
Residue THR  597 is missing expected H atoms. Skipping.
Residue ALA  598 is missing expected H atoms. Skipping.
Residue ALA  599 is missing expected H atoms. Skipping.
Residue THR  601 is missing expected H atoms. Skipping.
Residue THR  602 is missing expected H atoms. Skipping.
Residue LEU  604 is missing expected H atoms. Skipping.
Residue ILE  607 is missing expected H atoms. Skipping.
Residue LEU  608 is missing expected H atoms. Skipping.
Residue THR  612 is missing expected H atoms. Skipping.
Residue ALA  614 is missing expected H atoms. Skipping.
Residue ILE  616 is missing expected H atoms. Skipping.
Residue ALA  620 is missing expected H atoms. Skipping.
Residue ILE  622 is missing expected H atoms. Skipping.
Residue ILE   30 is missing expected H atoms. Skipping.
Residue THR   32 is missing expected H atoms. Skipping.
Residue THR   33 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LEU   43 is missing expected H atoms. Skipping.
Residue ALA   44 is missing expected H atoms. Skipping.
Residue VAL   45 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue ALA   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue LEU   59 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ALA   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   84 is missing expected H atoms. Skipping.
Residue ALA   87 is missing expected H atoms. Skipping.
Residue VAL   89 is missing expected H atoms. Skipping.
Residue LEU   90 is missing expected H atoms. Skipping.
Residue LEU   95 is missing expected H atoms. Skipping.
Residue VAL  106 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue VAL  109 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue ALA  115 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue VAL  133 is missing expected H atoms. Skipping.
Residue VAL  138 is missing expected H atoms. Skipping.
Residue ILE  140 is missing expected H atoms. Skipping.
Residue LEU  143 is missing expected H atoms. Skipping.
Residue MET  144 is missing expected H atoms. Skipping.
Residue LEU  146 is missing expected H atoms. Skipping.
Residue MET  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue ILE  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  162 is missing expected H atoms. Skipping.
Residue LEU  164 is missing expected H atoms. Skipping.
Residue ALA  165 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue MET  168 is missing expected H atoms. Skipping.
Residue LEU  171 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  181 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue MET  191 is missing expected H atoms. Skipping.
Residue ILE  193 is missing expected H atoms. Skipping.
Residue ALA  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  206 is missing expected H atoms. Skipping.
Residue THR  208 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue MET  213 is missing expected H atoms. Skipping.
Residue VAL  219 is missing expected H atoms. Skipping.
Residue LEU  220 is missing expected H atoms. Skipping.
Residue THR  221 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue THR  223 is missing expected H atoms. Skipping.
Residue VAL  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue ALA  244 is missing expected H atoms. Skipping.
Residue ALA  251 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue MET  253 is missing expected H atoms. Skipping.
Residue ALA  255 is missing expected H atoms. Skipping.
Residue THR  256 is missing expected H atoms. Skipping.
Residue VAL  257 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ALA  268 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue THR  275 is missing expected H atoms. Skipping.
Residue THR  276 is missing expected H atoms. Skipping.
Residue ALA  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue ILE  282 is missing expected H atoms. Skipping.
Residue ALA  283 is missing expected H atoms. Skipping.
Residue LEU  284 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue ALA  289 is missing expected H atoms. Skipping.
Residue ILE  291 is missing expected H atoms. Skipping.
Residue VAL  292 is missing expected H atoms. Skipping.
Residue VAL  301 is missing expected H atoms. Skipping.
Residue ALA  309 is missing expected H atoms. Skipping.
Residue THR  311 is missing expected H atoms. Skipping.
Residue THR  312 is missing expected H atoms. Skipping.
Residue MET  313 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue LEU  320 is missing expected H atoms. Skipping.
Residue MET  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  325 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue ILE  333 is missing expected H atoms. Skipping.
Residue ALA  335 is missing expected H atoms. Skipping.
Residue VAL  336 is missing expected H atoms. Skipping.
Residue THR  337 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue VAL  341 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  350 is missing expected H atoms. Skipping.
Residue ILE  351 is missing expected H atoms. Skipping.
Residue THR  354 is missing expected H atoms. Skipping.
