Starting phenix.real_space_refine
on Fri Jan 17 00:12:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xel_38293/01_2025/8xel_38293_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xel_38293/01_2025/8xel_38293.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xel_38293/01_2025/8xel_38293.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xel_38293/01_2025/8xel_38293.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xel_38293/01_2025/8xel_38293_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xel_38293/01_2025/8xel_38293_neut.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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    5203      2.51       5
     N    1409      2.21       5
     O    1614      1.98       5
     H    1837      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 10119
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 592, 5602
          Classifications: {'peptide': 592}
          Link IDs: {'CIS': 2, 'PTRANS': 28, 'TRANS': 561}
    Chain: "B"
      Number of atoms: 4517
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 479, 4517
          Classifications: {'peptide': 479}
          Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 452}
  Time building chain proxies: 9.47, per 1000 atoms: 0.94
  Number of scatterers: 10119
  At special positions: 0
  Unit cell: (66, 101.64, 131.34, 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    1614      8.00
     N    1409      7.00
     C    5203      6.00
     H    1837      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=2.05
    Simple disulfide: pdb=" SG  CYS A 138 " - pdb=" SG  CYS A 158 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 172 " - pdb=" SG  CYS A 185 " distance=2.02
    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=2.02
    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=2.04
    Simple disulfide: pdb=" SG  CYS B 258 " - pdb=" SG  CYS B 299 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 400 " - pdb=" SG  CYS B 412 " distance=2.05
    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=2.04
    Simple disulfide: pdb=" SG  CYS B 474 " - pdb=" SG  CYS B 486 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 488 " - pdb=" SG  CYS B 497 " distance=2.04

  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: 2.64
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1968

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 20 sheets defined
      17.5% alpha, 28.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 205 through 210
    Processing helix  chain 'A' and resid 218 through 225
    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
    Processing helix  chain 'A' and resid 457 through 459
      No H-bonds generated for 'chain 'A' and resid 457 through 459'
    Processing helix  chain 'A' and resid 531 through 534
      removed outlier: 4.045A  pdb=" N   GLN A 534 " --> pdb=" O   LYS A 531 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 531 through 534'
    Processing helix  chain 'A' and resid 594 through 599
    Processing helix  chain 'B' and resid 30 through 34
    Processing helix  chain 'B' and resid 38 through 46
      removed outlier: 4.319A  pdb=" N   SER B  46 " --> pdb=" O   CYS B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 73
    Processing helix  chain 'B' and resid 76 through 80
      removed outlier: 3.792A  pdb=" N   ILE B  80 " --> pdb=" O   PRO B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 106
    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: 3.640A  pdb=" N   LYS B 163 " --> pdb=" O   ASN B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 201
      removed outlier: 4.121A  pdb=" N   GLU B 200 " --> pdb=" O   PRO B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 207
    Processing helix  chain 'B' and resid 226 through 235
      removed outlier: 3.915A  pdb=" N   ASN B 230 " --> pdb=" O   VAL B 226 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   LYS B 235 " --> pdb=" O   GLU B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 258
      removed outlier: 3.717A  pdb=" N   ALA B 251 " --> pdb=" O   GLY B 247 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   GLN B 254 " --> pdb=" O   ASP B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 263
    Processing helix  chain 'B' and resid 284 through 290
      removed outlier: 3.597A  pdb=" N   ARG B 287 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 328
    Processing helix  chain 'B' and resid 340 through 349
    Processing helix  chain 'B' and resid 365 through 379
    Processing helix  chain 'B' and resid 461 through 467
    Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 42
      removed outlier: 6.558A  pdb=" N   ASP A 451 " --> pdb=" O   ALA A 441 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ALA A 441 " --> pdb=" O   ASP A 451 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   SER A 437 " --> 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: 7.101A  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: 3.669A  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 191 through 193
    Processing sheet with id=AA7, first strand: chain 'A' and resid 256 through 259
      removed outlier: 6.527A  pdb=" N   VAL A 283 " --> pdb=" O   ASN A 296 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   ASN A 296 " --> pdb=" O   VAL A 283 " (cutoff:3.500A)
      removed outlier: 6.768A  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: 6.543A  pdb=" N   ILE A 374 " --> pdb=" O   ALA A 391 " (cutoff:3.500A)
      removed outlier: 7.290A  pdb=" N   ALA A 391 " --> pdb=" O   ILE A 374 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   ALA A 389 " --> pdb=" O   PRO A 376 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   GLY A 378 " --> pdb=" O   ASP A 387 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLN A 419 " --> pdb=" O   ILE A 405 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 408 through 409
    Processing sheet with id=AB3, first strand: chain 'A' and resid 489 through 491
      removed outlier: 6.962A  pdb=" N   LYS A 489 " --> pdb=" O   CYS A 502 " (cutoff:3.500A)
      removed outlier: 6.998A  pdb=" N   CYS A 502 " --> pdb=" O   LYS A 489 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   SER A 501 " --> pdb=" O   LEU A 572 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 489 through 491
      removed outlier: 6.962A  pdb=" N   LYS A 489 " --> pdb=" O   CYS A 502 " (cutoff:3.500A)
      removed outlier: 6.998A  pdb=" N   CYS A 502 " --> pdb=" O   LYS A 489 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 550 through 558
    Processing sheet with id=AB6, first strand: chain 'B' and resid 50 through 51
    Processing sheet with id=AB7, first strand: chain 'B' and resid 86 through 91
      removed outlier: 3.692A  pdb=" N   GLU B  86 " --> pdb=" O   ARG B 117 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   ARG B 113 " --> pdb=" O   LEU B  90 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 123 through 131
    Processing sheet with id=AB9, first strand: chain 'B' and resid 216 through 223
      removed outlier: 7.183A  pdb=" N   VAL B 219 " --> pdb=" O   ALA B 181 " (cutoff:3.500A)
      removed outlier: 8.566A  pdb=" N   ALA B 181 " --> pdb=" O   VAL B 219 " (cutoff:3.500A)
      removed outlier: 5.275A  pdb=" N   THR B 221 " --> pdb=" O   PHE B 179 " (cutoff:3.500A)
      removed outlier: 5.788A  pdb=" N   PHE B 179 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   THR B 337 " --> pdb=" O   THR B 276 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 479 through 480
    Processing sheet with id=AC2, first strand: chain 'B' and resid 492 through 493

