Starting phenix.real_space_refine
on Tue Dec 31 01:51:40 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xez_38298/12_2024/8xez_38298_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xez_38298/12_2024/8xez_38298.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xez_38298/12_2024/8xez_38298.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xez_38298/12_2024/8xez_38298.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xez_38298/12_2024/8xez_38298_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xez_38298/12_2024/8xez_38298_neut.cif"
  }
  resolution = 3.15
  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=   0.006
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      96      5.16       5
     C    7377      2.51       5
     N    2010      2.21       5
     O    2309      1.98       5
     H    2609      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 14401
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 927, 8791
          Classifications: {'peptide': 927}
          Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 880}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 5610
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 601, 5610
          Classifications: {'peptide': 601}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 28, 'TRANS': 569}
  Time building chain proxies: 10.25, per 1000 atoms: 0.71
  Number of scatterers: 14401
  At special positions: 0
  Unit cell: (84.48, 121.44, 209.22, 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      96     16.00
     O    2309      8.00
     N    2010      7.00
     C    7377      6.00
     H    2609      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=31, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  89 " - pdb=" SG  CYS A  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 138 " - pdb=" SG  CYS A 158 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 172 " - pdb=" SG  CYS A 185 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 491 " - pdb=" SG  CYS A 502 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 508 " - pdb=" SG  CYS A 565 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 626 " - pdb=" SG  CYS A 632 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 698 " - pdb=" SG  CYS A 711 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 852 " - pdb=" SG  CYS A 914 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 904 " - pdb=" SG  CYS A 909 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  31 " - pdb=" SG  CYS B  49 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  39 " - pdb=" SG  CYS B 461 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  42 " - pdb=" SG  CYS B  64 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B  52 " - pdb=" SG  CYS B  75 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 203 " - pdb=" SG  CYS B 210 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 258 " - pdb=" SG  CYS B 299 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 400 " - pdb=" SG  CYS B 412 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 432 " - pdb=" SG  CYS B 459 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 463 " - pdb=" SG  CYS B 483 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 474 " - pdb=" SG  CYS B 486 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 488 " - pdb=" SG  CYS B 497 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 512 " - pdb=" SG  CYS B 527 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 521 " - pdb=" SG  CYS B 532 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 534 " - pdb=" SG  CYS B 547 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 549 " - pdb=" SG  CYS B 570 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 554 " - pdb=" SG  CYS B 568 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 562 " - pdb=" SG  CYS B 573 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 575 " - pdb=" SG  CYS B 584 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 586 " - pdb=" SG  CYS B 609 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 593 " - pdb=" SG  CYS B 607 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 601 " - pdb=" SG  CYS B 612 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 614 " - pdb=" SG  CYS B 624 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.65
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2812

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 33 sheets defined
      13.5% alpha, 31.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 205 through 210
    Processing helix  chain 'A' and resid 218 through 225
      removed outlier: 3.842A  pdb=" N   TYR A 225 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 248
    Processing helix  chain 'A' and resid 275 through 280
    Processing helix  chain 'A' and resid 396 through 400
      removed outlier: 3.611A  pdb=" N   LYS A 400 " --> pdb=" O   GLU A 397 " (cutoff:3.500A)
    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 530 through 536
      removed outlier: 3.920A  pdb=" N   LYS A 535 " --> pdb=" O   LEU A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 578
    Processing helix  chain 'A' and resid 594 through 599
    Processing helix  chain 'A' and resid 934 through 940
      removed outlier: 4.113A  pdb=" N   PHE A 938 " --> pdb=" O   TRP A 934 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 941 through 944
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 38 through 46
      removed outlier: 3.685A  pdb=" N   SER B  46 " --> pdb=" O   CYS B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 73
    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 170
      removed outlier: 3.664A  pdb=" N   LYS B 163 " --> pdb=" O   ASN B 159 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   LYS B 170 " --> pdb=" O   THR B 166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 201
      removed outlier: 3.646A  pdb=" N   GLU B 200 " --> pdb=" O   PRO B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 207
      removed outlier: 4.424A  pdb=" N   ASP B 205 " --> pdb=" O   PRO B 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 226 through 234
      removed outlier: 3.748A  pdb=" N   ASN B 230 " --> pdb=" O   VAL B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 258
      removed outlier: 3.998A  pdb=" N   ALA B 251 " --> pdb=" O   GLY B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 263
    Processing helix  chain 'B' and resid 285 through 289
    Processing helix  chain 'B' and resid 307 through 313
      removed outlier: 4.270A  pdb=" N   THR B 311 " --> pdb=" O   SER B 308 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   MET B 313 " --> pdb=" O   SER B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 329
    Processing helix  chain 'B' and resid 340 through 349
    Processing helix  chain 'B' and resid 365 through 378
    Processing helix  chain 'B' and resid 461 through 466
    Processing helix  chain 'B' and resid 599 through 603
    Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 42
    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
    Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 118
      removed outlier: 3.513A  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: 6.349A  pdb=" N   VAL A 283 " --> pdb=" O   ASN A 296 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   ASN A 296 " --> pdb=" O   VAL A 283 " (cutoff:3.500A)
      removed outlier: 6.831A  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: 5.829A  pdb=" N   ASP A 387 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 374 through 378
      removed outlier: 5.829A  pdb=" N   ASP A 387 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   GLN A 419 " --> pdb=" O   ILE A 405 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 509 through 512
      removed outlier: 3.520A  pdb=" N   LYS A 510 " --> pdb=" O   ASN A 474 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 491 through 492
      removed outlier: 3.541A  pdb=" N   CYS A 491 " --> pdb=" O   VAL A 500 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 502 through 507
    Processing sheet with id=AB6, first strand: chain 'A' and resid 550 through 557
    Processing sheet with id=AB7, first strand: chain 'A' and resid 638 through 642
      removed outlier: 6.950A  pdb=" N   SER A 730 " --> pdb=" O   PHE A 683 " (cutoff:3.500A)
      removed outlier: 5.382A  pdb=" N   PHE A 683 " --> pdb=" O   SER A 730 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 646 through 648
      removed outlier: 6.276A  pdb=" N   ILE A 647 " --> pdb=" O   ALA A 767 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   PHE A 743 " --> pdb=" O   HIS A 762 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   VAL A 764 " --> pdb=" O   VAL A 741 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ALA A 671 " --> pdb=" O   LEU A 713 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   SER A 697 " --> pdb=" O   ASP A 712 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 772 through 774
      removed outlier: 3.656A  pdb=" N   ARG A 813 " --> pdb=" O   GLU A 773 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 772 through 774
      removed outlier: 3.656A  pdb=" N   ARG A 813 " --> pdb=" O   GLU A 773 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   HIS A 843 " --> pdb=" O   LYS A 930 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   LEU A 932 " --> pdb=" O   ILE A 841 " (cutoff:3.500A)
      removed outlier: 5.545A  pdb=" N   ILE A 841 " --> pdb=" O   LEU A 932 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 782 through 785
      removed outlier: 3.795A  pdb=" N   ILE A 971 " --> pdb=" O   VAL A 958 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ASN A 973 " --> pdb=" O   PHE A 956 " (cutoff:3.500A)
      removed outlier: 12.494A  pdb=" N   SER A 949 " --> pdb=" O   LYS A 832 " (cutoff:3.500A)
      removed outlier: 11.254A  pdb=" N   LYS A 832 " --> pdb=" O   SER A 949 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   LYS A 951 " --> pdb=" O   PRO A 830 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   LYS A 822 " --> pdb=" O   ILE A 959 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   GLN A 908 " --> pdb=" O   TYR A 831 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'A' and resid 836 through 837
      removed outlier: 6.491A  pdb=" N   LYS A 822 " --> pdb=" O   ILE A 959 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   LYS A 951 " --> pdb=" O   PRO A 830 " (cutoff:3.500A)
      removed outlier: 11.254A  pdb=" N   LYS A 832 " --> pdb=" O   SER A 949 " (cutoff:3.500A)
      removed outlier: 12.494A  pdb=" N   SER A 949 " --> pdb=" O   LYS A 832 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 64 through 66
    Processing sheet with id=AC5, first strand: chain 'B' and resid 86 through 91
      removed outlier: 6.614A  pdb=" N   ARG B 113 " --> pdb=" O   LEU B  90 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   ILE B 114 " --> pdb=" O   GLN B 454 " (cutoff:3.500A)
      removed outlier: 7.451A  pdb=" N   THR B 456 " --> pdb=" O   ILE B 114 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   LEU B 116 " --> pdb=" O   THR B 456 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   VAL B 381 " --> pdb=" O   CYS B 412 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'B' and resid 109 through 110
      removed outlier: 3.618A  pdb=" N   SER B 422 " --> pdb=" O   THR B 399 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'B' and resid 217 through 223
      removed outlier: 7.043A  pdb=" N   VAL B 219 " --> pdb=" O   ALA B 181 " (cutoff:3.500A)
      removed outlier: 8.602A  pdb=" N   ALA B 181 " --> pdb=" O   VAL B 219 " (cutoff:3.500A)
      removed outlier: 5.599A  pdb=" N   THR B 221 " --> pdb=" O   PHE B 179 " (cutoff:3.500A)
      removed outlier: 5.702A  pdb=" N   PHE B 179 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   PHE B 182 " --> pdb=" O   MET B 144 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   HIS B 270 " --> pdb=" O   ASN B 331 " (cutoff:3.500A)
      removed outlier: 7.367A  pdb=" N   ILE B 333 " --> pdb=" O   HIS B 270 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   LEU B 272 " --> pdb=" O   ILE B 333 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   ALA B 335 " --> pdb=" O   LEU B 272 " (cutoff:3.500A)
      removed outlier: 6.096A  pdb=" N   PHE B 274 " --> pdb=" O   ALA B 335 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 479 through 482
    Processing sheet with id=AC9, first strand: chain 'B' and resid 492 through 493
    Processing sheet with id=AD1, first strand: chain 'B' and resid 526 through 528
    Processing sheet with id=AD2, first strand: chain 'B' and resid 542 through 543
    Processing sheet with id=AD3, first strand: chain 'B' and resid 556 through 557
    Processing sheet with id=AD4, first strand: chain 'B' and resid 566 through 569
    Processing sheet with id=AD5, first strand: chain 'B' and resid 579 through 580
      removed outlier: 3.668A  pdb=" N   CYS B 586 " --> pdb=" O   THR B 580 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'B' and resid 605 through 608

    398 hydrogen bonds defined for protein.
    1029 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: 6.54

  Time building geometry restraints manager: 4.22 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 2609
        1.03 -     1.23: 148
        1.23 -     1.43: 4896
        1.43 -     1.62: 6861
        1.62 -     1.82: 127
  Bond restraints: 14641
  Sorted by residual:
  bond pdb=" NE  ARG B 119 "
       pdb=" HE  ARG B 119 "
    ideal  model  delta    sigma   weight residual
    0.860  0.969 -0.109 2.00e-02 2.50e+03 2.96e+01
  bond pdb=" CA  HIS A 621 "
       pdb=" C   HIS A 621 "
    ideal  model  delta    sigma   weight residual
    1.523  1.488  0.035 1.23e-02 6.61e+03 8.00e+00
  bond pdb=" N   GLY B  27 "
       pdb=" CA  GLY B  27 "
    ideal  model  delta    sigma   weight residual
    1.451  1.491 -0.040 1.60e-02 3.91e+03 6.36e+00
  bond pdb=" CA  ILE A 622 "
       pdb=" C   ILE A 622 "
    ideal  model  delta    sigma   weight residual
    1.523  1.494  0.029 1.27e-02 6.20e+03 5.23e+00
  bond pdb=" CA  ASP A 176 "
       pdb=" C   ASP A 176 "
    ideal  model  delta    sigma   weight residual
    1.530  1.511  0.019 1.10e-02 8.26e+03 2.88e+00
  ... (remaining 14636 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 20673
        1.82 -     3.63: 279
        3.63 -     5.45: 23
        5.45 -     7.27: 2
        7.27 -     9.08: 1
  Bond angle restraints: 20978
  Sorted by residual:
  angle pdb=" C   ASP B 458 "
        pdb=" N   CYS B 459 "
        pdb=" CA  CYS B 459 "
      ideal   model   delta    sigma   weight residual
     121.70  130.78   -9.08 1.80e+00 3.09e-01 2.55e+01
  angle pdb=" N   VAL A 459 "
        pdb=" CA  VAL A 459 "
        pdb=" C   VAL A 459 "
      ideal   model   delta    sigma   weight residual
     112.43  108.86    3.57 9.20e-01 1.18e+00 1.51e+01
  angle pdb=" N   VAL A 906 "
        pdb=" CA  VAL A 906 "
        pdb=" C   VAL A 906 "
      ideal   model   delta    sigma   weight residual
     113.53  109.85    3.68 9.80e-01 1.04e+00 1.41e+01
  angle pdb=" N   ILE B 193 "
        pdb=" CA  ILE B 193 "
        pdb=" C   ILE B 193 "
      ideal   model   delta    sigma   weight residual
     111.91  108.70    3.21 8.90e-01 1.26e+00 1.30e+01
  angle pdb=" N   VAL B 292 "
        pdb=" CA  VAL B 292 "
        pdb=" C   VAL B 292 "
      ideal   model   delta    sigma   weight residual
     113.71  110.29    3.42 9.50e-01 1.11e+00 1.30e+01
  ... (remaining 20973 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.08: 8674
       18.08 -    36.16: 532
       36.16 -    54.24: 145
       54.24 -    72.32: 35
       72.32 -    90.40: 13
  Dihedral angle restraints: 9399
    sinusoidal: 4971
      harmonic: 4428
  Sorted by residual:
  dihedral pdb=" CB  CYS B 432 "
           pdb=" SG  CYS B 432 "
           pdb=" SG  CYS B 459 "
           pdb=" CB  CYS B 459 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  138.68  -45.68     1      1.00e+01 1.00e-02 2.89e+01
  dihedral pdb=" CB  CYS A 172 "
           pdb=" SG  CYS A 172 "
           pdb=" SG  CYS A 185 "
           pdb=" CB  CYS A 185 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   48.67   44.33     1      1.00e+01 1.00e-02 2.73e+01
  dihedral pdb=" CB  CYS A 626 "
           pdb=" SG  CYS A 626 "
           pdb=" SG  CYS A 632 "
           pdb=" CB  CYS A 632 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  131.13  -38.13     1      1.00e+01 1.00e-02 2.05e+01
  ... (remaining 9396 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1253
       0.038 -    0.077: 367
       0.077 -    0.115: 134
       0.115 -    0.153: 35
       0.153 -    0.191: 1
  Chirality restraints: 1790
  Sorted by residual:
  chirality pdb=" CA  ILE A 622 "
            pdb=" N   ILE A 622 "
            pdb=" C   ILE A 622 "
            pdb=" CB  ILE A 622 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 9.16e-01
  chirality pdb=" CA  ILE A 453 "
            pdb=" N   ILE A 453 "
            pdb=" C   ILE A 453 "
            pdb=" CB  ILE A 453 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.86e-01
  chirality pdb=" CA  ILE A 374 "
            pdb=" N   ILE A 374 "
            pdb=" C   ILE A 374 "
            pdb=" CB  ILE A 374 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.81e-01
  ... (remaining 1787 not shown)

  Planarity restraints: 3606
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 175 "   -0.113 2.00e-02 2.50e+03   1.23e-01 2.28e+02
        pdb=" CD  GLN A 175 "    0.008 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 175 "    0.108 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 175 "    0.001 2.00e-02 2.50e+03
        pdb="HE21 GLN A 175 "    0.181 2.00e-02 2.50e+03
        pdb="HE22 GLN A 175 "   -0.184 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 623 "    0.016 2.00e-02 2.50e+03   3.03e-02 9.20e+00
        pdb=" N   LEU A 624 "   -0.052 2.00e-02 2.50e+03
        pdb=" CA  LEU A 624 "    0.014 2.00e-02 2.50e+03
        pdb=" H   LEU A 624 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B  27 "    0.024 5.00e-02 4.00e+02   3.66e-02 2.15e+00
        pdb=" N   PRO B  28 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO B  28 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B  28 "    0.020 5.00e-02 4.00e+02
  ... (remaining 3603 not shown)