Residue THR  355 is missing expected H atoms. Skipping.
Residue VAL  356 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue LEU  359 is missing expected H atoms. Skipping.
Residue MET  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue LEU  367 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue VAL  371 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  377 is missing expected H atoms. Skipping.
Residue VAL  381 is missing expected H atoms. Skipping.
Residue LEU  383 is missing expected H atoms. Skipping.
Residue VAL  385 is missing expected H atoms. Skipping.
Residue LEU  388 is missing expected H atoms. Skipping.
Residue LEU  392 is missing expected H atoms. Skipping.
Residue LEU  394 is missing expected H atoms. Skipping.
Residue ALA  398 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue LEU  401 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue ILE  406 is missing expected H atoms. Skipping.
Residue LEU  409 is missing expected H atoms. Skipping.
Residue MET  413 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue ILE  417 is missing expected H atoms. Skipping.
Residue THR  420 is missing expected H atoms. Skipping.
Residue VAL  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  441 is missing expected H atoms. Skipping.
Residue ILE  442 is missing expected H atoms. Skipping.
Residue VAL  445 is missing expected H atoms. Skipping.
Residue LEU  451 is missing expected H atoms. Skipping.
Residue ILE  452 is missing expected H atoms. Skipping.
Residue VAL  453 is missing expected H atoms. Skipping.
Residue VAL  455 is missing expected H atoms. Skipping.
Residue THR  456 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ALA  465 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue THR  480 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Evaluate side-chains
  67 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 50
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.7985 (tmt90)
REVERT: A  563 MET cc_start: 0.8725 (tpp) cc_final: 0.8500 (ttt)
REVERT: B   40 GLN cc_start: 0.9131 (tp40) cc_final: 0.8791 (tm-30)
  outliers start: 17
  outliers final: 12
  residues processed: 64
  average time/residue: 0.7785
  time to fit residues: 53.1575
Evaluate side-chains
  62 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  145 ARG
Chi-restraints excluded: chain A residue  451 ASP
Chi-restraints excluded: chain A residue  508 CYS
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  547 ARG
Chi-restraints excluded: chain A residue  555 MET
Chi-restraints excluded: chain B residue   97 ASP
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  432 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 106 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 91 optimal weight:    0.8980
   chunk 80 optimal weight:    0.6980
   chunk 45 optimal weight:    7.9990
   chunk 10 optimal weight:    0.4980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.094370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.062140 restraints weight = 23502.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.2827 rms_B_bonded: 2.61
r_work: 0.2687 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2561 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8742
moved from start:          0.2134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8478  Z= 0.136
  Angle     :  0.523  12.162  11495  Z= 0.269
  Chirality :  0.043   0.190   1252
  Planarity :  0.003   0.025   1519
  Dihedral  :  4.296  52.210   1165
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 17.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 14.49 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.29 (0.26), residues: 1069
  helix:  0.56 (0.53), residues: 105
  sheet:  0.72 (0.28), residues: 339
  loop : -0.11 (0.25), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 242 
 TYR   0.015   0.001   TYR B 204 
 PHE   0.009   0.001   PHE B 274 
 TRP   0.034   0.002   TRP B  51 
 HIS   0.003   0.000   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8462)
  covalent geometry    : angle       0.49798 (11463)
  SS BOND              : bond        0.00185 (   16)
  SS BOND              : angle       3.07841 (   32)
  hydrogen bonds       : bond        0.02614 (  275)
  hydrogen bonds       : angle       5.47903 (  711)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   33 is missing expected H atoms. Skipping.
Residue VAL   35 is missing expected H atoms. Skipping.
Residue ALA   39 is missing expected H atoms. Skipping.
Residue ALA   52 is missing expected H atoms. Skipping.
Residue VAL   53 is missing expected H atoms. Skipping.
Residue VAL   57 is missing expected H atoms. Skipping.
Residue ALA   60 is missing expected H atoms. Skipping.
Residue MET   64 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue VAL   68 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue THR   75 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   86 is missing expected H atoms. Skipping.
Residue LEU   87 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ILE  100 is missing expected H atoms. Skipping.
Residue ALA  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue ALA  111 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue ALA  126 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue ALA  137 is missing expected H atoms. Skipping.