    289 hydrogen bonds defined for protein.
    747 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: 3.67

  Time building geometry restraints manager: 1.98 seconds

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

  Histogram of bond lengths:
        0.95 -     1.12: 1837
        1.12 -     1.30: 1486
        1.30 -     1.47: 3142
        1.47 -     1.65: 3747
        1.65 -     1.82: 79
  Bond restraints: 10291
  Sorted by residual:
  bond pdb=" N   GLY B 286 "
       pdb=" H   GLY B 286 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" N   CYS B 432 "
       pdb=" H   CYS B 432 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" NE  ARG A  95 "
       pdb=" HE  ARG A  95 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" N   ASP B 184 "
       pdb=" H   ASP B 184 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.65e+01
  bond pdb=" N   LEU A 582 "
       pdb=" H   LEU A 582 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.65e+01
  ... (remaining 10286 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.40: 10641
        2.40 -     4.79: 2946
        4.79 -     7.19: 1050
        7.19 -     9.58: 97
        9.58 -    11.98: 4
  Bond angle restraints: 14738
  Sorted by residual:
  angle pdb=" N   GLU B 482 "
        pdb=" CA  GLU B 482 "
        pdb=" C   GLU B 482 "
      ideal   model   delta    sigma   weight residual
     111.36  118.84   -7.48 1.09e+00 8.42e-01 4.71e+01
  angle pdb=" CA  ARG A 428 "
        pdb=" C   ARG A 428 "
        pdb=" N   SER A 429 "
      ideal   model   delta    sigma   weight residual
     115.97  124.02   -8.05 1.27e+00 6.20e-01 4.01e+01
  angle pdb=" CA  ASP A 332 "
        pdb=" CB  ASP A 332 "
        pdb=" CG  ASP A 332 "
      ideal   model   delta    sigma   weight residual
     112.60  118.82   -6.22 1.00e+00 1.00e+00 3.86e+01
  angle pdb=" C   ARG A 428 "
        pdb=" N   SER A 429 "
        pdb=" CA  SER A 429 "
      ideal   model   delta    sigma   weight residual
     121.70  131.47   -9.77 1.80e+00 3.09e-01 2.94e+01
  angle pdb=" CA  ASP B 503 "
        pdb=" CB  ASP B 503 "
        pdb=" CG  ASP B 503 "
      ideal   model   delta    sigma   weight residual
     112.60  117.99   -5.39 1.00e+00 1.00e+00 2.91e+01
  ... (remaining 14733 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 6106
       17.81 -    35.62: 330
       35.62 -    53.43: 90
       53.43 -    71.24: 32
       71.24 -    89.05: 8
  Dihedral angle restraints: 6566
    sinusoidal: 3469
      harmonic: 3097
  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  143.44  -50.44     1      1.00e+01 1.00e-02 3.49e+01
  dihedral pdb=" CA  CYS A 502 "
           pdb=" C   CYS A 502 "
           pdb=" N   PHE A 503 "
           pdb=" CA  PHE A 503 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.88   29.12     0      5.00e+00 4.00e-02 3.39e+01
  dihedral pdb=" CA  PHE B 481 "
           pdb=" C   PHE B 481 "
           pdb=" N   GLU B 482 "
           pdb=" CA  GLU B 482 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.04  -28.96     0      5.00e+00 4.00e-02 3.35e+01
  ... (remaining 6563 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.095: 849
       0.095 -    0.189: 328
       0.189 -    0.283: 59
       0.283 -    0.378: 12
       0.378 -    0.472: 2
  Chirality restraints: 1250
  Sorted by residual:
  chirality pdb=" CA  GLU B 482 "
            pdb=" N   GLU B 482 "
            pdb=" C   GLU B 482 "
            pdb=" CB  GLU B 482 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.58e+00
  chirality pdb=" CA  ASN A 316 "
            pdb=" N   ASN A 316 "
            pdb=" C   ASN A 316 "
            pdb=" CB  ASN A 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.28e+00
  chirality pdb=" CA  PRO B 120 "
            pdb=" N   PRO B 120 "
            pdb=" C   PRO B 120 "
            pdb=" CB  PRO B 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.35    0.37 2.00e-01 2.50e+01 3.44e+00
  ... (remaining 1247 not shown)