  Histogram of nonbonded interaction distances:
        1.52 -     2.14: 363
        2.14 -     2.75: 8668
        2.75 -     3.37: 23891
        3.37 -     3.98: 32836
        3.98 -     4.60: 47446
  Nonbonded interactions: 113204
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU B 435 "
            pdb=" HZ1 LYS B 438 "
     model   vdw
     1.520 2.450
  nonbonded pdb=" OE2 GLU A 478 "
            pdb="HH21 ARG A 506 "
     model   vdw
     1.567 2.450
  nonbonded pdb=" OE2 GLU A 220 "
            pdb=" H   ASN A 235 "
     model   vdw
     1.578 2.450
  nonbonded pdb=" H   LYS A 633 "
            pdb=" OE1 GLU A 666 "
     model   vdw
     1.582 2.450
  nonbonded pdb=" OE1 GLU A 117 "
            pdb=" HH  TYR A 142 "
     model   vdw
     1.591 2.450
  ... (remaining 113199 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:             19.230
  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:          2.160
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     36.880
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   61.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12032  Z= 0.235
  Angle     :  0.593   9.084  16302  Z= 0.349
  Chirality :  0.043   0.191   1790
  Planarity :  0.003   0.037   2157
  Dihedral  : 13.798  90.401   4455
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.68 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  8.14 %
    Favored  : 91.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.58 %
    Cis-general     : 0.07 %
    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: -0.30 (0.22), residues: 1522
  helix: -0.43 (0.48), residues: 131
  sheet:  0.20 (0.24), residues: 477
  loop : -0.31 (0.21), residues: 914

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 144 
 HIS   0.007   0.001   HIS A 621 
 PHE   0.014   0.001   PHE A 306 
 TYR   0.013   0.001   TYR A 305 
 ARG   0.003   0.000   ARG B 524 

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   33 is missing expected H atoms. Skipping.
Residue VAL   35 is missing expected H atoms. Skipping.
Residue ALA   39 is missing expected H atoms. Skipping.
Residue ALA   52 is missing expected H atoms. Skipping.
Residue VAL   53 is missing expected H atoms. Skipping.
Residue VAL   57 is missing expected H atoms. Skipping.
Residue ALA   60 is missing expected H atoms. Skipping.
Residue MET   64 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue VAL   68 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue THR   75 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   86 is missing expected H atoms. Skipping.
Residue LEU   87 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ILE  100 is missing expected H atoms. Skipping.
Residue ALA  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue ALA  111 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue ALA  126 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue ALA  137 is missing expected H atoms. Skipping.
Residue ALA  139 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  146 is missing expected H atoms. Skipping.
Residue MET  148 is missing expected H atoms. Skipping.
Residue VAL  155 is missing expected H atoms. Skipping.
Residue THR  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  164 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue VAL  167 is missing expected H atoms. Skipping.
Residue ALA  170 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  179 is missing expected H atoms. Skipping.
Residue ILE  191 is missing expected H atoms. Skipping.
Residue THR  194 is missing expected H atoms. Skipping.
Residue ALA  196 is missing expected H atoms. Skipping.
Residue VAL  199 is missing expected H atoms. Skipping.
Residue LEU  200 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LEU  213 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue ALA  219 is missing expected H atoms. Skipping.
Residue ILE  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Residue VAL  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LEU  238 is missing expected H atoms. Skipping.
Residue ALA  239 is missing expected H atoms. Skipping.
Residue THR  240 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue ALA  243 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue ILE  246 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue VAL  256 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  258 is missing expected H atoms. Skipping.
Residue ILE  266 is missing expected H atoms. Skipping.
Residue VAL  270 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue ALA  276 is missing expected H atoms. Skipping.
Residue ALA  277 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue LEU  280 is missing expected H atoms. Skipping.
Residue MET  282 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  285 is missing expected H atoms. Skipping.
Residue MET  291 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue THR  298 is missing expected H atoms. Skipping.
Residue MET  302 is missing expected H atoms. Skipping.
Residue ALA  303 is missing expected H atoms. Skipping.
Residue ALA  304 is missing expected H atoms. Skipping.
Residue VAL  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue ALA  312 is missing expected H atoms. Skipping.
Residue THR  313 is missing expected H atoms. Skipping.
Residue ILE  315 is missing expected H atoms. Skipping.
Residue ALA  321 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue ILE  325 is missing expected H atoms. Skipping.
Residue ALA  327 is missing expected H atoms. Skipping.
Residue LEU  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU  339 is missing expected H atoms. Skipping.
Residue VAL  342 is missing expected H atoms. Skipping.
Residue VAL  345 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  349 is missing expected H atoms. Skipping.
Residue ALA  352 is missing expected H atoms. Skipping.
Residue THR  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LEU  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue ALA  368 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  374 is missing expected H atoms. Skipping.
Residue ALA  375 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue LEU  380 is missing expected H atoms. Skipping.
Residue ILE  388 is missing expected H atoms. Skipping.
Residue ALA  389 is missing expected H atoms. Skipping.
Residue ILE  390 is missing expected H atoms. Skipping.
Residue ALA  391 is missing expected H atoms. Skipping.
Residue ALA  392 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue VAL  403 is missing expected H atoms. Skipping.
Residue ILE  405 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Residue ALA  415 is missing expected H atoms. Skipping.
Residue VAL  416 is missing expected H atoms. Skipping.
Residue ILE  420 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue ALA  426 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue MET  438 is missing expected H atoms. Skipping.
Residue ALA  441 is missing expected H atoms. Skipping.
Residue THR  442 is missing expected H atoms. Skipping.
Residue ILE  444 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue ILE  453 is missing expected H atoms. Skipping.
Residue VAL  454 is missing expected H atoms. Skipping.
Residue ALA  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue VAL  470 is missing expected H atoms. Skipping.
Residue ILE  471 is missing expected H atoms. Skipping.
Residue THR  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ALA  475 is missing expected H atoms. Skipping.
Residue LEU  477 is missing expected H atoms. Skipping.
Residue VAL  479 is missing expected H atoms. Skipping.
Residue ILE  483 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue THR  490 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue THR  496 is missing expected H atoms. Skipping.
Residue ALA  497 is missing expected H atoms. Skipping.
Residue LEU  498 is missing expected H atoms. Skipping.
Residue VAL  500 is missing expected H atoms. Skipping.
Residue VAL  505 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue ALA  511 is missing expected H atoms. Skipping.
Residue VAL  516 is missing expected H atoms. Skipping.
Residue LEU  517 is missing expected H atoms. Skipping.
Residue LEU  521 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  532 is missing expected H atoms. Skipping.
Residue ALA  537 is missing expected H atoms. Skipping.
Residue ILE  538 is missing expected H atoms. Skipping.
Residue ALA  541 is missing expected H atoms. Skipping.
Residue LEU  542 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue THR  556 is missing expected H atoms. Skipping.
Residue ILE  557 is missing expected H atoms. Skipping.
Residue LEU  562 is missing expected H atoms. Skipping.
Residue MET  563 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue ALA  570 is missing expected H atoms. Skipping.
Residue LEU  572 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue THR  583 is missing expected H atoms. Skipping.
Residue ILE  585 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue ILE  587 is missing expected H atoms. Skipping.
Residue MET  589 is missing expected H atoms. Skipping.
Residue LEU  593 is missing expected H atoms. Skipping.
Residue THR  597 is missing expected H atoms. Skipping.
Residue ALA  598 is missing expected H atoms. Skipping.
Residue ALA  599 is missing expected H atoms. Skipping.
Residue THR  601 is missing expected H atoms. Skipping.
Residue THR  602 is missing expected H atoms. Skipping.
Residue LEU  604 is missing expected H atoms. Skipping.
Residue ILE  607 is missing expected H atoms. Skipping.
Residue LEU  608 is missing expected H atoms. Skipping.
Residue THR  612 is missing expected H atoms. Skipping.
Residue ALA  614 is missing expected H atoms. Skipping.
Residue ILE  616 is missing expected H atoms. Skipping.
Residue ALA  620 is missing expected H atoms. Skipping.
Residue ILE  622 is missing expected H atoms. Skipping.
Residue LEU  623 is missing expected H atoms. Skipping.
Residue LEU  624 is missing expected H atoms. Skipping.
Residue VAL  631 is missing expected H atoms. Skipping.
Residue LEU  636 is missing expected H atoms. Skipping.
Residue VAL  638 is missing expected H atoms. Skipping.
Residue VAL  640 is missing expected H atoms. Skipping.
Residue ILE  647 is missing expected H atoms. Skipping.
Residue ILE  649 is missing expected H atoms. Skipping.
Residue LEU  655 is missing expected H atoms. Skipping.
Residue THR  656 is missing expected H atoms. Skipping.
Residue LEU  657 is missing expected H atoms. Skipping.
Residue ILE  658 is missing expected H atoms. Skipping.
Residue VAL  659 is missing expected H atoms. Skipping.
Residue ALA  661 is missing expected H atoms. Skipping.
Residue ALA  668 is missing expected H atoms. Skipping.
Residue ALA  671 is missing expected H atoms. Skipping.
Residue LEU  673 is missing expected H atoms. Skipping.
Residue ILE  674 is missing expected H atoms. Skipping.
Residue VAL  675 is missing expected H atoms. Skipping.
Residue ILE  677 is missing expected H atoms. Skipping.
Residue LEU  679 is missing expected H atoms. Skipping.
Residue ALA  681 is missing expected H atoms. Skipping.
Residue ILE  684 is missing expected H atoms. Skipping.
Residue VAL  686 is missing expected H atoms. Skipping.
Residue VAL  687 is missing expected H atoms. Skipping.
Residue ALA  692 is missing expected H atoms. Skipping.
Residue LEU  693 is missing expected H atoms. Skipping.
Residue ALA  694 is missing expected H atoms. Skipping.
Residue LEU  696 is missing expected H atoms. Skipping.
Residue ALA  699 is missing expected H atoms. Skipping.
Residue THR  702 is missing expected H atoms. Skipping.
Residue THR  706 is missing expected H atoms. Skipping.
Residue VAL  709 is missing expected H atoms. Skipping.
Residue VAL  710 is missing expected H atoms. Skipping.
Residue LEU  713 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue ALA  719 is missing expected H atoms. Skipping.
Residue THR  721 is missing expected H atoms. Skipping.
Residue LEU  723 is missing expected H atoms. Skipping.
Residue LEU  724 is missing expected H atoms. Skipping.
Residue ALA  725 is missing expected H atoms. Skipping.
Residue LEU  727 is missing expected H atoms. Skipping.
Residue VAL  731 is missing expected H atoms. Skipping.
Residue MET  737 is missing expected H atoms. Skipping.
Residue THR  739 is missing expected H atoms. Skipping.
Residue VAL  741 is missing expected H atoms. Skipping.
Residue LEU  745 is missing expected H atoms. Skipping.
Residue ILE  747 is missing expected H atoms. Skipping.
Residue LEU  752 is missing expected H atoms. Skipping.
Residue VAL  756 is missing expected H atoms. Skipping.
Residue VAL  759 is missing expected H atoms. Skipping.
Residue VAL  760 is missing expected H atoms. Skipping.
Residue VAL  764 is missing expected H atoms. Skipping.
Residue LEU  766 is missing expected H atoms. Skipping.
Residue ALA  767 is missing expected H atoms. Skipping.
Residue VAL  768 is missing expected H atoms. Skipping.
Residue LEU  769 is missing expected H atoms. Skipping.
Residue ALA  770 is missing expected H atoms. Skipping.
Residue ALA  771 is missing expected H atoms. Skipping.
Residue VAL  772 is missing expected H atoms. Skipping.
Residue ILE  774 is missing expected H atoms. Skipping.
Residue VAL  777 is missing expected H atoms. Skipping.
Residue VAL  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue THR  798 is missing expected H atoms. Skipping.
Residue VAL  802 is missing expected H atoms. Skipping.
Residue VAL  805 is missing expected H atoms. Skipping.
Residue VAL  806 is missing expected H atoms. Skipping.
Residue ILE  809 is missing expected H atoms. Skipping.
Residue LEU  812 is missing expected H atoms. Skipping.
Residue ALA  823 is missing expected H atoms. Skipping.
Residue MET  824 is missing expected H atoms. Skipping.
Residue LEU  825 is missing expected H atoms. Skipping.
Residue LEU  827 is missing expected H atoms. Skipping.
Residue THR  837 is missing expected H atoms. Skipping.
Residue LEU  838 is missing expected H atoms. Skipping.
Residue LEU  839 is missing expected H atoms. Skipping.
Residue ILE  841 is missing expected H atoms. Skipping.
Residue LEU  842 is missing expected H atoms. Skipping.
Residue ILE  846 is missing expected H atoms. Skipping.
Residue MET  850 is missing expected H atoms. Skipping.
Residue THR  853 is missing expected H atoms. Skipping.
Residue MET  856 is missing expected H atoms. Skipping.
Residue ILE  858 is missing expected H atoms. Skipping.
Residue LEU  861 is missing expected H atoms. Skipping.
Residue ILE  863 is missing expected H atoms. Skipping.
Residue ILE  865 is missing expected H atoms. Skipping.
Residue ILE  899 is missing expected H atoms. Skipping.
Residue THR  901 is missing expected H atoms. Skipping.
Residue LEU  902 is missing expected H atoms. Skipping.
Residue VAL  906 is missing expected H atoms. Skipping.
Residue ALA  907 is missing expected H atoms. Skipping.
Residue LEU  910 is missing expected H atoms. Skipping.
Residue ILE  912 is missing expected H atoms. Skipping.
Residue VAL  913 is missing expected H atoms. Skipping.
Residue VAL  916 is missing expected H atoms. Skipping.
Residue LEU  919 is missing expected H atoms. Skipping.
Residue ALA  925 is missing expected H atoms. Skipping.
Residue ILE  926 is missing expected H atoms. Skipping.
Residue LEU  927 is missing expected H atoms. Skipping.
Residue VAL  929 is missing expected H atoms. Skipping.
Residue LEU  932 is missing expected H atoms. Skipping.
Residue LEU  933 is missing expected H atoms. Skipping.
Residue THR  935 is missing expected H atoms. Skipping.
Residue THR  937 is missing expected H atoms. Skipping.
Residue MET  939 is missing expected H atoms. Skipping.
Residue LEU  950 is missing expected H atoms. Skipping.
Residue ALA  954 is missing expected H atoms. Skipping.
Residue VAL  958 is missing expected H atoms. Skipping.
Residue ILE  959 is missing expected H atoms. Skipping.
Residue LEU  966 is missing expected H atoms. Skipping.
Residue ILE  968 is missing expected H atoms. Skipping.
Residue ILE  971 is missing expected H atoms. Skipping.
Residue THR  972 is missing expected H atoms. Skipping.
Residue THR  975 is missing expected H atoms. Skipping.
Residue LEU  976 is missing expected H atoms. Skipping.
Residue VAL  977 is missing expected H atoms. Skipping.
Residue THR  978 is missing expected H atoms. Skipping.
Residue THR  979 is missing expected H atoms. Skipping.
Residue VAL  981 is missing expected H atoms. Skipping.
Residue THR  982 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue ALA  988 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.
Residue VAL  520 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  542 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Residue VAL  555 is missing expected H atoms. Skipping.
Residue MET  561 is missing expected H atoms. Skipping.
Residue LEU  574 is missing expected H atoms. Skipping.
Residue THR  580 is missing expected H atoms. Skipping.
Residue THR  587 is missing expected H atoms. Skipping.
Residue THR  588 is missing expected H atoms. Skipping.
Residue THR  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue LEU  599 is missing expected H atoms. Skipping.
Residue LEU  600 is missing expected H atoms. Skipping.
Residue VAL  613 is missing expected H atoms. Skipping.
Residue ILE  615 is missing expected H atoms. Skipping.
Residue THR  623 is missing expected H atoms. Skipping.
Evaluate side-chains
  67 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 1.311 
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
  outliers start: 5
  outliers final: 1
  residues processed: 66
  average time/residue: 0.3756
  time to fit residues: 35.2369
Evaluate side-chains
  57 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 1.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    6.9990
   chunk 115 optimal weight:    3.9990
   chunk 63 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 77 optimal weight:   40.0000
   chunk 61 optimal weight:    9.9990
   chunk 119 optimal weight:    1.9990
   chunk 46 optimal weight:    7.9990
   chunk 72 optimal weight:    3.9990
   chunk 88 optimal weight:    7.9990
   chunk 138 optimal weight:    0.8980
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 344 GLN
** A 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.1366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.043  12032  Z= 0.451
  Angle     :  0.607   6.689  16302  Z= 0.326
  Chirality :  0.047   0.156   1790
  Planarity :  0.004   0.050   2157
  Dihedral  :  5.283  52.223   1648
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 16.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  9.58 %
    Favored  : 88.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.58 %
    Cis-general     : 0.07 %
    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: -0.67 (0.22), residues: 1522
  helix: -0.88 (0.44), residues: 133
  sheet:  0.07 (0.24), residues: 470
  loop : -0.61 (0.21), residues: 919

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 144 
 HIS   0.005   0.001   HIS A 121 
 PHE   0.023   0.002   PHE A 306 
 TYR   0.023   0.002   TYR A 305 
 ARG   0.003   0.000   ARG B  93 