Residue ALA  139 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  146 is missing expected H atoms. Skipping.
Residue MET  148 is missing expected H atoms. Skipping.
Residue VAL  155 is missing expected H atoms. Skipping.
Residue THR  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  164 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue VAL  167 is missing expected H atoms. Skipping.
Residue ALA  170 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  179 is missing expected H atoms. Skipping.
Residue ILE  191 is missing expected H atoms. Skipping.
Residue THR  194 is missing expected H atoms. Skipping.
Residue ALA  196 is missing expected H atoms. Skipping.
Residue VAL  199 is missing expected H atoms. Skipping.
Residue LEU  200 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LEU  213 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue ALA  219 is missing expected H atoms. Skipping.
Residue ILE  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Residue VAL  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LEU  238 is missing expected H atoms. Skipping.
Residue ALA  239 is missing expected H atoms. Skipping.
Residue THR  240 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue ALA  243 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue ILE  246 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue VAL  256 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  258 is missing expected H atoms. Skipping.
Residue ILE  266 is missing expected H atoms. Skipping.
Residue VAL  270 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue ALA  276 is missing expected H atoms. Skipping.
Residue ALA  277 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue LEU  280 is missing expected H atoms. Skipping.
Residue MET  282 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  285 is missing expected H atoms. Skipping.
Residue MET  291 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue THR  298 is missing expected H atoms. Skipping.
Residue MET  302 is missing expected H atoms. Skipping.
Residue ALA  303 is missing expected H atoms. Skipping.
Residue ALA  304 is missing expected H atoms. Skipping.
Residue VAL  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue ALA  312 is missing expected H atoms. Skipping.
Residue THR  313 is missing expected H atoms. Skipping.
Residue ILE  315 is missing expected H atoms. Skipping.
Residue ALA  321 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue ILE  325 is missing expected H atoms. Skipping.
Residue ALA  327 is missing expected H atoms. Skipping.
Residue LEU  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU  339 is missing expected H atoms. Skipping.
Residue VAL  342 is missing expected H atoms. Skipping.
Residue VAL  345 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  349 is missing expected H atoms. Skipping.
Residue ALA  352 is missing expected H atoms. Skipping.
Residue THR  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LEU  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue ALA  368 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  374 is missing expected H atoms. Skipping.
Residue ALA  375 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue LEU  380 is missing expected H atoms. Skipping.
Residue ILE  388 is missing expected H atoms. Skipping.
Residue ALA  389 is missing expected H atoms. Skipping.
Residue ILE  390 is missing expected H atoms. Skipping.
Residue ALA  391 is missing expected H atoms. Skipping.
Residue ALA  392 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue VAL  403 is missing expected H atoms. Skipping.
Residue ILE  405 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Residue ALA  415 is missing expected H atoms. Skipping.
Residue VAL  416 is missing expected H atoms. Skipping.
Residue ILE  420 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue ALA  426 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue MET  438 is missing expected H atoms. Skipping.
Residue ALA  441 is missing expected H atoms. Skipping.
Residue THR  442 is missing expected H atoms. Skipping.
Residue ILE  444 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue ILE  453 is missing expected H atoms. Skipping.
Residue VAL  454 is missing expected H atoms. Skipping.
Residue ALA  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue VAL  470 is missing expected H atoms. Skipping.
Residue ILE  471 is missing expected H atoms. Skipping.
Residue THR  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ALA  475 is missing expected H atoms. Skipping.
Residue LEU  477 is missing expected H atoms. Skipping.
Residue VAL  479 is missing expected H atoms. Skipping.
Residue ILE  483 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue THR  490 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue THR  496 is missing expected H atoms. Skipping.
Residue ALA  497 is missing expected H atoms. Skipping.
Residue LEU  498 is missing expected H atoms. Skipping.
Residue VAL  500 is missing expected H atoms. Skipping.
Residue VAL  505 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue ALA  511 is missing expected H atoms. Skipping.
Residue VAL  516 is missing expected H atoms. Skipping.
Residue LEU  517 is missing expected H atoms. Skipping.
Residue LEU  521 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  532 is missing expected H atoms. Skipping.