  Planarity restraints: 2532
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 409 "    0.605 9.50e-02 1.11e+02   2.23e-01 2.48e+02
        pdb=" NE  ARG A 409 "    0.077 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 409 "    0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 409 "    0.018 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 409 "   -0.050 2.00e-02 2.50e+03
        pdb="HH11 ARG A 409 "   -0.197 2.00e-02 2.50e+03
        pdb="HH12 ARG A 409 "    0.182 2.00e-02 2.50e+03
        pdb="HH21 ARG A 409 "   -0.020 2.00e-02 2.50e+03
        pdb="HH22 ARG A 409 "   -0.046 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 204 "    0.190 2.00e-02 2.50e+03   9.99e-02 2.00e+02
        pdb=" CG  TYR B 204 "   -0.067 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 204 "   -0.093 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 204 "   -0.085 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 204 "   -0.042 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 204 "   -0.052 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 204 "    0.011 2.00e-02 2.50e+03
        pdb=" OH  TYR B 204 "    0.138 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 173 "   -0.141 9.50e-02 1.11e+02   9.66e-02 1.62e+02
        pdb=" NE  ARG A 173 "   -0.040 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 173 "   -0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 173 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 173 "    0.005 2.00e-02 2.50e+03
        pdb="HH11 ARG A 173 "    0.134 2.00e-02 2.50e+03
        pdb="HH12 ARG A 173 "   -0.173 2.00e-02 2.50e+03
        pdb="HH21 ARG A 173 "   -0.027 2.00e-02 2.50e+03
        pdb="HH22 ARG A 173 "    0.117 2.00e-02 2.50e+03
  ... (remaining 2529 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 664
        2.20 -     2.80: 5588
        2.80 -     3.40: 16626
        3.40 -     4.00: 23668
        4.00 -     4.60: 32879
  Nonbonded interactions: 79425
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 362 "
            pdb=" HG  SER B 364 "
     model   vdw
     1.599 2.450
  nonbonded pdb=" HH  TYR A 305 "
            pdb=" OD1 ASP B 285 "
     model   vdw
     1.608 2.450
  nonbonded pdb=" OD2 ASP B 153 "
            pdb=" HG  SER B 363 "
     model   vdw
     1.609 2.450
  nonbonded pdb=" HG  SER B 360 "
            pdb=" OD1 ASP B 362 "
     model   vdw
     1.613 2.450
  nonbonded pdb=" HG  SER B  61 "
            pdb=" OD2 ASP B  73 "
     model   vdw
     1.615 2.450
  ... (remaining 79420 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:             27.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     23.910
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   64.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0095
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      :  0.012   0.039   8454  Z= 0.784
  Angle     :  1.767  10.234  11451  Z= 1.188
  Chirality :  0.101   0.472   1250
  Planarity :  0.015   0.184   1517
  Dihedral  : 13.058  89.055   3127
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  4.40 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  5.27 %
    Favored  : 93.85 %
  Cbeta Deviations :  0.51 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.24), residues: 1067
  helix: -2.53 (0.33), residues: 123
  sheet:  0.95 (0.30), residues: 267
  loop : -0.42 (0.23), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.161   0.029   TRP A  91 
 HIS   0.010   0.004   HIS A 551 
 PHE   0.090   0.014   PHE A 184 
 TYR   0.190   0.019   TYR B 204 
 ARG   0.009   0.001   ARG B 386 

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 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   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
  110 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 102
  time to evaluate  : 0.865 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 ASN cc_start: 0.3322 (t0) cc_final: 0.2148 (t0)
REVERT: A  279 THR cc_start: 0.0389 (OUTLIER) cc_final: 0.0056 (m)
REVERT: B   63 ARG cc_start: 0.2372 (mtp85) cc_final: 0.1631 (mtp85)
REVERT: B  168 MET cc_start: -0.1927 (mmm) cc_final: -0.2609 (mtt)
REVERT: B  256 THR cc_start: -0.0303 (m) cc_final: -0.0627 (m)
REVERT: B  483 CYS cc_start: 0.1977 (OUTLIER) cc_final: 0.1407 (t)
  outliers start: 8
  outliers final: 3
  residues processed: 110
  average time/residue: 1.2761
  time to fit residues: 151.5888
Evaluate side-chains
  67 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  316 ASN
Chi-restraints excluded: chain A residue  486 GLN
Chi-restraints excluded: chain B residue  482 GLU
Chi-restraints excluded: chain B residue  483 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 80 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 27 optimal weight:    8.9990
   chunk 54 optimal weight:    0.6980
   chunk 42 optimal weight:    6.9990
   chunk 83 optimal weight:    5.9990
   chunk 32 optimal weight:    7.9990
   chunk 50 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 96 optimal weight:    4.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5486 r_free = 0.5486 target = 0.317688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.5430 r_free = 0.5430 target = 0.310025 restraints weight = 32156.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.5416 rms_B_bonded: 2.74
r_work: 0.5354 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.5354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1129
moved from start:          0.3756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8454  Z= 0.266
  Angle     :  0.745   7.783  11451  Z= 0.393
  Chirality :  0.049   0.197   1250
  Planarity :  0.005   0.050   1517
  Dihedral  :  7.140  79.647   1171
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 29.23
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.37 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  :  8.57 %
    Favored  : 88.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.25), residues: 1067
  helix: -1.12 (0.46), residues: 124
  sheet:  1.05 (0.28), residues: 329
  loop : -0.54 (0.25), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 492 
 HIS   0.006   0.002   HIS A 143 
 PHE   0.028   0.002   PHE A 193 
 TYR   0.019   0.002   TYR B 504 
 ARG   0.010   0.001   ARG A 428 