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   33 is missing expected H atoms. Skipping.
Residue VAL   35 is missing expected H atoms. Skipping.
Residue ALA   39 is missing expected H atoms. Skipping.
Residue ALA   52 is missing expected H atoms. Skipping.
Residue VAL   53 is missing expected H atoms. Skipping.
Residue VAL   57 is missing expected H atoms. Skipping.
Residue ALA   60 is missing expected H atoms. Skipping.
Residue MET   64 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue VAL   68 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue THR   75 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   86 is missing expected H atoms. Skipping.
Residue LEU   87 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ILE  100 is missing expected H atoms. Skipping.
Residue ALA  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue ALA  111 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue ALA  126 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue ALA  137 is missing expected H atoms. Skipping.
Residue ALA  139 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  146 is missing expected H atoms. Skipping.
Residue MET  148 is missing expected H atoms. Skipping.
Residue VAL  155 is missing expected H atoms. Skipping.
Residue THR  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  164 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue VAL  167 is missing expected H atoms. Skipping.
Residue ALA  170 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  179 is missing expected H atoms. Skipping.
Residue ILE  191 is missing expected H atoms. Skipping.
Residue THR  194 is missing expected H atoms. Skipping.
Residue ALA  196 is missing expected H atoms. Skipping.
Residue VAL  199 is missing expected H atoms. Skipping.
Residue LEU  200 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LEU  213 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue ALA  219 is missing expected H atoms. Skipping.
Residue ILE  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Residue VAL  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LEU  238 is missing expected H atoms. Skipping.
Residue ALA  239 is missing expected H atoms. Skipping.
Residue THR  240 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue ALA  243 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue ILE  246 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue VAL  256 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  258 is missing expected H atoms. Skipping.
Residue ILE  266 is missing expected H atoms. Skipping.
Residue VAL  270 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue ALA  276 is missing expected H atoms. Skipping.
Residue ALA  277 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue LEU  280 is missing expected H atoms. Skipping.
Residue MET  282 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  285 is missing expected H atoms. Skipping.
Residue MET  291 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue THR  298 is missing expected H atoms. Skipping.
Residue MET  302 is missing expected H atoms. Skipping.
Residue ALA  303 is missing expected H atoms. Skipping.
Residue ALA  304 is missing expected H atoms. Skipping.
Residue VAL  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue ALA  312 is missing expected H atoms. Skipping.
Residue THR  313 is missing expected H atoms. Skipping.
Residue ILE  315 is missing expected H atoms. Skipping.
Residue ALA  321 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue ILE  325 is missing expected H atoms. Skipping.
Residue ALA  327 is missing expected H atoms. Skipping.
Residue LEU  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU  339 is missing expected H atoms. Skipping.
Residue VAL  342 is missing expected H atoms. Skipping.
Residue VAL  345 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  349 is missing expected H atoms. Skipping.
Residue ALA  352 is missing expected H atoms. Skipping.
Residue THR  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LEU  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue ALA  368 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  374 is missing expected H atoms. Skipping.
Residue ALA  375 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue LEU  380 is missing expected H atoms. Skipping.
Residue ILE  388 is missing expected H atoms. Skipping.
Residue ALA  389 is missing expected H atoms. Skipping.
Residue ILE  390 is missing expected H atoms. Skipping.
Residue ALA  391 is missing expected H atoms. Skipping.
Residue ALA  392 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue VAL  403 is missing expected H atoms. Skipping.
Residue ILE  405 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Residue ALA  415 is missing expected H atoms. Skipping.
Residue VAL  416 is missing expected H atoms. Skipping.
Residue ILE  420 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue ALA  426 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue MET  438 is missing expected H atoms. Skipping.
Residue ALA  441 is missing expected H atoms. Skipping.
Residue THR  442 is missing expected H atoms. Skipping.
Residue ILE  444 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue ILE  453 is missing expected H atoms. Skipping.
Residue VAL  454 is missing expected H atoms. Skipping.
Residue ALA  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue VAL  470 is missing expected H atoms. Skipping.
Residue ILE  471 is missing expected H atoms. Skipping.
Residue THR  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ALA  475 is missing expected H atoms. Skipping.
Residue LEU  477 is missing expected H atoms. Skipping.
Residue VAL  479 is missing expected H atoms. Skipping.
Residue ILE  483 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue THR  490 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue THR  496 is missing expected H atoms. Skipping.
Residue ALA  497 is missing expected H atoms. Skipping.
Residue LEU  498 is missing expected H atoms. Skipping.
Residue VAL  500 is missing expected H atoms. Skipping.
Residue VAL  505 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue ALA  511 is missing expected H atoms. Skipping.
Residue VAL  516 is missing expected H atoms. Skipping.
Residue LEU  517 is missing expected H atoms. Skipping.
Residue LEU  521 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  532 is missing expected H atoms. Skipping.
Residue ALA  537 is missing expected H atoms. Skipping.
Residue ILE  538 is missing expected H atoms. Skipping.
Residue ALA  541 is missing expected H atoms. Skipping.
Residue LEU  542 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue THR  556 is missing expected H atoms. Skipping.
Residue ILE  557 is missing expected H atoms. Skipping.
Residue LEU  562 is missing expected H atoms. Skipping.
Residue MET  563 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue ALA  570 is missing expected H atoms. Skipping.
Residue LEU  572 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue THR  583 is missing expected H atoms. Skipping.
Residue ILE  585 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue ILE  587 is missing expected H atoms. Skipping.
Residue MET  589 is missing expected H atoms. Skipping.
Residue LEU  593 is missing expected H atoms. Skipping.
Residue THR  597 is missing expected H atoms. Skipping.
Residue ALA  598 is missing expected H atoms. Skipping.
Residue ALA  599 is missing expected H atoms. Skipping.
Residue THR  601 is missing expected H atoms. Skipping.
Residue THR  602 is missing expected H atoms. Skipping.
Residue LEU  604 is missing expected H atoms. Skipping.
Residue ILE  607 is missing expected H atoms. Skipping.
Residue LEU  608 is missing expected H atoms. Skipping.
Residue THR  612 is missing expected H atoms. Skipping.
Residue ALA  614 is missing expected H atoms. Skipping.
Residue ILE  616 is missing expected H atoms. Skipping.
Residue ALA  620 is missing expected H atoms. Skipping.
Residue ILE  622 is missing expected H atoms. Skipping.
Residue LEU  623 is missing expected H atoms. Skipping.
Residue LEU  624 is missing expected H atoms. Skipping.
Residue VAL  631 is missing expected H atoms. Skipping.
Residue LEU  636 is missing expected H atoms. Skipping.
Residue VAL  638 is missing expected H atoms. Skipping.
Residue VAL  640 is missing expected H atoms. Skipping.
Residue ILE  647 is missing expected H atoms. Skipping.
Residue ILE  649 is missing expected H atoms. Skipping.
Residue LEU  655 is missing expected H atoms. Skipping.
Residue THR  656 is missing expected H atoms. Skipping.
Residue LEU  657 is missing expected H atoms. Skipping.
Residue ILE  658 is missing expected H atoms. Skipping.
Residue VAL  659 is missing expected H atoms. Skipping.
Residue ALA  661 is missing expected H atoms. Skipping.
Residue ALA  668 is missing expected H atoms. Skipping.
Residue ALA  671 is missing expected H atoms. Skipping.
Residue LEU  673 is missing expected H atoms. Skipping.
Residue ILE  674 is missing expected H atoms. Skipping.
Residue VAL  675 is missing expected H atoms. Skipping.
Residue ILE  677 is missing expected H atoms. Skipping.
Residue LEU  679 is missing expected H atoms. Skipping.
Residue ALA  681 is missing expected H atoms. Skipping.
Residue ILE  684 is missing expected H atoms. Skipping.
Residue VAL  686 is missing expected H atoms. Skipping.
Residue VAL  687 is missing expected H atoms. Skipping.
Residue ALA  692 is missing expected H atoms. Skipping.
Residue LEU  693 is missing expected H atoms. Skipping.
Residue ALA  694 is missing expected H atoms. Skipping.
Residue LEU  696 is missing expected H atoms. Skipping.
Residue ALA  699 is missing expected H atoms. Skipping.
Residue THR  702 is missing expected H atoms. Skipping.
Residue THR  706 is missing expected H atoms. Skipping.
Residue VAL  709 is missing expected H atoms. Skipping.
Residue VAL  710 is missing expected H atoms. Skipping.
Residue LEU  713 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue ALA  719 is missing expected H atoms. Skipping.
Residue THR  721 is missing expected H atoms. Skipping.
Residue LEU  723 is missing expected H atoms. Skipping.
Residue LEU  724 is missing expected H atoms. Skipping.
Residue ALA  725 is missing expected H atoms. Skipping.
Residue LEU  727 is missing expected H atoms. Skipping.
Residue VAL  731 is missing expected H atoms. Skipping.
Residue MET  737 is missing expected H atoms. Skipping.
Residue THR  739 is missing expected H atoms. Skipping.
Residue VAL  741 is missing expected H atoms. Skipping.
Residue LEU  745 is missing expected H atoms. Skipping.
Residue ILE  747 is missing expected H atoms. Skipping.
Residue LEU  752 is missing expected H atoms. Skipping.
Residue VAL  756 is missing expected H atoms. Skipping.
Residue VAL  759 is missing expected H atoms. Skipping.
Residue VAL  760 is missing expected H atoms. Skipping.
Residue VAL  764 is missing expected H atoms. Skipping.
Residue LEU  766 is missing expected H atoms. Skipping.
Residue ALA  767 is missing expected H atoms. Skipping.
Residue VAL  768 is missing expected H atoms. Skipping.
Residue LEU  769 is missing expected H atoms. Skipping.
Residue ALA  770 is missing expected H atoms. Skipping.
Residue ALA  771 is missing expected H atoms. Skipping.
Residue VAL  772 is missing expected H atoms. Skipping.
Residue ILE  774 is missing expected H atoms. Skipping.
Residue VAL  777 is missing expected H atoms. Skipping.
Residue VAL  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue THR  798 is missing expected H atoms. Skipping.
Residue VAL  802 is missing expected H atoms. Skipping.
Residue VAL  805 is missing expected H atoms. Skipping.
Residue VAL  806 is missing expected H atoms. Skipping.
Residue ILE  809 is missing expected H atoms. Skipping.
Residue LEU  812 is missing expected H atoms. Skipping.
Residue ALA  823 is missing expected H atoms. Skipping.
Residue MET  824 is missing expected H atoms. Skipping.
Residue LEU  825 is missing expected H atoms. Skipping.
Residue LEU  827 is missing expected H atoms. Skipping.
Residue THR  837 is missing expected H atoms. Skipping.
Residue LEU  838 is missing expected H atoms. Skipping.
Residue LEU  839 is missing expected H atoms. Skipping.
Residue ILE  841 is missing expected H atoms. Skipping.
Residue LEU  842 is missing expected H atoms. Skipping.
Residue ILE  846 is missing expected H atoms. Skipping.
Residue MET  850 is missing expected H atoms. Skipping.
Residue THR  853 is missing expected H atoms. Skipping.
Residue MET  856 is missing expected H atoms. Skipping.
Residue ILE  858 is missing expected H atoms. Skipping.
Residue LEU  861 is missing expected H atoms. Skipping.
Residue ILE  863 is missing expected H atoms. Skipping.
Residue ILE  865 is missing expected H atoms. Skipping.
Residue ILE  899 is missing expected H atoms. Skipping.
Residue THR  901 is missing expected H atoms. Skipping.
Residue LEU  902 is missing expected H atoms. Skipping.
Residue VAL  906 is missing expected H atoms. Skipping.
Residue ALA  907 is missing expected H atoms. Skipping.
Residue LEU  910 is missing expected H atoms. Skipping.
Residue ILE  912 is missing expected H atoms. Skipping.
Residue VAL  913 is missing expected H atoms. Skipping.
Residue VAL  916 is missing expected H atoms. Skipping.
Residue LEU  919 is missing expected H atoms. Skipping.
Residue ALA  925 is missing expected H atoms. Skipping.
Residue ILE  926 is missing expected H atoms. Skipping.
Residue LEU  927 is missing expected H atoms. Skipping.
Residue VAL  929 is missing expected H atoms. Skipping.
Residue LEU  932 is missing expected H atoms. Skipping.
Residue LEU  933 is missing expected H atoms. Skipping.
Residue THR  935 is missing expected H atoms. Skipping.
Residue THR  937 is missing expected H atoms. Skipping.
Residue MET  939 is missing expected H atoms. Skipping.
Residue LEU  950 is missing expected H atoms. Skipping.
Residue ALA  954 is missing expected H atoms. Skipping.
Residue VAL  958 is missing expected H atoms. Skipping.
Residue ILE  959 is missing expected H atoms. Skipping.
Residue LEU  966 is missing expected H atoms. Skipping.
Residue ILE  968 is missing expected H atoms. Skipping.
Residue ILE  971 is missing expected H atoms. Skipping.
Residue THR  972 is missing expected H atoms. Skipping.
Residue THR  975 is missing expected H atoms. Skipping.
Residue LEU  976 is missing expected H atoms. Skipping.
Residue VAL  977 is missing expected H atoms. Skipping.
Residue THR  978 is missing expected H atoms. Skipping.
Residue THR  979 is missing expected H atoms. Skipping.
Residue VAL  981 is missing expected H atoms. Skipping.
Residue THR  982 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue ALA  988 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.
Residue VAL  520 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  542 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Residue VAL  555 is missing expected H atoms. Skipping.
Residue MET  561 is missing expected H atoms. Skipping.
Residue LEU  574 is missing expected H atoms. Skipping.
Residue THR  580 is missing expected H atoms. Skipping.
Residue THR  587 is missing expected H atoms. Skipping.
Residue THR  588 is missing expected H atoms. Skipping.
Residue THR  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue LEU  599 is missing expected H atoms. Skipping.
Residue LEU  600 is missing expected H atoms. Skipping.
Residue VAL  613 is missing expected H atoms. Skipping.
Residue ILE  615 is missing expected H atoms. Skipping.
Residue THR  623 is missing expected H atoms. Skipping.
Evaluate side-chains
  77 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 58
  time to evaluate  : 1.663 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 TRP cc_start: 0.8490 (OUTLIER) cc_final: 0.7954 (t-100)
REVERT: A  216 ASP cc_start: 0.6857 (OUTLIER) cc_final: 0.6613 (m-30)
REVERT: A  507 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.7175 (p90)
REVERT: A  563 MET cc_start: 0.6582 (OUTLIER) cc_final: 0.6041 (mtm)
  outliers start: 19
  outliers final: 10
  residues processed: 70
  average time/residue: 0.3247
  time to fit residues: 33.9137
Evaluate side-chains
  66 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 52
  time to evaluate  : 1.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 TRP
Chi-restraints excluded: chain A residue  216 ASP
Chi-restraints excluded: chain A residue  451 ASP
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  503 PHE
Chi-restraints excluded: chain A residue  507 PHE
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain A residue  732 HIS
Chi-restraints excluded: chain A residue  747 ILE
Chi-restraints excluded: chain A residue  826 HIS
Chi-restraints excluded: chain B residue  451 LEU
Chi-restraints excluded: chain B residue  493 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 76 optimal weight:   50.0000
   chunk 42 optimal weight:    0.7980
   chunk 114 optimal weight:    0.6980
   chunk 93 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 138 optimal weight:    5.9990
   chunk 149 optimal weight:   30.0000
   chunk 123 optimal weight:    0.5980
   chunk 137 optimal weight:    4.9990
   chunk 47 optimal weight:    0.8980
   chunk 110 optimal weight:    1.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.1676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  12032  Z= 0.153
  Angle     :  0.450   6.117  16302  Z= 0.243
  Chirality :  0.042   0.136   1790
  Planarity :  0.003   0.035   2157
  Dihedral  :  4.616  59.680   1648
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 18.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 10.49 %
    Favored  : 88.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.58 %
    Cis-general     : 0.07 %
    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: -0.49 (0.22), residues: 1522
  helix: -0.46 (0.46), residues: 134
  sheet:  0.05 (0.23), residues: 477
  loop : -0.46 (0.21), residues: 911

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 144 
 HIS   0.004   0.001   HIS A 621 
 PHE   0.008   0.001   PHE A  49 
 TYR   0.011   0.001   TYR A 305 
 ARG   0.002   0.000   ARG A 728 