Residue ALA  537 is missing expected H atoms. Skipping.
Residue ILE  538 is missing expected H atoms. Skipping.
Residue ALA  541 is missing expected H atoms. Skipping.
Residue LEU  542 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue THR  556 is missing expected H atoms. Skipping.
Residue ILE  557 is missing expected H atoms. Skipping.
Residue LEU  562 is missing expected H atoms. Skipping.
Residue MET  563 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue ALA  570 is missing expected H atoms. Skipping.
Residue LEU  572 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue THR  583 is missing expected H atoms. Skipping.
Residue ILE  585 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue ILE  587 is missing expected H atoms. Skipping.
Residue MET  589 is missing expected H atoms. Skipping.
Residue LEU  593 is missing expected H atoms. Skipping.
Residue THR  597 is missing expected H atoms. Skipping.
Residue ALA  598 is missing expected H atoms. Skipping.
Residue ALA  599 is missing expected H atoms. Skipping.
Residue THR  601 is missing expected H atoms. Skipping.
Residue THR  602 is missing expected H atoms. Skipping.
Residue LEU  604 is missing expected H atoms. Skipping.
Residue ILE  607 is missing expected H atoms. Skipping.
Residue LEU  608 is missing expected H atoms. Skipping.
Residue THR  612 is missing expected H atoms. Skipping.
Residue ALA  614 is missing expected H atoms. Skipping.
Residue ILE  616 is missing expected H atoms. Skipping.
Residue ALA  620 is missing expected H atoms. Skipping.
Residue ILE  622 is missing expected H atoms. Skipping.
Residue ILE   30 is missing expected H atoms. Skipping.
Residue THR   32 is missing expected H atoms. Skipping.
Residue THR   33 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LEU   43 is missing expected H atoms. Skipping.
Residue ALA   44 is missing expected H atoms. Skipping.
Residue VAL   45 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue ALA   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue LEU   59 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ALA   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   84 is missing expected H atoms. Skipping.
Residue ALA   87 is missing expected H atoms. Skipping.
Residue VAL   89 is missing expected H atoms. Skipping.
Residue LEU   90 is missing expected H atoms. Skipping.
Residue LEU   95 is missing expected H atoms. Skipping.
Residue VAL  106 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue VAL  109 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue ALA  115 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue VAL  133 is missing expected H atoms. Skipping.
Residue VAL  138 is missing expected H atoms. Skipping.
Residue ILE  140 is missing expected H atoms. Skipping.
Residue LEU  143 is missing expected H atoms. Skipping.
Residue MET  144 is missing expected H atoms. Skipping.
Residue LEU  146 is missing expected H atoms. Skipping.
Residue MET  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue ILE  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  162 is missing expected H atoms. Skipping.
Residue LEU  164 is missing expected H atoms. Skipping.
Residue ALA  165 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue MET  168 is missing expected H atoms. Skipping.
Residue LEU  171 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  181 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue MET  191 is missing expected H atoms. Skipping.
Residue ILE  193 is missing expected H atoms. Skipping.
Residue ALA  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  206 is missing expected H atoms. Skipping.
Residue THR  208 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue MET  213 is missing expected H atoms. Skipping.
Residue VAL  219 is missing expected H atoms. Skipping.
Residue LEU  220 is missing expected H atoms. Skipping.
Residue THR  221 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue THR  223 is missing expected H atoms. Skipping.
Residue VAL  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue ALA  244 is missing expected H atoms. Skipping.
Residue ALA  251 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue MET  253 is missing expected H atoms. Skipping.
Residue ALA  255 is missing expected H atoms. Skipping.
Residue THR  256 is missing expected H atoms. Skipping.
Residue VAL  257 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ALA  268 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue THR  275 is missing expected H atoms. Skipping.
Residue THR  276 is missing expected H atoms. Skipping.
Residue ALA  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue ILE  282 is missing expected H atoms. Skipping.
Residue ALA  283 is missing expected H atoms. Skipping.
Residue LEU  284 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue ALA  289 is missing expected H atoms. Skipping.
Residue ILE  291 is missing expected H atoms. Skipping.
Residue VAL  292 is missing expected H atoms. Skipping.
Residue VAL  301 is missing expected H atoms. Skipping.