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 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   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
  96 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 65
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 LYS cc_start: -0.3543 (OUTLIER) cc_final: -0.3831 (tttp)
REVERT: A  539 ARG cc_start: 0.2944 (mpt180) cc_final: 0.1826 (ptp-170)
REVERT: B  184 ASP cc_start: 0.4182 (t70) cc_final: 0.2129 (t70)
  outliers start: 31
  outliers final: 15
  residues processed: 87
  average time/residue: 1.5529
  time to fit residues: 144.6734
Evaluate side-chains
  73 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 57
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  305 TYR
Chi-restraints excluded: chain A residue  338 LYS
Chi-restraints excluded: chain A residue  468 ARG
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  543 PHE
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain B residue  241 ASN
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  482 GLU
Chi-restraints excluded: chain B residue  483 CYS
Chi-restraints excluded: chain B residue  498 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 84 optimal weight:   10.0000
   chunk 59 optimal weight:    0.9990
   chunk 27 optimal weight:   30.0000
   chunk 30 optimal weight:    8.9990
   chunk 100 optimal weight:    0.9990
   chunk 17 optimal weight:   10.0000
   chunk 48 optimal weight:    2.9990
   chunk 4 optimal weight:   10.0000
   chunk 58 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 619 GLN
** A 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  41 GLN
B 496 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5451 r_free = 0.5451 target = 0.313140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5390 r_free = 0.5390 target = 0.302958 restraints weight = 31503.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.5365 rms_B_bonded: 3.29
r_work: 0.5290 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.5290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1772
moved from start:          0.5623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   8454  Z= 0.247
  Angle     :  0.679   8.867  11451  Z= 0.353
  Chirality :  0.047   0.199   1250
  Planarity :  0.005   0.073   1517
  Dihedral  :  6.205  66.922   1165
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 43.27
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.06 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 11.43 %
    Favored  : 86.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.25), residues: 1067
  helix: -0.63 (0.47), residues: 119
  sheet:  0.47 (0.28), residues: 326
  loop : -0.78 (0.24), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  51 
 HIS   0.006   0.001   HIS A 551 
 PHE   0.027   0.002   PHE A 578 
 TYR   0.023   0.002   TYR B 504 
 ARG   0.010   0.001   ARG A 409 

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 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   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
  94 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 72
  time to evaluate  : 0.958 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  539 ARG cc_start: 0.3239 (mpt180) cc_final: 0.2470 (mpt180)
REVERT: A  574 ASP cc_start: 0.2256 (OUTLIER) cc_final: 0.1596 (m-30)
REVERT: A  575 GLU cc_start: 0.5881 (OUTLIER) cc_final: 0.4288 (pt0)
REVERT: A  578 PHE cc_start: 0.2521 (p90) cc_final: 0.2114 (p90)
REVERT: A  581 LYS cc_start: 0.3304 (OUTLIER) cc_final: 0.2466 (tttt)
REVERT: A  612 THR cc_start: 0.4108 (m) cc_final: 0.3679 (m)
REVERT: B  334 PHE cc_start: 0.1899 (m-80) cc_final: 0.1586 (m-10)
  outliers start: 22
  outliers final: 11
  residues processed: 87
  average time/residue: 1.3374
  time to fit residues: 125.6390
Evaluate side-chains
  77 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  543 PHE
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  575 GLU
Chi-restraints excluded: chain A residue  581 LYS
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  241 ASN
Chi-restraints excluded: chain B residue  253 MET
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  482 GLU
Chi-restraints excluded: chain B residue  498 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 95 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 75 optimal weight:    9.9990
   chunk 17 optimal weight:   10.0000
   chunk 15 optimal weight:    6.9990
   chunk 97 optimal weight:    0.7980
   chunk 43 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 554 ASN
A 564 GLN
** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 464 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5418 r_free = 0.5418 target = 0.308617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.5380 r_free = 0.5380 target = 0.288696 restraints weight = 28311.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.5299 rms_B_bonded: 5.48
r_work (final): 0.5299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2504
moved from start:          0.7795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066   8454  Z= 0.383
  Angle     :  0.879  10.933  11451  Z= 0.462
  Chirality :  0.052   0.199   1250
  Planarity :  0.007   0.085   1517
  Dihedral  :  7.375  73.051   1164
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 65.76
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.78 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 13.08 %
    Favored  : 81.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.30 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.25), residues: 1067
  helix: -0.54 (0.50), residues: 108
  sheet: -0.19 (0.30), residues: 322
  loop : -1.24 (0.24), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 492 
 HIS   0.011   0.002   HIS B 218 
 PHE   0.051   0.003   PHE A 578 
 TYR   0.029   0.002   TYR B 504 
 ARG   0.007   0.001   ARG A 409 