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   33 is missing expected H atoms. Skipping.
Residue VAL   35 is missing expected H atoms. Skipping.
Residue ALA   39 is missing expected H atoms. Skipping.
Residue ALA   52 is missing expected H atoms. Skipping.
Residue VAL   53 is missing expected H atoms. Skipping.
Residue VAL   57 is missing expected H atoms. Skipping.
Residue ALA   60 is missing expected H atoms. Skipping.
Residue MET   64 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue VAL   68 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue THR   75 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   86 is missing expected H atoms. Skipping.
Residue LEU   87 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ILE  100 is missing expected H atoms. Skipping.
Residue ALA  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue ALA  111 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue ALA  126 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue ALA  137 is missing expected H atoms. Skipping.
Residue ALA  139 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  146 is missing expected H atoms. Skipping.
Residue MET  148 is missing expected H atoms. Skipping.
Residue VAL  155 is missing expected H atoms. Skipping.
Residue THR  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  164 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue VAL  167 is missing expected H atoms. Skipping.
Residue ALA  170 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  179 is missing expected H atoms. Skipping.
Residue ILE  191 is missing expected H atoms. Skipping.
Residue THR  194 is missing expected H atoms. Skipping.
Residue ALA  196 is missing expected H atoms. Skipping.
Residue VAL  199 is missing expected H atoms. Skipping.
Residue LEU  200 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LEU  213 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue ALA  219 is missing expected H atoms. Skipping.
Residue ILE  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Residue VAL  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LEU  238 is missing expected H atoms. Skipping.
Residue ALA  239 is missing expected H atoms. Skipping.
Residue THR  240 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue ALA  243 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue ILE  246 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue VAL  256 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  258 is missing expected H atoms. Skipping.
Residue ILE  266 is missing expected H atoms. Skipping.
Residue VAL  270 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue ALA  276 is missing expected H atoms. Skipping.
Residue ALA  277 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue LEU  280 is missing expected H atoms. Skipping.
Residue MET  282 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  285 is missing expected H atoms. Skipping.
Residue MET  291 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue THR  298 is missing expected H atoms. Skipping.
Residue MET  302 is missing expected H atoms. Skipping.
Residue ALA  303 is missing expected H atoms. Skipping.
Residue ALA  304 is missing expected H atoms. Skipping.
Residue VAL  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue ALA  312 is missing expected H atoms. Skipping.
Residue THR  313 is missing expected H atoms. Skipping.
Residue ILE  315 is missing expected H atoms. Skipping.
Residue ALA  321 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue ILE  325 is missing expected H atoms. Skipping.
Residue ALA  327 is missing expected H atoms. Skipping.
Residue LEU  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU  339 is missing expected H atoms. Skipping.
Residue VAL  342 is missing expected H atoms. Skipping.
Residue VAL  345 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  349 is missing expected H atoms. Skipping.
Residue ALA  352 is missing expected H atoms. Skipping.
Residue THR  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LEU  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue ALA  368 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  374 is missing expected H atoms. Skipping.
Residue ALA  375 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue LEU  380 is missing expected H atoms. Skipping.
Residue ILE  388 is missing expected H atoms. Skipping.
Residue ALA  389 is missing expected H atoms. Skipping.
Residue ILE  390 is missing expected H atoms. Skipping.
Residue ALA  391 is missing expected H atoms. Skipping.
Residue ALA  392 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue VAL  403 is missing expected H atoms. Skipping.
Residue ILE  405 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Residue ALA  415 is missing expected H atoms. Skipping.
Residue VAL  416 is missing expected H atoms. Skipping.
Residue ILE  420 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue ALA  426 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue MET  438 is missing expected H atoms. Skipping.
Residue ALA  441 is missing expected H atoms. Skipping.
Residue THR  442 is missing expected H atoms. Skipping.
Residue ILE  444 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue ILE  453 is missing expected H atoms. Skipping.
Residue VAL  454 is missing expected H atoms. Skipping.
Residue ALA  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue VAL  470 is missing expected H atoms. Skipping.
Residue ILE  471 is missing expected H atoms. Skipping.
Residue THR  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ALA  475 is missing expected H atoms. Skipping.
Residue LEU  477 is missing expected H atoms. Skipping.
Residue VAL  479 is missing expected H atoms. Skipping.
Residue ILE  483 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue THR  490 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue THR  496 is missing expected H atoms. Skipping.
Residue ALA  497 is missing expected H atoms. Skipping.
Residue LEU  498 is missing expected H atoms. Skipping.
Residue VAL  500 is missing expected H atoms. Skipping.
Residue VAL  505 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue ALA  511 is missing expected H atoms. Skipping.
Residue VAL  516 is missing expected H atoms. Skipping.
Residue LEU  517 is missing expected H atoms. Skipping.
Residue LEU  521 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  532 is missing expected H atoms. Skipping.
Residue ALA  537 is missing expected H atoms. Skipping.
Residue ILE  538 is missing expected H atoms. Skipping.
Residue ALA  541 is missing expected H atoms. Skipping.
Residue LEU  542 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue THR  556 is missing expected H atoms. Skipping.
Residue ILE  557 is missing expected H atoms. Skipping.
Residue LEU  562 is missing expected H atoms. Skipping.
Residue MET  563 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue ALA  570 is missing expected H atoms. Skipping.
Residue LEU  572 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue THR  583 is missing expected H atoms. Skipping.
Residue ILE  585 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue ILE  587 is missing expected H atoms. Skipping.
Residue MET  589 is missing expected H atoms. Skipping.
Residue LEU  593 is missing expected H atoms. Skipping.
Residue THR  597 is missing expected H atoms. Skipping.
Residue ALA  598 is missing expected H atoms. Skipping.
Residue ALA  599 is missing expected H atoms. Skipping.
Residue THR  601 is missing expected H atoms. Skipping.
Residue THR  602 is missing expected H atoms. Skipping.
Residue LEU  604 is missing expected H atoms. Skipping.
Residue ILE  607 is missing expected H atoms. Skipping.
Residue LEU  608 is missing expected H atoms. Skipping.
Residue THR  612 is missing expected H atoms. Skipping.
Residue ALA  614 is missing expected H atoms. Skipping.
Residue ILE  616 is missing expected H atoms. Skipping.
Residue ALA  620 is missing expected H atoms. Skipping.
Residue ILE  622 is missing expected H atoms. Skipping.
Residue LEU  623 is missing expected H atoms. Skipping.
Residue LEU  624 is missing expected H atoms. Skipping.
Residue VAL  631 is missing expected H atoms. Skipping.
Residue LEU  636 is missing expected H atoms. Skipping.
Residue VAL  638 is missing expected H atoms. Skipping.
Residue VAL  640 is missing expected H atoms. Skipping.
Residue ILE  647 is missing expected H atoms. Skipping.
Residue ILE  649 is missing expected H atoms. Skipping.
Residue LEU  655 is missing expected H atoms. Skipping.
Residue THR  656 is missing expected H atoms. Skipping.
Residue LEU  657 is missing expected H atoms. Skipping.
Residue ILE  658 is missing expected H atoms. Skipping.
Residue VAL  659 is missing expected H atoms. Skipping.
Residue ALA  661 is missing expected H atoms. Skipping.
Residue ALA  668 is missing expected H atoms. Skipping.
Residue ALA  671 is missing expected H atoms. Skipping.
Residue LEU  673 is missing expected H atoms. Skipping.
Residue ILE  674 is missing expected H atoms. Skipping.
Residue VAL  675 is missing expected H atoms. Skipping.
Residue ILE  677 is missing expected H atoms. Skipping.
Residue LEU  679 is missing expected H atoms. Skipping.
Residue ALA  681 is missing expected H atoms. Skipping.
Residue ILE  684 is missing expected H atoms. Skipping.
Residue VAL  686 is missing expected H atoms. Skipping.
Residue VAL  687 is missing expected H atoms. Skipping.
Residue ALA  692 is missing expected H atoms. Skipping.
Residue LEU  693 is missing expected H atoms. Skipping.
Residue ALA  694 is missing expected H atoms. Skipping.
Residue LEU  696 is missing expected H atoms. Skipping.
Residue ALA  699 is missing expected H atoms. Skipping.
Residue THR  702 is missing expected H atoms. Skipping.
Residue THR  706 is missing expected H atoms. Skipping.
Residue VAL  709 is missing expected H atoms. Skipping.
Residue VAL  710 is missing expected H atoms. Skipping.
Residue LEU  713 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue ALA  719 is missing expected H atoms. Skipping.
Residue THR  721 is missing expected H atoms. Skipping.
Residue LEU  723 is missing expected H atoms. Skipping.
Residue LEU  724 is missing expected H atoms. Skipping.
Residue ALA  725 is missing expected H atoms. Skipping.
Residue LEU  727 is missing expected H atoms. Skipping.
Residue VAL  731 is missing expected H atoms. Skipping.
Residue MET  737 is missing expected H atoms. Skipping.
Residue THR  739 is missing expected H atoms. Skipping.
Residue VAL  741 is missing expected H atoms. Skipping.
Residue LEU  745 is missing expected H atoms. Skipping.
Residue ILE  747 is missing expected H atoms. Skipping.
Residue LEU  752 is missing expected H atoms. Skipping.
Residue VAL  756 is missing expected H atoms. Skipping.
Residue VAL  759 is missing expected H atoms. Skipping.
Residue VAL  760 is missing expected H atoms. Skipping.
Residue VAL  764 is missing expected H atoms. Skipping.
Residue LEU  766 is missing expected H atoms. Skipping.
Residue ALA  767 is missing expected H atoms. Skipping.
Residue VAL  768 is missing expected H atoms. Skipping.
Residue LEU  769 is missing expected H atoms. Skipping.
Residue ALA  770 is missing expected H atoms. Skipping.
Residue ALA  771 is missing expected H atoms. Skipping.
Residue VAL  772 is missing expected H atoms. Skipping.
Residue ILE  774 is missing expected H atoms. Skipping.
Residue VAL  777 is missing expected H atoms. Skipping.
Residue VAL  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue THR  798 is missing expected H atoms. Skipping.
Residue VAL  802 is missing expected H atoms. Skipping.
Residue VAL  805 is missing expected H atoms. Skipping.
Residue VAL  806 is missing expected H atoms. Skipping.
Residue ILE  809 is missing expected H atoms. Skipping.
Residue LEU  812 is missing expected H atoms. Skipping.
Residue ALA  823 is missing expected H atoms. Skipping.
Residue MET  824 is missing expected H atoms. Skipping.
Residue LEU  825 is missing expected H atoms. Skipping.
Residue LEU  827 is missing expected H atoms. Skipping.
Residue THR  837 is missing expected H atoms. Skipping.
Residue LEU  838 is missing expected H atoms. Skipping.
Residue LEU  839 is missing expected H atoms. Skipping.
Residue ILE  841 is missing expected H atoms. Skipping.
Residue LEU  842 is missing expected H atoms. Skipping.
Residue ILE  846 is missing expected H atoms. Skipping.
Residue MET  850 is missing expected H atoms. Skipping.
Residue THR  853 is missing expected H atoms. Skipping.
Residue MET  856 is missing expected H atoms. Skipping.
Residue ILE  858 is missing expected H atoms. Skipping.
Residue LEU  861 is missing expected H atoms. Skipping.
Residue ILE  863 is missing expected H atoms. Skipping.
Residue ILE  865 is missing expected H atoms. Skipping.
Residue ILE  899 is missing expected H atoms. Skipping.
Residue THR  901 is missing expected H atoms. Skipping.
Residue LEU  902 is missing expected H atoms. Skipping.
Residue VAL  906 is missing expected H atoms. Skipping.
Residue ALA  907 is missing expected H atoms. Skipping.
Residue LEU  910 is missing expected H atoms. Skipping.
Residue ILE  912 is missing expected H atoms. Skipping.
Residue VAL  913 is missing expected H atoms. Skipping.
Residue VAL  916 is missing expected H atoms. Skipping.
Residue LEU  919 is missing expected H atoms. Skipping.
Residue ALA  925 is missing expected H atoms. Skipping.
Residue ILE  926 is missing expected H atoms. Skipping.
Residue LEU  927 is missing expected H atoms. Skipping.
Residue VAL  929 is missing expected H atoms. Skipping.
Residue LEU  932 is missing expected H atoms. Skipping.
Residue LEU  933 is missing expected H atoms. Skipping.
Residue THR  935 is missing expected H atoms. Skipping.
Residue THR  937 is missing expected H atoms. Skipping.
Residue MET  939 is missing expected H atoms. Skipping.
Residue LEU  950 is missing expected H atoms. Skipping.
Residue ALA  954 is missing expected H atoms. Skipping.
Residue VAL  958 is missing expected H atoms. Skipping.
Residue ILE  959 is missing expected H atoms. Skipping.
Residue LEU  966 is missing expected H atoms. Skipping.
Residue ILE  968 is missing expected H atoms. Skipping.
Residue ILE  971 is missing expected H atoms. Skipping.
Residue THR  972 is missing expected H atoms. Skipping.
Residue THR  975 is missing expected H atoms. Skipping.
Residue LEU  976 is missing expected H atoms. Skipping.
Residue VAL  977 is missing expected H atoms. Skipping.
Residue THR  978 is missing expected H atoms. Skipping.
Residue THR  979 is missing expected H atoms. Skipping.
Residue VAL  981 is missing expected H atoms. Skipping.
Residue THR  982 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue ALA  988 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.
Residue VAL  520 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  542 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Residue VAL  555 is missing expected H atoms. Skipping.
Residue MET  561 is missing expected H atoms. Skipping.
Residue LEU  574 is missing expected H atoms. Skipping.
Residue THR  580 is missing expected H atoms. Skipping.
Residue THR  587 is missing expected H atoms. Skipping.
Residue THR  588 is missing expected H atoms. Skipping.
Residue THR  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue LEU  599 is missing expected H atoms. Skipping.
Residue LEU  600 is missing expected H atoms. Skipping.
Residue VAL  613 is missing expected H atoms. Skipping.
Residue ILE  615 is missing expected H atoms. Skipping.
Residue THR  623 is missing expected H atoms. Skipping.
Evaluate side-chains
  75 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 1.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 TRP cc_start: 0.8368 (OUTLIER) cc_final: 0.8132 (t-100)
REVERT: A  145 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7104 (tmt170)
REVERT: A  824 MET cc_start: 0.8848 (mmm) cc_final: 0.7774 (tpp)
  outliers start: 15
  outliers final: 8
  residues processed: 68
  average time/residue: 0.3296
  time to fit residues: 33.2149
Evaluate side-chains
  65 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 1.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 TRP
Chi-restraints excluded: chain A residue  145 ARG
Chi-restraints excluded: chain A residue  503 PHE
Chi-restraints excluded: chain A residue  747 ILE
Chi-restraints excluded: chain A residue  826 HIS
Chi-restraints excluded: chain A residue  829 TRP
Chi-restraints excluded: chain A residue  850 MET
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  474 CYS
Chi-restraints excluded: chain B residue  493 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 136 optimal weight:    5.9990
   chunk 103 optimal weight:    2.9990
   chunk 71 optimal weight:   10.0000
   chunk 15 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 92 optimal weight:    0.1980
   chunk 138 optimal weight:    4.9990
   chunk 146 optimal weight:    1.9990
   chunk 72 optimal weight:    9.9990
   chunk 131 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    2.4388

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

Flipped N/Q/H residues before XYZ refinement:
** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.2068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043  12032  Z= 0.404
  Angle     :  0.560   6.953  16302  Z= 0.298
  Chirality :  0.045   0.151   1790
  Planarity :  0.004   0.037   2157
  Dihedral  :  4.799  20.821   1646
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 24.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 10.42 %
    Favored  : 87.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.58 %
    Cis-general     : 0.07 %
    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: -0.76 (0.22), residues: 1522
  helix: -0.78 (0.44), residues: 133
  sheet: -0.14 (0.24), residues: 470
  loop : -0.61 (0.21), residues: 919

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 144 
 HIS   0.006   0.001   HIS B 565 
 PHE   0.021   0.002   PHE A 507 
 TYR   0.024   0.002   TYR A 305 
 ARG   0.003   0.000   ARG A 506 