Residue ALA  309 is missing expected H atoms. Skipping.
Residue THR  311 is missing expected H atoms. Skipping.
Residue THR  312 is missing expected H atoms. Skipping.
Residue MET  313 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue LEU  320 is missing expected H atoms. Skipping.
Residue MET  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  325 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue ILE  333 is missing expected H atoms. Skipping.
Residue ALA  335 is missing expected H atoms. Skipping.
Residue VAL  336 is missing expected H atoms. Skipping.
Residue THR  337 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue VAL  341 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  350 is missing expected H atoms. Skipping.
Residue ILE  351 is missing expected H atoms. Skipping.
Residue THR  354 is missing expected H atoms. Skipping.
Residue THR  355 is missing expected H atoms. Skipping.
Residue VAL  356 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue LEU  359 is missing expected H atoms. Skipping.
Residue MET  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue LEU  367 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue VAL  371 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  377 is missing expected H atoms. Skipping.
Residue VAL  381 is missing expected H atoms. Skipping.
Residue LEU  383 is missing expected H atoms. Skipping.
Residue VAL  385 is missing expected H atoms. Skipping.
Residue LEU  388 is missing expected H atoms. Skipping.
Residue LEU  392 is missing expected H atoms. Skipping.
Residue LEU  394 is missing expected H atoms. Skipping.
Residue ALA  398 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue LEU  401 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue ILE  406 is missing expected H atoms. Skipping.
Residue LEU  409 is missing expected H atoms. Skipping.
Residue MET  413 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue ILE  417 is missing expected H atoms. Skipping.
Residue THR  420 is missing expected H atoms. Skipping.
Residue VAL  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  441 is missing expected H atoms. Skipping.
Residue ILE  442 is missing expected H atoms. Skipping.
Residue VAL  445 is missing expected H atoms. Skipping.
Residue LEU  451 is missing expected H atoms. Skipping.
Residue ILE  452 is missing expected H atoms. Skipping.
Residue VAL  453 is missing expected H atoms. Skipping.
Residue VAL  455 is missing expected H atoms. Skipping.
Residue THR  456 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ALA  465 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue THR  480 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Evaluate side-chains
  64 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.7946 (tmt90)
REVERT: B   40 GLN cc_start: 0.9088 (tp40) cc_final: 0.8800 (mp10)
  outliers start: 14
  outliers final: 10
  residues processed: 62
  average time/residue: 0.8803
  time to fit residues: 58.1190
Evaluate side-chains
  61 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  145 ARG
Chi-restraints excluded: chain A residue  451 ASP
Chi-restraints excluded: chain A residue  508 CYS
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  547 ARG
Chi-restraints excluded: chain A residue  555 MET
Chi-restraints excluded: chain B residue   97 ASP
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  429 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 88 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 21 optimal weight:    0.4980
   chunk 17 optimal weight:    0.5980
   chunk 72 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0770
   chunk 59 optimal weight:    9.9990
   overall best weight:    0.8342

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.094314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.061954 restraints weight = 23799.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.2824 rms_B_bonded: 2.63
r_work: 0.2686 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2557 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8750
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8478  Z= 0.148
  Angle     :  0.531  13.491  11495  Z= 0.273
  Chirality :  0.043   0.230   1252
  Planarity :  0.003   0.025   1519
  Dihedral  :  4.315  52.507   1165
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 18.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 14.38 %
    Favored  : 84.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.26), residues: 1069
  helix:  0.56 (0.53), residues: 105
  sheet:  0.76 (0.28), residues: 337
  loop : -0.11 (0.25), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  63 
 TYR   0.014   0.001   TYR B 204 
 PHE   0.009   0.001   PHE B 274 
 TRP   0.012   0.001   TRP B  51 
 HIS   0.003   0.000   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 8462)
  covalent geometry    : angle       0.50221 (11463)
  SS BOND              : bond        0.00162 (   16)
  SS BOND              : angle       3.32985 (   32)
  hydrogen bonds       : bond        0.02665 (  275)
  hydrogen bonds       : angle       5.45776 (  711)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3986.15 seconds
wall clock time: 68 minutes 40.70 seconds (4120.70 seconds total)