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 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   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
  120 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 73
  time to evaluate  : 1.079 
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  331 MET cc_start: -0.2511 (mmm) cc_final: -0.2888 (mmm)
REVERT: A  388 ILE cc_start: 0.6687 (OUTLIER) cc_final: 0.5766 (pp)
REVERT: A  533 LYS cc_start: -0.1001 (OUTLIER) cc_final: -0.2103 (mmtm)
REVERT: A  554 ASN cc_start: 0.0044 (OUTLIER) cc_final: -0.0175 (m110)
REVERT: A  575 GLU cc_start: 0.5663 (OUTLIER) cc_final: 0.4879 (pt0)
REVERT: A  581 LYS cc_start: 0.3615 (OUTLIER) cc_final: 0.3281 (tttt)
REVERT: B  122 ASP cc_start: 0.0386 (OUTLIER) cc_final: 0.0047 (m-30)
REVERT: B  191 MET cc_start: 0.1648 (mtm) cc_final: 0.1359 (mtm)
REVERT: B  253 MET cc_start: 0.2295 (OUTLIER) cc_final: 0.1778 (mpm)
REVERT: B  334 PHE cc_start: 0.2935 (m-80) cc_final: 0.2701 (m-10)
  outliers start: 47
  outliers final: 22
  residues processed: 110
  average time/residue: 1.2681
  time to fit residues: 150.9402
Evaluate side-chains
  97 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 68
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
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  148 MET
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  498 LEU
Chi-restraints excluded: chain A residue  499 LYS
Chi-restraints excluded: chain A residue  533 LYS
Chi-restraints excluded: chain A residue  543 PHE
Chi-restraints excluded: chain A residue  546 SER
Chi-restraints excluded: chain A residue  554 ASN
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  575 GLU
Chi-restraints excluded: chain A residue  581 LYS
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  122 ASP
Chi-restraints excluded: chain B residue  124 LYS
Chi-restraints excluded: chain B residue  253 MET
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  344 TYR
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  438 LYS
Chi-restraints excluded: chain B residue  472 HIS
Chi-restraints excluded: chain B residue  482 GLU
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  507 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 58 optimal weight:    0.6980
   chunk 39 optimal weight:    6.9990
   chunk 22 optimal weight:   20.0000
   chunk 89 optimal weight:    5.9990
   chunk 81 optimal weight:    2.9990
   chunk 79 optimal weight:   10.0000
   chunk 7 optimal weight:    7.9990
   chunk 57 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 105 optimal weight:    0.1980
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 344 GLN
A 554 ASN
** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5405 r_free = 0.5405 target = 0.307751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.5357 r_free = 0.5357 target = 0.286709 restraints weight = 28857.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.5265 rms_B_bonded: 6.08
r_work: 0.5155 rms_B_bonded: 5.47 restraints_weight: 2.0000
r_work (final): 0.5155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2941
moved from start:          0.8715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075   8454  Z= 0.343
  Angle     :  0.791  10.142  11451  Z= 0.416
  Chirality :  0.050   0.213   1250
  Planarity :  0.006   0.060   1517
  Dihedral  :  7.166  66.165   1164
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 68.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.62 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 15.05 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.48 (0.25), residues: 1067
  helix: -0.40 (0.50), residues: 112
  sheet: -0.39 (0.30), residues: 321
  loop : -1.44 (0.23), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A  91 
 HIS   0.012   0.002   HIS B 472 
 PHE   0.038   0.002   PHE A 578 
 TYR   0.036   0.002   TYR A 545 
 ARG   0.006   0.001   ARG A 173 

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 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   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
  124 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 70
  time to evaluate  : 0.961 
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: symmetry clash
REVERT: A  331 MET cc_start: -0.2275 (mmm) cc_final: -0.2710 (mmm)
REVERT: A  472 THR cc_start: 0.2100 (OUTLIER) cc_final: 0.1754 (t)
REVERT: A  483 ILE cc_start: -0.0982 (OUTLIER) cc_final: -0.1416 (mm)
REVERT: A  575 GLU cc_start: 0.6167 (OUTLIER) cc_final: 0.5188 (pt0)
REVERT: B   59 LEU cc_start: 0.2047 (OUTLIER) cc_final: 0.1311 (mp)
REVERT: B  116 LEU cc_start: 0.2064 (OUTLIER) cc_final: 0.1633 (tp)
REVERT: B  122 ASP cc_start: 0.1538 (OUTLIER) cc_final: 0.0999 (m-30)
REVERT: B  253 MET cc_start: 0.2491 (OUTLIER) cc_final: 0.1888 (mpm)
REVERT: B  361 MET cc_start: 0.3243 (ttt) cc_final: 0.2992 (mtt)
  outliers start: 54
  outliers final: 32
  residues processed: 107
  average time/residue: 1.2671
  time to fit residues: 147.0033
Evaluate side-chains
  104 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 65
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ASN
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  144 TRP
Chi-restraints excluded: chain A residue  145 ARG
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  498 LEU
Chi-restraints excluded: chain A residue  499 LYS
Chi-restraints excluded: chain A residue  543 PHE
Chi-restraints excluded: chain A residue  546 SER
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  575 GLU
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  122 ASP
Chi-restraints excluded: chain B residue  126 PHE
Chi-restraints excluded: chain B residue  213 MET
Chi-restraints excluded: chain B residue  241 ASN
Chi-restraints excluded: chain B residue  253 MET
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  307 TYR
Chi-restraints excluded: chain B residue  321 MET
Chi-restraints excluded: chain B residue  347 TYR
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  442 ILE
Chi-restraints excluded: chain B residue  453 VAL
Chi-restraints excluded: chain B residue  482 GLU
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  507 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 36 optimal weight:   10.0000
   chunk 62 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 72 optimal weight:    9.9990
   chunk 83 optimal weight:    9.9990
   chunk 44 optimal weight:    0.6980
   chunk 5 optimal weight:    9.9990
   chunk 87 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 407 ASN
** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 346 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5436 r_free = 0.5436 target = 0.309339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.5368 r_free = 0.5368 target = 0.292748 restraints weight = 26921.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.5297 rms_B_bonded: 4.33
r_work (final): 0.5297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2461
moved from start:          0.9017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8454  Z= 0.212
  Angle     :  0.611   8.259  11451  Z= 0.324
  Chirality :  0.045   0.182   1250
  Planarity :  0.005   0.055   1517
  Dihedral  :  6.543  70.775   1164
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 62.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 17.36 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.26), residues: 1067
  helix: -0.27 (0.49), residues: 116
  sheet: -0.46 (0.30), residues: 332
  loop : -1.39 (0.24), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  91 
 HIS   0.003   0.001   HIS B 472 
 PHE   0.026   0.002   PHE A 578 
 TYR   0.021   0.001   TYR A 545 
 ARG   0.005   0.001   ARG A 573 