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   33 is missing expected H atoms. Skipping.
Residue VAL   35 is missing expected H atoms. Skipping.
Residue ALA   39 is missing expected H atoms. Skipping.
Residue ALA   52 is missing expected H atoms. Skipping.
Residue VAL   53 is missing expected H atoms. Skipping.
Residue VAL   57 is missing expected H atoms. Skipping.
Residue ALA   60 is missing expected H atoms. Skipping.
Residue MET   64 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue VAL   68 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue THR   75 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   86 is missing expected H atoms. Skipping.
Residue LEU   87 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ILE  100 is missing expected H atoms. Skipping.
Residue ALA  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue ALA  111 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue ALA  126 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue ALA  137 is missing expected H atoms. Skipping.
Residue ALA  139 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  146 is missing expected H atoms. Skipping.
Residue MET  148 is missing expected H atoms. Skipping.
Residue VAL  155 is missing expected H atoms. Skipping.
Residue THR  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  164 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue VAL  167 is missing expected H atoms. Skipping.
Residue ALA  170 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  179 is missing expected H atoms. Skipping.
Residue ILE  191 is missing expected H atoms. Skipping.
Residue THR  194 is missing expected H atoms. Skipping.
Residue ALA  196 is missing expected H atoms. Skipping.
Residue VAL  199 is missing expected H atoms. Skipping.
Residue LEU  200 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LEU  213 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue ALA  219 is missing expected H atoms. Skipping.
Residue ILE  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Residue VAL  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LEU  238 is missing expected H atoms. Skipping.
Residue ALA  239 is missing expected H atoms. Skipping.
Residue THR  240 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue ALA  243 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue ILE  246 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue VAL  256 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  258 is missing expected H atoms. Skipping.
Residue ILE  266 is missing expected H atoms. Skipping.
Residue VAL  270 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue ALA  276 is missing expected H atoms. Skipping.
Residue ALA  277 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue LEU  280 is missing expected H atoms. Skipping.
Residue MET  282 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  285 is missing expected H atoms. Skipping.
Residue MET  291 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue THR  298 is missing expected H atoms. Skipping.
Residue MET  302 is missing expected H atoms. Skipping.
Residue ALA  303 is missing expected H atoms. Skipping.
Residue ALA  304 is missing expected H atoms. Skipping.
Residue VAL  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue ALA  312 is missing expected H atoms. Skipping.
Residue THR  313 is missing expected H atoms. Skipping.
Residue ILE  315 is missing expected H atoms. Skipping.
Residue ALA  321 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue ILE  325 is missing expected H atoms. Skipping.
Residue ALA  327 is missing expected H atoms. Skipping.
Residue LEU  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU  339 is missing expected H atoms. Skipping.
Residue VAL  342 is missing expected H atoms. Skipping.
Residue VAL  345 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  349 is missing expected H atoms. Skipping.
Residue ALA  352 is missing expected H atoms. Skipping.
Residue THR  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LEU  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue ALA  368 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  374 is missing expected H atoms. Skipping.
Residue ALA  375 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue LEU  380 is missing expected H atoms. Skipping.
Residue ILE  388 is missing expected H atoms. Skipping.
Residue ALA  389 is missing expected H atoms. Skipping.
Residue ILE  390 is missing expected H atoms. Skipping.
Residue ALA  391 is missing expected H atoms. Skipping.
Residue ALA  392 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue VAL  403 is missing expected H atoms. Skipping.
Residue ILE  405 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Residue ALA  415 is missing expected H atoms. Skipping.
Residue VAL  416 is missing expected H atoms. Skipping.
Residue ILE  420 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue ALA  426 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue MET  438 is missing expected H atoms. Skipping.
Residue ALA  441 is missing expected H atoms. Skipping.
Residue THR  442 is missing expected H atoms. Skipping.
Residue ILE  444 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue ILE  453 is missing expected H atoms. Skipping.
Residue VAL  454 is missing expected H atoms. Skipping.
Residue ALA  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue VAL  470 is missing expected H atoms. Skipping.
Residue ILE  471 is missing expected H atoms. Skipping.
Residue THR  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ALA  475 is missing expected H atoms. Skipping.
Residue LEU  477 is missing expected H atoms. Skipping.
Residue VAL  479 is missing expected H atoms. Skipping.
Residue ILE  483 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue THR  490 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue THR  496 is missing expected H atoms. Skipping.
Residue ALA  497 is missing expected H atoms. Skipping.
Residue LEU  498 is missing expected H atoms. Skipping.
Residue VAL  500 is missing expected H atoms. Skipping.
Residue VAL  505 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue ALA  511 is missing expected H atoms. Skipping.
Residue VAL  516 is missing expected H atoms. Skipping.
Residue LEU  517 is missing expected H atoms. Skipping.
Residue LEU  521 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  532 is missing expected H atoms. Skipping.
Residue ALA  537 is missing expected H atoms. Skipping.
Residue ILE  538 is missing expected H atoms. Skipping.
Residue ALA  541 is missing expected H atoms. Skipping.
Residue LEU  542 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue THR  556 is missing expected H atoms. Skipping.
Residue ILE  557 is missing expected H atoms. Skipping.
Residue LEU  562 is missing expected H atoms. Skipping.
Residue MET  563 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue ALA  570 is missing expected H atoms. Skipping.
Residue LEU  572 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue THR  583 is missing expected H atoms. Skipping.
Residue ILE  585 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue ILE  587 is missing expected H atoms. Skipping.
Residue MET  589 is missing expected H atoms. Skipping.
Residue LEU  593 is missing expected H atoms. Skipping.
Residue THR  597 is missing expected H atoms. Skipping.
Residue ALA  598 is missing expected H atoms. Skipping.
Residue ALA  599 is missing expected H atoms. Skipping.
Residue THR  601 is missing expected H atoms. Skipping.
Residue THR  602 is missing expected H atoms. Skipping.
Residue LEU  604 is missing expected H atoms. Skipping.
Residue ILE  607 is missing expected H atoms. Skipping.
Residue LEU  608 is missing expected H atoms. Skipping.
Residue THR  612 is missing expected H atoms. Skipping.
Residue ALA  614 is missing expected H atoms. Skipping.
Residue ILE  616 is missing expected H atoms. Skipping.
Residue ALA  620 is missing expected H atoms. Skipping.
Residue ILE  622 is missing expected H atoms. Skipping.
Residue LEU  623 is missing expected H atoms. Skipping.
Residue LEU  624 is missing expected H atoms. Skipping.
Residue VAL  631 is missing expected H atoms. Skipping.
Residue LEU  636 is missing expected H atoms. Skipping.
Residue VAL  638 is missing expected H atoms. Skipping.
Residue VAL  640 is missing expected H atoms. Skipping.
Residue ILE  647 is missing expected H atoms. Skipping.
Residue ILE  649 is missing expected H atoms. Skipping.
Residue LEU  655 is missing expected H atoms. Skipping.
Residue THR  656 is missing expected H atoms. Skipping.
Residue LEU  657 is missing expected H atoms. Skipping.
Residue ILE  658 is missing expected H atoms. Skipping.
Residue VAL  659 is missing expected H atoms. Skipping.
Residue ALA  661 is missing expected H atoms. Skipping.
Residue ALA  668 is missing expected H atoms. Skipping.
Residue ALA  671 is missing expected H atoms. Skipping.
Residue LEU  673 is missing expected H atoms. Skipping.
Residue ILE  674 is missing expected H atoms. Skipping.
Residue VAL  675 is missing expected H atoms. Skipping.
Residue ILE  677 is missing expected H atoms. Skipping.
Residue LEU  679 is missing expected H atoms. Skipping.
Residue ALA  681 is missing expected H atoms. Skipping.
Residue ILE  684 is missing expected H atoms. Skipping.
Residue VAL  686 is missing expected H atoms. Skipping.
Residue VAL  687 is missing expected H atoms. Skipping.
Residue ALA  692 is missing expected H atoms. Skipping.
Residue LEU  693 is missing expected H atoms. Skipping.
Residue ALA  694 is missing expected H atoms. Skipping.
Residue LEU  696 is missing expected H atoms. Skipping.
Residue ALA  699 is missing expected H atoms. Skipping.
Residue THR  702 is missing expected H atoms. Skipping.
Residue THR  706 is missing expected H atoms. Skipping.
Residue VAL  709 is missing expected H atoms. Skipping.
Residue VAL  710 is missing expected H atoms. Skipping.
Residue LEU  713 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue ALA  719 is missing expected H atoms. Skipping.
Residue THR  721 is missing expected H atoms. Skipping.
Residue LEU  723 is missing expected H atoms. Skipping.
Residue LEU  724 is missing expected H atoms. Skipping.
Residue ALA  725 is missing expected H atoms. Skipping.
Residue LEU  727 is missing expected H atoms. Skipping.
Residue VAL  731 is missing expected H atoms. Skipping.
Residue MET  737 is missing expected H atoms. Skipping.
Residue THR  739 is missing expected H atoms. Skipping.
Residue VAL  741 is missing expected H atoms. Skipping.
Residue LEU  745 is missing expected H atoms. Skipping.
Residue ILE  747 is missing expected H atoms. Skipping.
Residue LEU  752 is missing expected H atoms. Skipping.
Residue VAL  756 is missing expected H atoms. Skipping.
Residue VAL  759 is missing expected H atoms. Skipping.
Residue VAL  760 is missing expected H atoms. Skipping.
Residue VAL  764 is missing expected H atoms. Skipping.
Residue LEU  766 is missing expected H atoms. Skipping.
Residue ALA  767 is missing expected H atoms. Skipping.
Residue VAL  768 is missing expected H atoms. Skipping.
Residue LEU  769 is missing expected H atoms. Skipping.
Residue ALA  770 is missing expected H atoms. Skipping.
Residue ALA  771 is missing expected H atoms. Skipping.
Residue VAL  772 is missing expected H atoms. Skipping.
Residue ILE  774 is missing expected H atoms. Skipping.
Residue VAL  777 is missing expected H atoms. Skipping.
Residue VAL  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue THR  798 is missing expected H atoms. Skipping.
Residue VAL  802 is missing expected H atoms. Skipping.
Residue VAL  805 is missing expected H atoms. Skipping.
Residue VAL  806 is missing expected H atoms. Skipping.
Residue ILE  809 is missing expected H atoms. Skipping.
Residue LEU  812 is missing expected H atoms. Skipping.
Residue ALA  823 is missing expected H atoms. Skipping.
Residue MET  824 is missing expected H atoms. Skipping.
Residue LEU  825 is missing expected H atoms. Skipping.
Residue LEU  827 is missing expected H atoms. Skipping.
Residue THR  837 is missing expected H atoms. Skipping.
Residue LEU  838 is missing expected H atoms. Skipping.
Residue LEU  839 is missing expected H atoms. Skipping.
Residue ILE  841 is missing expected H atoms. Skipping.
Residue LEU  842 is missing expected H atoms. Skipping.
Residue ILE  846 is missing expected H atoms. Skipping.
Residue MET  850 is missing expected H atoms. Skipping.
Residue THR  853 is missing expected H atoms. Skipping.
Residue MET  856 is missing expected H atoms. Skipping.
Residue ILE  858 is missing expected H atoms. Skipping.
Residue LEU  861 is missing expected H atoms. Skipping.
Residue ILE  863 is missing expected H atoms. Skipping.
Residue ILE  865 is missing expected H atoms. Skipping.
Residue ILE  899 is missing expected H atoms. Skipping.
Residue THR  901 is missing expected H atoms. Skipping.
Residue LEU  902 is missing expected H atoms. Skipping.
Residue VAL  906 is missing expected H atoms. Skipping.
Residue ALA  907 is missing expected H atoms. Skipping.
Residue LEU  910 is missing expected H atoms. Skipping.
Residue ILE  912 is missing expected H atoms. Skipping.
Residue VAL  913 is missing expected H atoms. Skipping.
Residue VAL  916 is missing expected H atoms. Skipping.
Residue LEU  919 is missing expected H atoms. Skipping.
Residue ALA  925 is missing expected H atoms. Skipping.
Residue ILE  926 is missing expected H atoms. Skipping.
Residue LEU  927 is missing expected H atoms. Skipping.
Residue VAL  929 is missing expected H atoms. Skipping.
Residue LEU  932 is missing expected H atoms. Skipping.
Residue LEU  933 is missing expected H atoms. Skipping.
Residue THR  935 is missing expected H atoms. Skipping.
Residue THR  937 is missing expected H atoms. Skipping.
Residue MET  939 is missing expected H atoms. Skipping.
Residue LEU  950 is missing expected H atoms. Skipping.
Residue ALA  954 is missing expected H atoms. Skipping.
Residue VAL  958 is missing expected H atoms. Skipping.
Residue ILE  959 is missing expected H atoms. Skipping.
Residue LEU  966 is missing expected H atoms. Skipping.
Residue ILE  968 is missing expected H atoms. Skipping.
Residue ILE  971 is missing expected H atoms. Skipping.
Residue THR  972 is missing expected H atoms. Skipping.
Residue THR  975 is missing expected H atoms. Skipping.
Residue LEU  976 is missing expected H atoms. Skipping.
Residue VAL  977 is missing expected H atoms. Skipping.
Residue THR  978 is missing expected H atoms. Skipping.
Residue THR  979 is missing expected H atoms. Skipping.
Residue VAL  981 is missing expected H atoms. Skipping.
Residue THR  982 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue ALA  988 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.
Residue VAL  520 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  542 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Residue VAL  555 is missing expected H atoms. Skipping.
Residue MET  561 is missing expected H atoms. Skipping.
Residue LEU  574 is missing expected H atoms. Skipping.
Residue THR  580 is missing expected H atoms. Skipping.
Residue THR  587 is missing expected H atoms. Skipping.
Residue THR  588 is missing expected H atoms. Skipping.
Residue THR  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue LEU  599 is missing expected H atoms. Skipping.
Residue LEU  600 is missing expected H atoms. Skipping.
Residue VAL  613 is missing expected H atoms. Skipping.
Residue ILE  615 is missing expected H atoms. Skipping.
Residue THR  623 is missing expected H atoms. Skipping.
Evaluate side-chains
  84 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 55
  time to evaluate  : 1.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 TRP cc_start: 0.8510 (OUTLIER) cc_final: 0.8045 (t-100)
REVERT: A  145 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7240 (tmt170)
REVERT: A  737 MET cc_start: 0.8207 (ppp) cc_final: 0.6033 (mpp)
  outliers start: 29
  outliers final: 18
  residues processed: 74
  average time/residue: 0.3509
  time to fit residues: 39.8646
Evaluate side-chains
  72 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 52
  time to evaluate  : 1.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 TRP
Chi-restraints excluded: chain A residue  145 ARG
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  185 CYS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  451 ASP
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  503 PHE
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain A residue  747 ILE
Chi-restraints excluded: chain A residue  826 HIS
Chi-restraints excluded: chain A residue  829 TRP
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  321 MET
Chi-restraints excluded: chain B residue  451 LEU
Chi-restraints excluded: chain B residue  474 CYS
Chi-restraints excluded: chain B residue  493 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 122 optimal weight:    2.9990
   chunk 83 optimal weight:   50.0000
   chunk 2 optimal weight:    0.6980
   chunk 109 optimal weight:    1.9990
   chunk 60 optimal weight:    8.9990
   chunk 125 optimal weight:    0.9980
   chunk 101 optimal weight:    5.9990
   chunk 0 optimal weight:    2.9990
   chunk 75 optimal weight:   10.0000
   chunk 131 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 478 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.2257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025  12032  Z= 0.244
  Angle     :  0.474   7.817  16302  Z= 0.254
  Chirality :  0.043   0.138   1790
  Planarity :  0.003   0.035   2157
  Dihedral  :  4.421  18.850   1646
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 25.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 11.56 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.58 %
    Cis-general     : 0.07 %
    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: -0.74 (0.22), residues: 1522
  helix: -0.74 (0.44), residues: 140
  sheet: -0.17 (0.23), residues: 472
  loop : -0.57 (0.21), residues: 910

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 144 
 HIS   0.004   0.001   HIS A 621 
 PHE   0.013   0.001   PHE A 306 
 TYR   0.017   0.001   TYR A 305 
 ARG   0.002   0.000   ARG A 540 

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   33 is missing expected H atoms. Skipping.
Residue VAL   35 is missing expected H atoms. Skipping.
Residue ALA   39 is missing expected H atoms. Skipping.
Residue ALA   52 is missing expected H atoms. Skipping.
Residue VAL   53 is missing expected H atoms. Skipping.
Residue VAL   57 is missing expected H atoms. Skipping.
Residue ALA   60 is missing expected H atoms. Skipping.
Residue MET   64 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue VAL   68 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue THR   75 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   86 is missing expected H atoms. Skipping.
Residue LEU   87 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ILE  100 is missing expected H atoms. Skipping.
Residue ALA  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue ALA  111 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue ALA  126 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue ALA  137 is missing expected H atoms. Skipping.
Residue ALA  139 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  146 is missing expected H atoms. Skipping.
Residue MET  148 is missing expected H atoms. Skipping.
Residue VAL  155 is missing expected H atoms. Skipping.
Residue THR  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  164 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue VAL  167 is missing expected H atoms. Skipping.
Residue ALA  170 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  179 is missing expected H atoms. Skipping.
Residue ILE  191 is missing expected H atoms. Skipping.
Residue THR  194 is missing expected H atoms. Skipping.
Residue ALA  196 is missing expected H atoms. Skipping.
Residue VAL  199 is missing expected H atoms. Skipping.
Residue LEU  200 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LEU  213 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue ALA  219 is missing expected H atoms. Skipping.
Residue ILE  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Residue VAL  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LEU  238 is missing expected H atoms. Skipping.
Residue ALA  239 is missing expected H atoms. Skipping.
Residue THR  240 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue ALA  243 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue ILE  246 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue VAL  256 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  258 is missing expected H atoms. Skipping.
Residue ILE  266 is missing expected H atoms. Skipping.
Residue VAL  270 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue ALA  276 is missing expected H atoms. Skipping.
Residue ALA  277 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue LEU  280 is missing expected H atoms. Skipping.
Residue MET  282 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  285 is missing expected H atoms. Skipping.
Residue MET  291 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue THR  298 is missing expected H atoms. Skipping.
Residue MET  302 is missing expected H atoms. Skipping.
Residue ALA  303 is missing expected H atoms. Skipping.
Residue ALA  304 is missing expected H atoms. Skipping.
Residue VAL  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue ALA  312 is missing expected H atoms. Skipping.
Residue THR  313 is missing expected H atoms. Skipping.
Residue ILE  315 is missing expected H atoms. Skipping.
Residue ALA  321 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue ILE  325 is missing expected H atoms. Skipping.
Residue ALA  327 is missing expected H atoms. Skipping.
Residue LEU  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU  339 is missing expected H atoms. Skipping.
Residue VAL  342 is missing expected H atoms. Skipping.
Residue VAL  345 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  349 is missing expected H atoms. Skipping.
Residue ALA  352 is missing expected H atoms. Skipping.
Residue THR  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LEU  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue ALA  368 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  374 is missing expected H atoms. Skipping.
Residue ALA  375 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue LEU  380 is missing expected H atoms. Skipping.
Residue ILE  388 is missing expected H atoms. Skipping.
Residue ALA  389 is missing expected H atoms. Skipping.
Residue ILE  390 is missing expected H atoms. Skipping.
Residue ALA  391 is missing expected H atoms. Skipping.
Residue ALA  392 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue VAL  403 is missing expected H atoms. Skipping.
Residue ILE  405 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Residue ALA  415 is missing expected H atoms. Skipping.
Residue VAL  416 is missing expected H atoms. Skipping.
Residue ILE  420 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue ALA  426 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue MET  438 is missing expected H atoms. Skipping.
Residue ALA  441 is missing expected H atoms. Skipping.
Residue THR  442 is missing expected H atoms. Skipping.
Residue ILE  444 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue ILE  453 is missing expected H atoms. Skipping.
Residue VAL  454 is missing expected H atoms. Skipping.
Residue ALA  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue VAL  470 is missing expected H atoms. Skipping.
Residue ILE  471 is missing expected H atoms. Skipping.
Residue THR  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ALA  475 is missing expected H atoms. Skipping.
Residue LEU  477 is missing expected H atoms. Skipping.
Residue VAL  479 is missing expected H atoms. Skipping.
Residue ILE  483 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue THR  490 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue THR  496 is missing expected H atoms. Skipping.
Residue ALA  497 is missing expected H atoms. Skipping.
Residue LEU  498 is missing expected H atoms. Skipping.
Residue VAL  500 is missing expected H atoms. Skipping.
Residue VAL  505 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue ALA  511 is missing expected H atoms. Skipping.
Residue VAL  516 is missing expected H atoms. Skipping.
Residue LEU  517 is missing expected H atoms. Skipping.
Residue LEU  521 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  532 is missing expected H atoms. Skipping.
Residue ALA  537 is missing expected H atoms. Skipping.
Residue ILE  538 is missing expected H atoms. Skipping.
Residue ALA  541 is missing expected H atoms. Skipping.
Residue LEU  542 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue THR  556 is missing expected H atoms. Skipping.
Residue ILE  557 is missing expected H atoms. Skipping.
Residue LEU  562 is missing expected H atoms. Skipping.
Residue MET  563 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue ALA  570 is missing expected H atoms. Skipping.
Residue LEU  572 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue THR  583 is missing expected H atoms. Skipping.
Residue ILE  585 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue ILE  587 is missing expected H atoms. Skipping.
Residue MET  589 is missing expected H atoms. Skipping.
Residue LEU  593 is missing expected H atoms. Skipping.
Residue THR  597 is missing expected H atoms. Skipping.
Residue ALA  598 is missing expected H atoms. Skipping.
Residue ALA  599 is missing expected H atoms. Skipping.
Residue THR  601 is missing expected H atoms. Skipping.
Residue THR  602 is missing expected H atoms. Skipping.
Residue LEU  604 is missing expected H atoms. Skipping.
Residue ILE  607 is missing expected H atoms. Skipping.
Residue LEU  608 is missing expected H atoms. Skipping.
Residue THR  612 is missing expected H atoms. Skipping.
Residue ALA  614 is missing expected H atoms. Skipping.
Residue ILE  616 is missing expected H atoms. Skipping.
Residue ALA  620 is missing expected H atoms. Skipping.
Residue ILE  622 is missing expected H atoms. Skipping.
Residue LEU  623 is missing expected H atoms. Skipping.
Residue LEU  624 is missing expected H atoms. Skipping.
Residue VAL  631 is missing expected H atoms. Skipping.
Residue LEU  636 is missing expected H atoms. Skipping.
Residue VAL  638 is missing expected H atoms. Skipping.
Residue VAL  640 is missing expected H atoms. Skipping.
Residue ILE  647 is missing expected H atoms. Skipping.
Residue ILE  649 is missing expected H atoms. Skipping.
Residue LEU  655 is missing expected H atoms. Skipping.
Residue THR  656 is missing expected H atoms. Skipping.
Residue LEU  657 is missing expected H atoms. Skipping.
Residue ILE  658 is missing expected H atoms. Skipping.
Residue VAL  659 is missing expected H atoms. Skipping.
Residue ALA  661 is missing expected H atoms. Skipping.
Residue ALA  668 is missing expected H atoms. Skipping.
Residue ALA  671 is missing expected H atoms. Skipping.
Residue LEU  673 is missing expected H atoms. Skipping.
Residue ILE  674 is missing expected H atoms. Skipping.
Residue VAL  675 is missing expected H atoms. Skipping.
Residue ILE  677 is missing expected H atoms. Skipping.
Residue LEU  679 is missing expected H atoms. Skipping.
Residue ALA  681 is missing expected H atoms. Skipping.
Residue ILE  684 is missing expected H atoms. Skipping.
Residue VAL  686 is missing expected H atoms. Skipping.
Residue VAL  687 is missing expected H atoms. Skipping.
Residue ALA  692 is missing expected H atoms. Skipping.
Residue LEU  693 is missing expected H atoms. Skipping.
Residue ALA  694 is missing expected H atoms. Skipping.
Residue LEU  696 is missing expected H atoms. Skipping.
Residue ALA  699 is missing expected H atoms. Skipping.
Residue THR  702 is missing expected H atoms. Skipping.
Residue THR  706 is missing expected H atoms. Skipping.
Residue VAL  709 is missing expected H atoms. Skipping.
Residue VAL  710 is missing expected H atoms. Skipping.
Residue LEU  713 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue ALA  719 is missing expected H atoms. Skipping.
Residue THR  721 is missing expected H atoms. Skipping.
Residue LEU  723 is missing expected H atoms. Skipping.
Residue LEU  724 is missing expected H atoms. Skipping.
Residue ALA  725 is missing expected H atoms. Skipping.
Residue LEU  727 is missing expected H atoms. Skipping.
Residue VAL  731 is missing expected H atoms. Skipping.
Residue MET  737 is missing expected H atoms. Skipping.
Residue THR  739 is missing expected H atoms. Skipping.
Residue VAL  741 is missing expected H atoms. Skipping.
Residue LEU  745 is missing expected H atoms. Skipping.
Residue ILE  747 is missing expected H atoms. Skipping.
Residue LEU  752 is missing expected H atoms. Skipping.
Residue VAL  756 is missing expected H atoms. Skipping.
Residue VAL  759 is missing expected H atoms. Skipping.
Residue VAL  760 is missing expected H atoms. Skipping.
Residue VAL  764 is missing expected H atoms. Skipping.
Residue LEU  766 is missing expected H atoms. Skipping.
Residue ALA  767 is missing expected H atoms. Skipping.
Residue VAL  768 is missing expected H atoms. Skipping.
Residue LEU  769 is missing expected H atoms. Skipping.
Residue ALA  770 is missing expected H atoms. Skipping.
Residue ALA  771 is missing expected H atoms. Skipping.
Residue VAL  772 is missing expected H atoms. Skipping.
Residue ILE  774 is missing expected H atoms. Skipping.
Residue VAL  777 is missing expected H atoms. Skipping.
Residue VAL  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue THR  798 is missing expected H atoms. Skipping.
Residue VAL  802 is missing expected H atoms. Skipping.
Residue VAL  805 is missing expected H atoms. Skipping.
Residue VAL  806 is missing expected H atoms. Skipping.
Residue ILE  809 is missing expected H atoms. Skipping.
Residue LEU  812 is missing expected H atoms. Skipping.
Residue ALA  823 is missing expected H atoms. Skipping.
Residue MET  824 is missing expected H atoms. Skipping.
Residue LEU  825 is missing expected H atoms. Skipping.
Residue LEU  827 is missing expected H atoms. Skipping.
Residue THR  837 is missing expected H atoms. Skipping.
Residue LEU  838 is missing expected H atoms. Skipping.
Residue LEU  839 is missing expected H atoms. Skipping.
Residue ILE  841 is missing expected H atoms. Skipping.
Residue LEU  842 is missing expected H atoms. Skipping.
Residue ILE  846 is missing expected H atoms. Skipping.
Residue MET  850 is missing expected H atoms. Skipping.
Residue THR  853 is missing expected H atoms. Skipping.
Residue MET  856 is missing expected H atoms. Skipping.
Residue ILE  858 is missing expected H atoms. Skipping.
Residue LEU  861 is missing expected H atoms. Skipping.
Residue ILE  863 is missing expected H atoms. Skipping.
Residue ILE  865 is missing expected H atoms. Skipping.
Residue ILE  899 is missing expected H atoms. Skipping.
Residue THR  901 is missing expected H atoms. Skipping.
Residue LEU  902 is missing expected H atoms. Skipping.
Residue VAL  906 is missing expected H atoms. Skipping.
Residue ALA  907 is missing expected H atoms. Skipping.
Residue LEU  910 is missing expected H atoms. Skipping.
Residue ILE  912 is missing expected H atoms. Skipping.
Residue VAL  913 is missing expected H atoms. Skipping.
Residue VAL  916 is missing expected H atoms. Skipping.
Residue LEU  919 is missing expected H atoms. Skipping.
Residue ALA  925 is missing expected H atoms. Skipping.
Residue ILE  926 is missing expected H atoms. Skipping.
Residue LEU  927 is missing expected H atoms. Skipping.
Residue VAL  929 is missing expected H atoms. Skipping.
Residue LEU  932 is missing expected H atoms. Skipping.
Residue LEU  933 is missing expected H atoms. Skipping.
Residue THR  935 is missing expected H atoms. Skipping.
Residue THR  937 is missing expected H atoms. Skipping.
Residue MET  939 is missing expected H atoms. Skipping.
Residue LEU  950 is missing expected H atoms. Skipping.
Residue ALA  954 is missing expected H atoms. Skipping.
Residue VAL  958 is missing expected H atoms. Skipping.
Residue ILE  959 is missing expected H atoms. Skipping.
Residue LEU  966 is missing expected H atoms. Skipping.
Residue ILE  968 is missing expected H atoms. Skipping.
Residue ILE  971 is missing expected H atoms. Skipping.
Residue THR  972 is missing expected H atoms. Skipping.
Residue THR  975 is missing expected H atoms. Skipping.
Residue LEU  976 is missing expected H atoms. Skipping.
Residue VAL  977 is missing expected H atoms. Skipping.
Residue THR  978 is missing expected H atoms. Skipping.
Residue THR  979 is missing expected H atoms. Skipping.
Residue VAL  981 is missing expected H atoms. Skipping.
Residue THR  982 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue ALA  988 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.
Residue VAL  520 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  542 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Residue VAL  555 is missing expected H atoms. Skipping.
Residue MET  561 is missing expected H atoms. Skipping.
Residue LEU  574 is missing expected H atoms. Skipping.
Residue THR  580 is missing expected H atoms. Skipping.
Residue THR  587 is missing expected H atoms. Skipping.
Residue THR  588 is missing expected H atoms. Skipping.
Residue THR  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue LEU  599 is missing expected H atoms. Skipping.
Residue LEU  600 is missing expected H atoms. Skipping.
Residue VAL  613 is missing expected H atoms. Skipping.
Residue ILE  615 is missing expected H atoms. Skipping.
Residue THR  623 is missing expected H atoms. Skipping.
Evaluate side-chains
  76 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 53
  time to evaluate  : 1.561 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 TRP cc_start: 0.8482 (OUTLIER) cc_final: 0.8155 (t-100)
REVERT: A  145 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7204 (tmt170)
REVERT: A  737 MET cc_start: 0.8245 (ppp) cc_final: 0.6044 (mpp)
REVERT: A  824 MET cc_start: 0.8883 (mmm) cc_final: 0.7821 (tpp)
REVERT: B  135 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.6976 (t70)
  outliers start: 23
  outliers final: 14
  residues processed: 69
  average time/residue: 0.3159
  time to fit residues: 33.0098
Evaluate side-chains
  70 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 53
  time to evaluate  : 1.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 TRP
Chi-restraints excluded: chain A residue  145 ARG
Chi-restraints excluded: chain A residue  185 CYS
Chi-restraints excluded: chain A residue  305 TYR
Chi-restraints excluded: chain A residue  451 ASP
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  503 PHE
Chi-restraints excluded: chain A residue  578 PHE
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain A residue  747 ILE
Chi-restraints excluded: chain A residue  826 HIS
Chi-restraints excluded: chain B residue  135 ASP
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  474 CYS
Chi-restraints excluded: chain B residue  493 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 132 optimal weight:    0.3980
   chunk 29 optimal weight:    3.9990
   chunk 86 optimal weight:    5.9990
   chunk 36 optimal weight:    4.9990
   chunk 147 optimal weight:    9.9990
   chunk 122 optimal weight:    2.9990
   chunk 68 optimal weight:   10.0000
   chunk 12 optimal weight:    0.0970
   chunk 48 optimal weight:    0.9980
   chunk 77 optimal weight:    8.9990
   overall best weight:    1.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 715 ASN
** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 466 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  12032  Z= 0.281
  Angle     :  0.488   7.922  16302  Z= 0.260
  Chirality :  0.043   0.156   1790
  Planarity :  0.003   0.032   2157
  Dihedral  :  4.406  19.168   1646
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 26.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 10.95 %
    Favored  : 86.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.58 %
    Cis-general     : 0.07 %
    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: -0.81 (0.22), residues: 1522
  helix: -0.69 (0.44), residues: 140
  sheet: -0.25 (0.24), residues: 478
  loop : -0.62 (0.21), residues: 904

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 144 
 HIS   0.004   0.001   HIS B 565 
 PHE   0.015   0.001   PHE A 306 
 TYR   0.019   0.001   TYR A 305 
 ARG   0.002   0.000   ARG A 918 