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 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   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
  112 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 70
  time to evaluate  : 0.933 
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  100 ILE cc_start: -0.2086 (OUTLIER) cc_final: -0.2519 (mp)
REVERT: A  331 MET cc_start: -0.2085 (mmm) cc_final: -0.2728 (mmm)
REVERT: A  388 ILE cc_start: 0.5313 (OUTLIER) cc_final: 0.4811 (pp)
REVERT: A  483 ILE cc_start: -0.1010 (OUTLIER) cc_final: -0.1546 (mm)
REVERT: A  575 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.4944 (pt0)
REVERT: B   59 LEU cc_start: 0.1980 (OUTLIER) cc_final: 0.1697 (mp)
REVERT: B  253 MET cc_start: 0.1865 (OUTLIER) cc_final: 0.0982 (mpm)
REVERT: B  361 MET cc_start: 0.3255 (ttt) cc_final: 0.2844 (mtt)
  outliers start: 42
  outliers final: 25
  residues processed: 101
  average time/residue: 1.2644
  time to fit residues: 138.4415
Evaluate side-chains
  100 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 69
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 PHE
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  144 TRP
Chi-restraints excluded: chain A residue  145 ARG
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  498 LEU
Chi-restraints excluded: chain A residue  502 CYS
Chi-restraints excluded: chain A residue  543 PHE
Chi-restraints excluded: chain A residue  546 SER
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  575 GLU
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  213 MET
Chi-restraints excluded: chain B residue  241 ASN
Chi-restraints excluded: chain B residue  253 MET
Chi-restraints excluded: chain B residue  321 MET
Chi-restraints excluded: chain B residue  347 TYR
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  482 GLU
Chi-restraints excluded: chain B residue  507 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 23 optimal weight:    0.0070
   chunk 1 optimal weight:   20.0000
   chunk 90 optimal weight:   10.0000
   chunk 96 optimal weight:    6.9990
   chunk 32 optimal weight:    6.9990
   chunk 11 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9980
   chunk 55 optimal weight:    0.6980
   chunk 101 optimal weight:    0.7980
   chunk 31 optimal weight:    5.9990
   chunk 89 optimal weight:    3.9990
   overall best weight:    1.3000

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

Flipped N/Q/H residues before XYZ refinement:
** A  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5405 r_free = 0.5405 target = 0.305910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.5355 r_free = 0.5355 target = 0.295480 restraints weight = 32372.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.5301 rms_B_bonded: 2.88
r_work: 0.5237 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.5237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2735
moved from start:          0.9553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   8454  Z= 0.255
  Angle     :  0.670   9.130  11451  Z= 0.353
  Chirality :  0.046   0.195   1250
  Planarity :  0.005   0.077   1517
  Dihedral  :  6.690  71.870   1164
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 67.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 16.48 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.57 (0.26), residues: 1067
  helix: -0.18 (0.50), residues: 115
  sheet: -0.61 (0.30), residues: 330
  loop : -1.47 (0.24), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B  51 
 HIS   0.002   0.001   HIS A 621 
 PHE   0.027   0.002   PHE A 578 
 TYR   0.031   0.002   TYR A 545 
 ARG   0.007   0.001   ARG B 430 

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 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   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
  117 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 66
  time to evaluate  : 1.018 
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: symmetry clash
REVERT: A  184 PHE cc_start: 0.5924 (m-80) cc_final: 0.5666 (m-10)
REVERT: A  483 ILE cc_start: -0.0372 (OUTLIER) cc_final: -0.0915 (mm)
REVERT: A  504 ASN cc_start: 0.2635 (OUTLIER) cc_final: 0.0824 (m110)
REVERT: A  575 GLU cc_start: 0.6153 (OUTLIER) cc_final: 0.4964 (pt0)
REVERT: A  610 GLN cc_start: 0.1065 (OUTLIER) cc_final: -0.0305 (mt0)
REVERT: B   59 LEU cc_start: 0.1699 (OUTLIER) cc_final: 0.1059 (mt)
REVERT: B  253 MET cc_start: 0.2092 (OUTLIER) cc_final: 0.1099 (mpm)
REVERT: B  361 MET cc_start: 0.3300 (ttt) cc_final: 0.3010 (mtt)
  outliers start: 51
  outliers final: 32
  residues processed: 104
  average time/residue: 1.2101
  time to fit residues: 136.7007
Evaluate side-chains
  103 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 65
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ASN
Chi-restraints excluded: chain A residue  144 TRP
Chi-restraints excluded: chain A residue  145 ARG
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  498 LEU
Chi-restraints excluded: chain A residue  504 ASN
Chi-restraints excluded: chain A residue  543 PHE
Chi-restraints excluded: chain A residue  546 SER
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  575 GLU
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  610 GLN
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  213 MET
Chi-restraints excluded: chain B residue  241 ASN
Chi-restraints excluded: chain B residue  253 MET
Chi-restraints excluded: chain B residue  307 TYR
Chi-restraints excluded: chain B residue  313 MET
Chi-restraints excluded: chain B residue  321 MET
Chi-restraints excluded: chain B residue  347 TYR
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  438 LYS
Chi-restraints excluded: chain B residue  442 ILE
Chi-restraints excluded: chain B residue  472 HIS
Chi-restraints excluded: chain B residue  482 GLU
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  507 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 19 optimal weight:    7.9990
   chunk 89 optimal weight:    5.9990
   chunk 61 optimal weight:    0.8980
   chunk 71 optimal weight:   10.0000
   chunk 25 optimal weight:   20.0000
   chunk 69 optimal weight:    8.9990
   chunk 103 optimal weight:    0.6980
   chunk 21 optimal weight:   20.0000
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 316 ASN
** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5520 r_free = 0.5520 target = 0.324898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.5563 r_free = 0.5563 target = 0.315422 restraints weight = 33761.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.5344 rms_B_bonded: 1.56
r_work: 0.5296 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.5230 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.5230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2886
moved from start:          1.0218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   8454  Z= 0.257
  Angle     :  0.668  10.611  11451  Z= 0.348
  Chirality :  0.046   0.208   1250
  Planarity :  0.005   0.054   1517
  Dihedral  :  6.737  65.378   1164
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 71.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.53 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 17.58 %
    Favored  : 76.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.69 (0.25), residues: 1067
  helix: -0.18 (0.50), residues: 117
  sheet: -0.78 (0.29), residues: 331
  loop : -1.52 (0.24), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  51 
 HIS   0.004   0.001   HIS B 472 
 PHE   0.025   0.002   PHE A 578 
 TYR   0.032   0.002   TYR A 545 
 ARG   0.009   0.001   ARG A 573 