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   33 is missing expected H atoms. Skipping.
Residue VAL   35 is missing expected H atoms. Skipping.
Residue ALA   39 is missing expected H atoms. Skipping.
Residue ALA   52 is missing expected H atoms. Skipping.
Residue VAL   53 is missing expected H atoms. Skipping.
Residue VAL   57 is missing expected H atoms. Skipping.
Residue ALA   60 is missing expected H atoms. Skipping.
Residue MET   64 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue VAL   68 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue THR   75 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   86 is missing expected H atoms. Skipping.
Residue LEU   87 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ILE  100 is missing expected H atoms. Skipping.
Residue ALA  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue ALA  111 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue ALA  126 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue ALA  137 is missing expected H atoms. Skipping.
Residue ALA  139 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  146 is missing expected H atoms. Skipping.
Residue MET  148 is missing expected H atoms. Skipping.
Residue VAL  155 is missing expected H atoms. Skipping.
Residue THR  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  164 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue VAL  167 is missing expected H atoms. Skipping.
Residue ALA  170 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  179 is missing expected H atoms. Skipping.
Residue ILE  191 is missing expected H atoms. Skipping.
Residue THR  194 is missing expected H atoms. Skipping.
Residue ALA  196 is missing expected H atoms. Skipping.
Residue VAL  199 is missing expected H atoms. Skipping.
Residue LEU  200 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LEU  213 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue ALA  219 is missing expected H atoms. Skipping.
Residue ILE  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Residue VAL  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LEU  238 is missing expected H atoms. Skipping.
Residue ALA  239 is missing expected H atoms. Skipping.
Residue THR  240 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue ALA  243 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue ILE  246 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue VAL  256 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  258 is missing expected H atoms. Skipping.
Residue ILE  266 is missing expected H atoms. Skipping.
Residue VAL  270 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue ALA  276 is missing expected H atoms. Skipping.
Residue ALA  277 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue LEU  280 is missing expected H atoms. Skipping.
Residue MET  282 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  285 is missing expected H atoms. Skipping.
Residue MET  291 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue THR  298 is missing expected H atoms. Skipping.
Residue MET  302 is missing expected H atoms. Skipping.
Residue ALA  303 is missing expected H atoms. Skipping.
Residue ALA  304 is missing expected H atoms. Skipping.
Residue VAL  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue ALA  312 is missing expected H atoms. Skipping.
Residue THR  313 is missing expected H atoms. Skipping.
Residue ILE  315 is missing expected H atoms. Skipping.
Residue ALA  321 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue ILE  325 is missing expected H atoms. Skipping.
Residue ALA  327 is missing expected H atoms. Skipping.
Residue LEU  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU  339 is missing expected H atoms. Skipping.
Residue VAL  342 is missing expected H atoms. Skipping.
Residue VAL  345 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  349 is missing expected H atoms. Skipping.
Residue ALA  352 is missing expected H atoms. Skipping.
Residue THR  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LEU  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue ALA  368 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  374 is missing expected H atoms. Skipping.
Residue ALA  375 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue LEU  380 is missing expected H atoms. Skipping.
Residue ILE  388 is missing expected H atoms. Skipping.
Residue ALA  389 is missing expected H atoms. Skipping.
Residue ILE  390 is missing expected H atoms. Skipping.
Residue ALA  391 is missing expected H atoms. Skipping.
Residue ALA  392 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue VAL  403 is missing expected H atoms. Skipping.
Residue ILE  405 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Residue ALA  415 is missing expected H atoms. Skipping.
Residue VAL  416 is missing expected H atoms. Skipping.
Residue ILE  420 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue ALA  426 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue MET  438 is missing expected H atoms. Skipping.
Residue ALA  441 is missing expected H atoms. Skipping.
Residue THR  442 is missing expected H atoms. Skipping.
Residue ILE  444 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue ILE  453 is missing expected H atoms. Skipping.
Residue VAL  454 is missing expected H atoms. Skipping.
Residue ALA  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue VAL  470 is missing expected H atoms. Skipping.
Residue ILE  471 is missing expected H atoms. Skipping.
Residue THR  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ALA  475 is missing expected H atoms. Skipping.
Residue LEU  477 is missing expected H atoms. Skipping.
Residue VAL  479 is missing expected H atoms. Skipping.
Residue ILE  483 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue THR  490 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue THR  496 is missing expected H atoms. Skipping.
Residue ALA  497 is missing expected H atoms. Skipping.
Residue LEU  498 is missing expected H atoms. Skipping.
Residue VAL  500 is missing expected H atoms. Skipping.
Residue VAL  505 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue ALA  511 is missing expected H atoms. Skipping.
Residue VAL  516 is missing expected H atoms. Skipping.
Residue LEU  517 is missing expected H atoms. Skipping.
Residue LEU  521 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  532 is missing expected H atoms. Skipping.
Residue ALA  537 is missing expected H atoms. Skipping.
Residue ILE  538 is missing expected H atoms. Skipping.
Residue ALA  541 is missing expected H atoms. Skipping.
Residue LEU  542 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue THR  556 is missing expected H atoms. Skipping.
Residue ILE  557 is missing expected H atoms. Skipping.
Residue LEU  562 is missing expected H atoms. Skipping.
Residue MET  563 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue ALA  570 is missing expected H atoms. Skipping.
Residue LEU  572 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue THR  583 is missing expected H atoms. Skipping.
Residue ILE  585 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue ILE  587 is missing expected H atoms. Skipping.
Residue MET  589 is missing expected H atoms. Skipping.
Residue LEU  593 is missing expected H atoms. Skipping.
Residue THR  597 is missing expected H atoms. Skipping.
Residue ALA  598 is missing expected H atoms. Skipping.
Residue ALA  599 is missing expected H atoms. Skipping.
Residue THR  601 is missing expected H atoms. Skipping.
Residue THR  602 is missing expected H atoms. Skipping.
Residue LEU  604 is missing expected H atoms. Skipping.
Residue ILE  607 is missing expected H atoms. Skipping.
Residue LEU  608 is missing expected H atoms. Skipping.
Residue THR  612 is missing expected H atoms. Skipping.
Residue ALA  614 is missing expected H atoms. Skipping.
Residue ILE  616 is missing expected H atoms. Skipping.
Residue ALA  620 is missing expected H atoms. Skipping.
Residue ILE  622 is missing expected H atoms. Skipping.
Residue LEU  623 is missing expected H atoms. Skipping.
Residue LEU  624 is missing expected H atoms. Skipping.
Residue VAL  631 is missing expected H atoms. Skipping.
Residue LEU  636 is missing expected H atoms. Skipping.
Residue VAL  638 is missing expected H atoms. Skipping.
Residue VAL  640 is missing expected H atoms. Skipping.
Residue ILE  647 is missing expected H atoms. Skipping.
Residue ILE  649 is missing expected H atoms. Skipping.
Residue LEU  655 is missing expected H atoms. Skipping.
Residue THR  656 is missing expected H atoms. Skipping.
Residue LEU  657 is missing expected H atoms. Skipping.
Residue ILE  658 is missing expected H atoms. Skipping.
Residue VAL  659 is missing expected H atoms. Skipping.
Residue ALA  661 is missing expected H atoms. Skipping.
Residue ALA  668 is missing expected H atoms. Skipping.
Residue ALA  671 is missing expected H atoms. Skipping.
Residue LEU  673 is missing expected H atoms. Skipping.
Residue ILE  674 is missing expected H atoms. Skipping.
Residue VAL  675 is missing expected H atoms. Skipping.
Residue ILE  677 is missing expected H atoms. Skipping.
Residue LEU  679 is missing expected H atoms. Skipping.
Residue ALA  681 is missing expected H atoms. Skipping.
Residue ILE  684 is missing expected H atoms. Skipping.
Residue VAL  686 is missing expected H atoms. Skipping.
Residue VAL  687 is missing expected H atoms. Skipping.
Residue ALA  692 is missing expected H atoms. Skipping.
Residue LEU  693 is missing expected H atoms. Skipping.
Residue ALA  694 is missing expected H atoms. Skipping.
Residue LEU  696 is missing expected H atoms. Skipping.
Residue ALA  699 is missing expected H atoms. Skipping.
Residue THR  702 is missing expected H atoms. Skipping.
Residue THR  706 is missing expected H atoms. Skipping.
Residue VAL  709 is missing expected H atoms. Skipping.
Residue VAL  710 is missing expected H atoms. Skipping.
Residue LEU  713 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue ALA  719 is missing expected H atoms. Skipping.
Residue THR  721 is missing expected H atoms. Skipping.
Residue LEU  723 is missing expected H atoms. Skipping.
Residue LEU  724 is missing expected H atoms. Skipping.
Residue ALA  725 is missing expected H atoms. Skipping.
Residue LEU  727 is missing expected H atoms. Skipping.
Residue VAL  731 is missing expected H atoms. Skipping.
Residue MET  737 is missing expected H atoms. Skipping.
Residue THR  739 is missing expected H atoms. Skipping.
Residue VAL  741 is missing expected H atoms. Skipping.
Residue LEU  745 is missing expected H atoms. Skipping.
Residue ILE  747 is missing expected H atoms. Skipping.
Residue LEU  752 is missing expected H atoms. Skipping.
Residue VAL  756 is missing expected H atoms. Skipping.
Residue VAL  759 is missing expected H atoms. Skipping.
Residue VAL  760 is missing expected H atoms. Skipping.
Residue VAL  764 is missing expected H atoms. Skipping.
Residue LEU  766 is missing expected H atoms. Skipping.
Residue ALA  767 is missing expected H atoms. Skipping.
Residue VAL  768 is missing expected H atoms. Skipping.
Residue LEU  769 is missing expected H atoms. Skipping.
Residue ALA  770 is missing expected H atoms. Skipping.
Residue ALA  771 is missing expected H atoms. Skipping.
Residue VAL  772 is missing expected H atoms. Skipping.
Residue ILE  774 is missing expected H atoms. Skipping.
Residue VAL  777 is missing expected H atoms. Skipping.
Residue VAL  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue THR  798 is missing expected H atoms. Skipping.
Residue VAL  802 is missing expected H atoms. Skipping.
Residue VAL  805 is missing expected H atoms. Skipping.
Residue VAL  806 is missing expected H atoms. Skipping.
Residue ILE  809 is missing expected H atoms. Skipping.
Residue LEU  812 is missing expected H atoms. Skipping.
Residue ALA  823 is missing expected H atoms. Skipping.
Residue MET  824 is missing expected H atoms. Skipping.
Residue LEU  825 is missing expected H atoms. Skipping.
Residue LEU  827 is missing expected H atoms. Skipping.
Residue THR  837 is missing expected H atoms. Skipping.
Residue LEU  838 is missing expected H atoms. Skipping.
Residue LEU  839 is missing expected H atoms. Skipping.
Residue ILE  841 is missing expected H atoms. Skipping.
Residue LEU  842 is missing expected H atoms. Skipping.
Residue ILE  846 is missing expected H atoms. Skipping.
Residue MET  850 is missing expected H atoms. Skipping.
Residue THR  853 is missing expected H atoms. Skipping.
Residue MET  856 is missing expected H atoms. Skipping.
Residue ILE  858 is missing expected H atoms. Skipping.
Residue LEU  861 is missing expected H atoms. Skipping.
Residue ILE  863 is missing expected H atoms. Skipping.
Residue ILE  865 is missing expected H atoms. Skipping.
Residue ILE  899 is missing expected H atoms. Skipping.
Residue THR  901 is missing expected H atoms. Skipping.
Residue LEU  902 is missing expected H atoms. Skipping.
Residue VAL  906 is missing expected H atoms. Skipping.
Residue ALA  907 is missing expected H atoms. Skipping.
Residue LEU  910 is missing expected H atoms. Skipping.
Residue ILE  912 is missing expected H atoms. Skipping.
Residue VAL  913 is missing expected H atoms. Skipping.
Residue VAL  916 is missing expected H atoms. Skipping.
Residue LEU  919 is missing expected H atoms. Skipping.
Residue ALA  925 is missing expected H atoms. Skipping.
Residue ILE  926 is missing expected H atoms. Skipping.
Residue LEU  927 is missing expected H atoms. Skipping.
Residue VAL  929 is missing expected H atoms. Skipping.
Residue LEU  932 is missing expected H atoms. Skipping.
Residue LEU  933 is missing expected H atoms. Skipping.
Residue THR  935 is missing expected H atoms. Skipping.
Residue THR  937 is missing expected H atoms. Skipping.
Residue MET  939 is missing expected H atoms. Skipping.
Residue LEU  950 is missing expected H atoms. Skipping.
Residue ALA  954 is missing expected H atoms. Skipping.
Residue VAL  958 is missing expected H atoms. Skipping.
Residue ILE  959 is missing expected H atoms. Skipping.
Residue LEU  966 is missing expected H atoms. Skipping.
Residue ILE  968 is missing expected H atoms. Skipping.
Residue ILE  971 is missing expected H atoms. Skipping.
Residue THR  972 is missing expected H atoms. Skipping.
Residue THR  975 is missing expected H atoms. Skipping.
Residue LEU  976 is missing expected H atoms. Skipping.
Residue VAL  977 is missing expected H atoms. Skipping.
Residue THR  978 is missing expected H atoms. Skipping.
Residue THR  979 is missing expected H atoms. Skipping.
Residue VAL  981 is missing expected H atoms. Skipping.
Residue THR  982 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue ALA  988 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.
Residue VAL  520 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  542 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Residue VAL  555 is missing expected H atoms. Skipping.
Residue MET  561 is missing expected H atoms. Skipping.
Residue LEU  574 is missing expected H atoms. Skipping.
Residue THR  580 is missing expected H atoms. Skipping.
Residue THR  587 is missing expected H atoms. Skipping.
Residue THR  588 is missing expected H atoms. Skipping.
Residue THR  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue LEU  599 is missing expected H atoms. Skipping.
Residue LEU  600 is missing expected H atoms. Skipping.
Residue VAL  613 is missing expected H atoms. Skipping.
Residue ILE  615 is missing expected H atoms. Skipping.
Residue THR  623 is missing expected H atoms. Skipping.
Evaluate side-chains
  83 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 53
  time to evaluate  : 1.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 TRP cc_start: 0.8502 (OUTLIER) cc_final: 0.8160 (t-100)
REVERT: A  145 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7223 (tmt170)
REVERT: A  737 MET cc_start: 0.8219 (ppp) cc_final: 0.7829 (ppp)
REVERT: B  135 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7077 (t70)
REVERT: B  204 TYR cc_start: 0.7599 (OUTLIER) cc_final: 0.7184 (p90)
  outliers start: 30
  outliers final: 22
  residues processed: 75
  average time/residue: 0.3100
  time to fit residues: 35.1212
Evaluate side-chains
  78 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 52
  time to evaluate  : 1.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 TRP
Chi-restraints excluded: chain A residue  145 ARG
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  185 CYS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  305 TYR
Chi-restraints excluded: chain A residue  451 ASP
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  471 ILE
Chi-restraints excluded: chain A residue  503 PHE
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  578 PHE
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain A residue  747 ILE
Chi-restraints excluded: chain A residue  826 HIS
Chi-restraints excluded: chain A residue  829 TRP
Chi-restraints excluded: chain B residue  135 ASP
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  204 TYR
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  451 LEU
Chi-restraints excluded: chain B residue  474 CYS
Chi-restraints excluded: chain B residue  493 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 141 optimal weight:    0.0970
   chunk 16 optimal weight:    0.9990
   chunk 83 optimal weight:   50.0000
   chunk 107 optimal weight:    0.8980
   chunk 123 optimal weight:    1.9990
   chunk 82 optimal weight:    6.9990
   chunk 146 optimal weight:    9.9990
   chunk 91 optimal weight:   20.0000
   chunk 89 optimal weight:    5.9990
   chunk 67 optimal weight:    7.9990
   chunk 90 optimal weight:    7.9990
   overall best weight:    1.9984

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

Flipped N/Q/H residues before XYZ refinement:
** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.2719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  12032  Z= 0.328
  Angle     :  0.507   7.965  16302  Z= 0.271
  Chirality :  0.044   0.146   1790
  Planarity :  0.003   0.033   2157
  Dihedral  :  4.512  19.749   1646
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 29.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 11.10 %
    Favored  : 86.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.58 %
    Cis-general     : 0.07 %
    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: -0.83 (0.22), residues: 1522
  helix: -0.95 (0.42), residues: 146
  sheet: -0.10 (0.24), residues: 474
  loop : -0.69 (0.21), residues: 902

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 144 
 HIS   0.004   0.001   HIS A 121 
 PHE   0.017   0.001   PHE A 306 
 TYR   0.021   0.001   TYR A 305 
 ARG   0.002   0.000   ARG A 519 