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 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   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
  123 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 71
  time to evaluate  : 0.986 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  233 LYS cc_start: 0.4590 (OUTLIER) cc_final: 0.4369 (mptt)
REVERT: A  483 ILE cc_start: -0.0325 (OUTLIER) cc_final: -0.0849 (mm)
REVERT: A  519 ARG cc_start: 0.6527 (OUTLIER) cc_final: 0.6199 (mtm110)
REVERT: A  575 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.5248 (pm20)
REVERT: B   59 LEU cc_start: 0.1896 (OUTLIER) cc_final: 0.1203 (mp)
REVERT: B  117 ARG cc_start: 0.3313 (mtp180) cc_final: 0.3068 (ttm170)
REVERT: B  168 MET cc_start: -0.3749 (OUTLIER) cc_final: -0.3975 (mtt)
REVERT: B  253 MET cc_start: 0.2077 (OUTLIER) cc_final: 0.1087 (mpm)
REVERT: B  361 MET cc_start: 0.3536 (ttt) cc_final: 0.3015 (mtt)
  outliers start: 52
  outliers final: 29
  residues processed: 108
  average time/residue: 1.2717
  time to fit residues: 148.4354
Evaluate side-chains
  104 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 68
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ASN
Chi-restraints excluded: chain A residue   65 PHE
Chi-restraints excluded: chain A residue  144 TRP
Chi-restraints excluded: chain A residue  145 ARG
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  233 LYS
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  499 LYS
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain A residue  519 ARG
Chi-restraints excluded: chain A residue  543 PHE
Chi-restraints excluded: chain A residue  546 SER
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  575 GLU
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  144 MET
Chi-restraints excluded: chain B residue  168 MET
Chi-restraints excluded: chain B residue  253 MET
Chi-restraints excluded: chain B residue  307 TYR
Chi-restraints excluded: chain B residue  313 MET
Chi-restraints excluded: chain B residue  321 MET
Chi-restraints excluded: chain B residue  347 TYR
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  442 ILE
Chi-restraints excluded: chain B residue  453 VAL
Chi-restraints excluded: chain B residue  482 GLU
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  507 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 3 optimal weight:    7.9990
   chunk 79 optimal weight:    9.9990
   chunk 26 optimal weight:    7.9990
   chunk 43 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 72 optimal weight:    0.0870
   chunk 39 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 21 optimal weight:   30.0000
   chunk 100 optimal weight:    2.9990
   overall best weight:    2.0166

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

Flipped N/Q/H residues before XYZ refinement:
** A  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 485 ASN
** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5382 r_free = 0.5382 target = 0.301807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.5314 r_free = 0.5314 target = 0.289562 restraints weight = 32387.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.5248 rms_B_bonded: 3.09
r_work: 0.5185 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.5185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3090
moved from start:          1.1271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.088   8454  Z= 0.368
  Angle     :  0.859  15.798  11451  Z= 0.443
  Chirality :  0.050   0.214   1250
  Planarity :  0.007   0.067   1517
  Dihedral  :  7.674  69.779   1164
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 86.54
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 10.59 %
    Favored  : 89.32 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 17.91 %
    Favored  : 76.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.39 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.19 (0.25), residues: 1067
  helix: -0.41 (0.50), residues: 117
  sheet: -1.13 (0.29), residues: 322
  loop : -1.88 (0.24), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  91 
 HIS   0.008   0.002   HIS B 472 
 PHE   0.037   0.003   PHE A 578 
 TYR   0.044   0.002   TYR A 545 
 ARG   0.015   0.001   ARG B 505 

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 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   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
  121 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 70
  time to evaluate  : 0.972 
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: symmetry clash
   revert: symmetry clash
REVERT: A  184 PHE cc_start: 0.5721 (m-10) cc_final: 0.5499 (m-10)
REVERT: A  207 PHE cc_start: 0.3254 (m-10) cc_final: 0.2354 (m-80)
REVERT: A  483 ILE cc_start: -0.0499 (OUTLIER) cc_final: -0.0838 (mm)
REVERT: A  504 ASN cc_start: 0.2331 (OUTLIER) cc_final: 0.0664 (m-40)
REVERT: A  575 GLU cc_start: 0.6212 (OUTLIER) cc_final: 0.5807 (pt0)
REVERT: B   59 LEU cc_start: 0.1499 (OUTLIER) cc_final: 0.0766 (mp)
REVERT: B  168 MET cc_start: -0.4542 (OUTLIER) cc_final: -0.4907 (mtt)
REVERT: B  253 MET cc_start: 0.2390 (OUTLIER) cc_final: 0.1278 (mpm)
REVERT: B  361 MET cc_start: 0.3256 (ttt) cc_final: 0.2961 (mtt)
REVERT: B  413 MET cc_start: -0.2982 (OUTLIER) cc_final: -0.4204 (pmm)
  outliers start: 51
  outliers final: 34
  residues processed: 105
  average time/residue: 1.2016
  time to fit residues: 137.4930
Evaluate side-chains
  108 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 67
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ASN
Chi-restraints excluded: chain A residue   65 PHE
Chi-restraints excluded: chain A residue  144 TRP
Chi-restraints excluded: chain A residue  145 ARG
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  499 LYS
Chi-restraints excluded: chain A residue  504 ASN
Chi-restraints excluded: chain A residue  507 PHE
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain A residue  543 PHE
Chi-restraints excluded: chain A residue  546 SER
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  575 GLU
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  144 MET
Chi-restraints excluded: chain B residue  168 MET
Chi-restraints excluded: chain B residue  253 MET
Chi-restraints excluded: chain B residue  307 TYR
Chi-restraints excluded: chain B residue  321 MET
Chi-restraints excluded: chain B residue  347 TYR
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  413 MET
Chi-restraints excluded: chain B residue  442 ILE
Chi-restraints excluded: chain B residue  451 LEU
Chi-restraints excluded: chain B residue  453 VAL
Chi-restraints excluded: chain B residue  482 GLU
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  507 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 31 optimal weight:   20.0000
   chunk 32 optimal weight:    0.9990
   chunk 24 optimal weight:   30.0000
   chunk 48 optimal weight:    0.0970
   chunk 85 optimal weight:    6.9990
   chunk 67 optimal weight:    1.9990
   chunk 92 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 97 optimal weight:    7.9990
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5396 r_free = 0.5396 target = 0.303890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.5346 r_free = 0.5346 target = 0.293671 restraints weight = 32212.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.5289 rms_B_bonded: 2.96
r_work: 0.5222 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.5222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2842
moved from start:          1.1070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   8454  Z= 0.187
  Angle     :  0.608   9.415  11451  Z= 0.319
  Chirality :  0.045   0.157   1250
  Planarity :  0.005   0.062   1517
  Dihedral  :  6.565  60.789   1164
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 72.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.78 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 19.67 %
    Favored  : 76.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.89 (0.25), residues: 1067
  helix: -0.19 (0.50), residues: 118
  sheet: -0.96 (0.29), residues: 333
  loop : -1.66 (0.24), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  51 
 HIS   0.003   0.001   HIS A 551 
 PHE   0.019   0.002   PHE A  55 
 TYR   0.018   0.001   TYR A 545 
 ARG   0.006   0.001   ARG A 409 

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 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   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
  110 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 73
  time to evaluate  : 0.928 
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: symmetry clash
   revert: symmetry clash
REVERT: A  207 PHE cc_start: 0.2967 (m-10) cc_final: 0.2010 (m-80)
REVERT: A  483 ILE cc_start: -0.0496 (OUTLIER) cc_final: -0.0856 (mm)
REVERT: A  504 ASN cc_start: 0.2288 (OUTLIER) cc_final: 0.0684 (m110)
REVERT: B  168 MET cc_start: -0.3684 (OUTLIER) cc_final: -0.3947 (mtt)
REVERT: B  191 MET cc_start: 0.2308 (mtp) cc_final: 0.1346 (mtt)
REVERT: B  253 MET cc_start: 0.1743 (OUTLIER) cc_final: 0.0633 (mpm)
REVERT: B  361 MET cc_start: 0.3375 (ttt) cc_final: 0.2950 (mtt)
  outliers start: 37
  outliers final: 29
  residues processed: 96
  average time/residue: 1.1546
  time to fit residues: 120.5899
Evaluate side-chains
  104 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 71
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ASN
Chi-restraints excluded: chain A residue   65 PHE
Chi-restraints excluded: chain A residue  144 TRP
Chi-restraints excluded: chain A residue  145 ARG
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  499 LYS
Chi-restraints excluded: chain A residue  504 ASN
Chi-restraints excluded: chain A residue  507 PHE
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain A residue  543 PHE
Chi-restraints excluded: chain A residue  546 SER
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain B residue  144 MET
Chi-restraints excluded: chain B residue  168 MET
Chi-restraints excluded: chain B residue  253 MET
Chi-restraints excluded: chain B residue  307 TYR
Chi-restraints excluded: chain B residue  313 MET
Chi-restraints excluded: chain B residue  321 MET
Chi-restraints excluded: chain B residue  347 TYR
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  453 VAL
Chi-restraints excluded: chain B residue  482 GLU
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  507 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 74 optimal weight:    9.9990
   chunk 67 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 93 optimal weight:   10.0000
   chunk 13 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 69 optimal weight:    7.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5371 r_free = 0.5371 target = 0.298318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.5316 r_free = 0.5316 target = 0.276286 restraints weight = 29563.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.5216 rms_B_bonded: 6.88
r_work: 0.5101 rms_B_bonded: 5.80 restraints_weight: 2.0000
r_work (final): 0.5101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3293
moved from start:          1.1329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   8454  Z= 0.224
  Angle     :  0.640   9.130  11451  Z= 0.335
  Chirality :  0.045   0.176   1250
  Planarity :  0.005   0.064   1517
  Dihedral  :  6.608  62.736   1164
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 75.69
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.90 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 19.56 %
    Favored  : 76.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.01 (0.25), residues: 1067
  helix: -0.09 (0.50), residues: 117
  sheet: -1.02 (0.30), residues: 319
  loop : -1.78 (0.23), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  51 
 HIS   0.003   0.001   HIS B 472 
 PHE   0.020   0.002   PHE A  55 
 TYR   0.026   0.002   TYR A 545 
 ARG   0.010   0.001   ARG A  63 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8685.46 seconds
wall clock time: 155 minutes 37.43 seconds (9337.43 seconds total)