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   33 is missing expected H atoms. Skipping.
Residue VAL   35 is missing expected H atoms. Skipping.
Residue ALA   39 is missing expected H atoms. Skipping.
Residue ALA   52 is missing expected H atoms. Skipping.
Residue VAL   53 is missing expected H atoms. Skipping.
Residue VAL   57 is missing expected H atoms. Skipping.
Residue ALA   60 is missing expected H atoms. Skipping.
Residue MET   64 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue VAL   68 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue THR   75 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   86 is missing expected H atoms. Skipping.
Residue LEU   87 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ILE  100 is missing expected H atoms. Skipping.
Residue ALA  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue ALA  111 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue ALA  126 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue ALA  137 is missing expected H atoms. Skipping.
Residue ALA  139 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  146 is missing expected H atoms. Skipping.
Residue MET  148 is missing expected H atoms. Skipping.
Residue VAL  155 is missing expected H atoms. Skipping.
Residue THR  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  164 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue VAL  167 is missing expected H atoms. Skipping.
Residue ALA  170 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  179 is missing expected H atoms. Skipping.
Residue ILE  191 is missing expected H atoms. Skipping.
Residue THR  194 is missing expected H atoms. Skipping.
Residue ALA  196 is missing expected H atoms. Skipping.
Residue VAL  199 is missing expected H atoms. Skipping.
Residue LEU  200 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LEU  213 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue ALA  219 is missing expected H atoms. Skipping.
Residue ILE  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Residue VAL  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LEU  238 is missing expected H atoms. Skipping.
Residue ALA  239 is missing expected H atoms. Skipping.
Residue THR  240 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue ALA  243 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue ILE  246 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue VAL  256 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  258 is missing expected H atoms. Skipping.
Residue ILE  266 is missing expected H atoms. Skipping.
Residue VAL  270 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue ALA  276 is missing expected H atoms. Skipping.
Residue ALA  277 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue LEU  280 is missing expected H atoms. Skipping.
Residue MET  282 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  285 is missing expected H atoms. Skipping.
Residue MET  291 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue THR  298 is missing expected H atoms. Skipping.
Residue MET  302 is missing expected H atoms. Skipping.
Residue ALA  303 is missing expected H atoms. Skipping.
Residue ALA  304 is missing expected H atoms. Skipping.
Residue VAL  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue ALA  312 is missing expected H atoms. Skipping.
Residue THR  313 is missing expected H atoms. Skipping.
Residue ILE  315 is missing expected H atoms. Skipping.
Residue ALA  321 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue ILE  325 is missing expected H atoms. Skipping.
Residue ALA  327 is missing expected H atoms. Skipping.
Residue LEU  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU  339 is missing expected H atoms. Skipping.
Residue VAL  342 is missing expected H atoms. Skipping.
Residue VAL  345 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  349 is missing expected H atoms. Skipping.
Residue ALA  352 is missing expected H atoms. Skipping.
Residue THR  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LEU  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue ALA  368 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  374 is missing expected H atoms. Skipping.
Residue ALA  375 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue LEU  380 is missing expected H atoms. Skipping.
Residue ILE  388 is missing expected H atoms. Skipping.
Residue ALA  389 is missing expected H atoms. Skipping.
Residue ILE  390 is missing expected H atoms. Skipping.
Residue ALA  391 is missing expected H atoms. Skipping.
Residue ALA  392 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue VAL  403 is missing expected H atoms. Skipping.
Residue ILE  405 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Residue ALA  415 is missing expected H atoms. Skipping.
Residue VAL  416 is missing expected H atoms. Skipping.
Residue ILE  420 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue ALA  426 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue MET  438 is missing expected H atoms. Skipping.
Residue ALA  441 is missing expected H atoms. Skipping.
Residue THR  442 is missing expected H atoms. Skipping.
Residue ILE  444 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue ILE  453 is missing expected H atoms. Skipping.
Residue VAL  454 is missing expected H atoms. Skipping.
Residue ALA  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue VAL  470 is missing expected H atoms. Skipping.
Residue ILE  471 is missing expected H atoms. Skipping.
Residue THR  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ALA  475 is missing expected H atoms. Skipping.
Residue LEU  477 is missing expected H atoms. Skipping.
Residue VAL  479 is missing expected H atoms. Skipping.
Residue ILE  483 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue THR  490 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue THR  496 is missing expected H atoms. Skipping.
Residue ALA  497 is missing expected H atoms. Skipping.
Residue LEU  498 is missing expected H atoms. Skipping.
Residue VAL  500 is missing expected H atoms. Skipping.
Residue VAL  505 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue ALA  511 is missing expected H atoms. Skipping.
Residue VAL  516 is missing expected H atoms. Skipping.
Residue LEU  517 is missing expected H atoms. Skipping.
Residue LEU  521 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  532 is missing expected H atoms. Skipping.
Residue ALA  537 is missing expected H atoms. Skipping.
Residue ILE  538 is missing expected H atoms. Skipping.
Residue ALA  541 is missing expected H atoms. Skipping.
Residue LEU  542 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue THR  556 is missing expected H atoms. Skipping.
Residue ILE  557 is missing expected H atoms. Skipping.
Residue LEU  562 is missing expected H atoms. Skipping.
Residue MET  563 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue ALA  570 is missing expected H atoms. Skipping.
Residue LEU  572 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue THR  583 is missing expected H atoms. Skipping.
Residue ILE  585 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue ILE  587 is missing expected H atoms. Skipping.
Residue MET  589 is missing expected H atoms. Skipping.
Residue LEU  593 is missing expected H atoms. Skipping.
Residue THR  597 is missing expected H atoms. Skipping.
Residue ALA  598 is missing expected H atoms. Skipping.
Residue ALA  599 is missing expected H atoms. Skipping.
Residue THR  601 is missing expected H atoms. Skipping.
Residue THR  602 is missing expected H atoms. Skipping.
Residue LEU  604 is missing expected H atoms. Skipping.
Residue ILE  607 is missing expected H atoms. Skipping.
Residue LEU  608 is missing expected H atoms. Skipping.
Residue THR  612 is missing expected H atoms. Skipping.
Residue ALA  614 is missing expected H atoms. Skipping.
Residue ILE  616 is missing expected H atoms. Skipping.
Residue ALA  620 is missing expected H atoms. Skipping.
Residue ILE  622 is missing expected H atoms. Skipping.
Residue LEU  623 is missing expected H atoms. Skipping.
Residue LEU  624 is missing expected H atoms. Skipping.
Residue VAL  631 is missing expected H atoms. Skipping.
Residue LEU  636 is missing expected H atoms. Skipping.
Residue VAL  638 is missing expected H atoms. Skipping.
Residue VAL  640 is missing expected H atoms. Skipping.
Residue ILE  647 is missing expected H atoms. Skipping.
Residue ILE  649 is missing expected H atoms. Skipping.
Residue LEU  655 is missing expected H atoms. Skipping.
Residue THR  656 is missing expected H atoms. Skipping.
Residue LEU  657 is missing expected H atoms. Skipping.
Residue ILE  658 is missing expected H atoms. Skipping.
Residue VAL  659 is missing expected H atoms. Skipping.
Residue ALA  661 is missing expected H atoms. Skipping.
Residue ALA  668 is missing expected H atoms. Skipping.
Residue ALA  671 is missing expected H atoms. Skipping.
Residue LEU  673 is missing expected H atoms. Skipping.
Residue ILE  674 is missing expected H atoms. Skipping.
Residue VAL  675 is missing expected H atoms. Skipping.
Residue ILE  677 is missing expected H atoms. Skipping.
Residue LEU  679 is missing expected H atoms. Skipping.
Residue ALA  681 is missing expected H atoms. Skipping.
Residue ILE  684 is missing expected H atoms. Skipping.
Residue VAL  686 is missing expected H atoms. Skipping.
Residue VAL  687 is missing expected H atoms. Skipping.
Residue ALA  692 is missing expected H atoms. Skipping.
Residue LEU  693 is missing expected H atoms. Skipping.
Residue ALA  694 is missing expected H atoms. Skipping.
Residue LEU  696 is missing expected H atoms. Skipping.
Residue ALA  699 is missing expected H atoms. Skipping.
Residue THR  702 is missing expected H atoms. Skipping.
Residue THR  706 is missing expected H atoms. Skipping.
Residue VAL  709 is missing expected H atoms. Skipping.
Residue VAL  710 is missing expected H atoms. Skipping.
Residue LEU  713 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue ALA  719 is missing expected H atoms. Skipping.
Residue THR  721 is missing expected H atoms. Skipping.
Residue LEU  723 is missing expected H atoms. Skipping.
Residue LEU  724 is missing expected H atoms. Skipping.
Residue ALA  725 is missing expected H atoms. Skipping.
Residue LEU  727 is missing expected H atoms. Skipping.
Residue VAL  731 is missing expected H atoms. Skipping.
Residue MET  737 is missing expected H atoms. Skipping.
Residue THR  739 is missing expected H atoms. Skipping.
Residue VAL  741 is missing expected H atoms. Skipping.
Residue LEU  745 is missing expected H atoms. Skipping.
Residue ILE  747 is missing expected H atoms. Skipping.
Residue LEU  752 is missing expected H atoms. Skipping.
Residue VAL  756 is missing expected H atoms. Skipping.
Residue VAL  759 is missing expected H atoms. Skipping.
Residue VAL  760 is missing expected H atoms. Skipping.
Residue VAL  764 is missing expected H atoms. Skipping.
Residue LEU  766 is missing expected H atoms. Skipping.
Residue ALA  767 is missing expected H atoms. Skipping.
Residue VAL  768 is missing expected H atoms. Skipping.
Residue LEU  769 is missing expected H atoms. Skipping.
Residue ALA  770 is missing expected H atoms. Skipping.
Residue ALA  771 is missing expected H atoms. Skipping.
Residue VAL  772 is missing expected H atoms. Skipping.
Residue ILE  774 is missing expected H atoms. Skipping.
Residue VAL  777 is missing expected H atoms. Skipping.
Residue VAL  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue THR  798 is missing expected H atoms. Skipping.
Residue VAL  802 is missing expected H atoms. Skipping.
Residue VAL  805 is missing expected H atoms. Skipping.
Residue VAL  806 is missing expected H atoms. Skipping.
Residue ILE  809 is missing expected H atoms. Skipping.
Residue LEU  812 is missing expected H atoms. Skipping.
Residue ALA  823 is missing expected H atoms. Skipping.
Residue MET  824 is missing expected H atoms. Skipping.
Residue LEU  825 is missing expected H atoms. Skipping.
Residue LEU  827 is missing expected H atoms. Skipping.
Residue THR  837 is missing expected H atoms. Skipping.
Residue LEU  838 is missing expected H atoms. Skipping.
Residue LEU  839 is missing expected H atoms. Skipping.
Residue ILE  841 is missing expected H atoms. Skipping.
Residue LEU  842 is missing expected H atoms. Skipping.
Residue ILE  846 is missing expected H atoms. Skipping.
Residue MET  850 is missing expected H atoms. Skipping.
Residue THR  853 is missing expected H atoms. Skipping.
Residue MET  856 is missing expected H atoms. Skipping.
Residue ILE  858 is missing expected H atoms. Skipping.
Residue LEU  861 is missing expected H atoms. Skipping.
Residue ILE  863 is missing expected H atoms. Skipping.
Residue ILE  865 is missing expected H atoms. Skipping.
Residue ILE  899 is missing expected H atoms. Skipping.
Residue THR  901 is missing expected H atoms. Skipping.
Residue LEU  902 is missing expected H atoms. Skipping.
Residue VAL  906 is missing expected H atoms. Skipping.
Residue ALA  907 is missing expected H atoms. Skipping.
Residue LEU  910 is missing expected H atoms. Skipping.
Residue ILE  912 is missing expected H atoms. Skipping.
Residue VAL  913 is missing expected H atoms. Skipping.
Residue VAL  916 is missing expected H atoms. Skipping.
Residue LEU  919 is missing expected H atoms. Skipping.
Residue ALA  925 is missing expected H atoms. Skipping.
Residue ILE  926 is missing expected H atoms. Skipping.
Residue LEU  927 is missing expected H atoms. Skipping.
Residue VAL  929 is missing expected H atoms. Skipping.
Residue LEU  932 is missing expected H atoms. Skipping.
Residue LEU  933 is missing expected H atoms. Skipping.
Residue THR  935 is missing expected H atoms. Skipping.
Residue THR  937 is missing expected H atoms. Skipping.
Residue MET  939 is missing expected H atoms. Skipping.
Residue LEU  950 is missing expected H atoms. Skipping.
Residue ALA  954 is missing expected H atoms. Skipping.
Residue VAL  958 is missing expected H atoms. Skipping.
Residue ILE  959 is missing expected H atoms. Skipping.
Residue LEU  966 is missing expected H atoms. Skipping.
Residue ILE  968 is missing expected H atoms. Skipping.
Residue ILE  971 is missing expected H atoms. Skipping.
Residue THR  972 is missing expected H atoms. Skipping.
Residue THR  975 is missing expected H atoms. Skipping.
Residue LEU  976 is missing expected H atoms. Skipping.
Residue VAL  977 is missing expected H atoms. Skipping.
Residue THR  978 is missing expected H atoms. Skipping.
Residue THR  979 is missing expected H atoms. Skipping.
Residue VAL  981 is missing expected H atoms. Skipping.
Residue THR  982 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue ALA  988 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.
Residue VAL  520 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  542 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Residue VAL  555 is missing expected H atoms. Skipping.
Residue MET  561 is missing expected H atoms. Skipping.
Residue LEU  574 is missing expected H atoms. Skipping.
Residue THR  580 is missing expected H atoms. Skipping.
Residue THR  587 is missing expected H atoms. Skipping.
Residue THR  588 is missing expected H atoms. Skipping.
Residue THR  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue LEU  599 is missing expected H atoms. Skipping.
Residue LEU  600 is missing expected H atoms. Skipping.
Residue VAL  613 is missing expected H atoms. Skipping.
Residue ILE  615 is missing expected H atoms. Skipping.
Residue THR  623 is missing expected H atoms. Skipping.
Evaluate side-chains
  88 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 56
  time to evaluate  : 1.679 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 TRP cc_start: 0.8513 (OUTLIER) cc_final: 0.8105 (t-100)
REVERT: A  145 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7315 (tmt170)
REVERT: A  737 MET cc_start: 0.8220 (ppp) cc_final: 0.7806 (ppp)
REVERT: A  824 MET cc_start: 0.8882 (mmm) cc_final: 0.7807 (tpp)
REVERT: B  135 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7135 (t70)
REVERT: B  204 TYR cc_start: 0.7634 (OUTLIER) cc_final: 0.7146 (p90)
REVERT: B  608 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8289 (pm20)
  outliers start: 32
  outliers final: 25
  residues processed: 80
  average time/residue: 0.3122
  time to fit residues: 37.8368
Evaluate side-chains
  82 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 53
  time to evaluate  : 1.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 TRP
Chi-restraints excluded: chain A residue  145 ARG
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  185 CYS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  451 ASP
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  471 ILE
Chi-restraints excluded: chain A residue  503 PHE
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  578 PHE
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain A residue  712 ASP
Chi-restraints excluded: chain A residue  747 ILE
Chi-restraints excluded: chain A residue  826 HIS
Chi-restraints excluded: chain A residue  829 TRP
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  135 ASP
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  204 TYR
Chi-restraints excluded: chain B residue  321 MET
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  451 LEU
Chi-restraints excluded: chain B residue  459 CYS
Chi-restraints excluded: chain B residue  474 CYS
Chi-restraints excluded: chain B residue  493 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 58 optimal weight:    5.9990
   chunk 87 optimal weight:   30.0000
   chunk 44 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 93 optimal weight:    3.9990
   chunk 99 optimal weight:    8.9990
   chunk 72 optimal weight:    8.9990
   chunk 13 optimal weight:    1.9990
   chunk 115 optimal weight:    1.9990
   chunk 133 optimal weight:    5.9990
   chunk 140 optimal weight:    9.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.3019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.048  12032  Z= 0.481
  Angle     :  0.591   8.078  16302  Z= 0.315
  Chirality :  0.046   0.159   1790
  Planarity :  0.004   0.035   2157
  Dihedral  :  4.916  22.368   1646
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 33.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.49 %
    Favored  : 92.51 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 11.18 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.58 %
    Cis-general     : 0.07 %
    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: -1.09 (0.22), residues: 1522
  helix: -1.25 (0.41), residues: 146
  sheet: -0.23 (0.24), residues: 474
  loop : -0.87 (0.21), residues: 902

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 144 
 HIS   0.005   0.001   HIS A 121 
 PHE   0.024   0.002   PHE A 306 
 TYR   0.029   0.002   TYR A 305 
 ARG   0.003   0.000   ARG A 506 

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   33 is missing expected H atoms. Skipping.
Residue VAL   35 is missing expected H atoms. Skipping.
Residue ALA   39 is missing expected H atoms. Skipping.
Residue ALA   52 is missing expected H atoms. Skipping.
Residue VAL   53 is missing expected H atoms. Skipping.
Residue VAL   57 is missing expected H atoms. Skipping.
Residue ALA   60 is missing expected H atoms. Skipping.
Residue MET   64 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue VAL   68 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue THR   75 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   86 is missing expected H atoms. Skipping.
Residue LEU   87 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ILE  100 is missing expected H atoms. Skipping.
Residue ALA  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue ALA  111 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue ALA  126 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue ALA  137 is missing expected H atoms. Skipping.
Residue ALA  139 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  146 is missing expected H atoms. Skipping.
Residue MET  148 is missing expected H atoms. Skipping.
Residue VAL  155 is missing expected H atoms. Skipping.
Residue THR  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  164 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue VAL  167 is missing expected H atoms. Skipping.
Residue ALA  170 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  179 is missing expected H atoms. Skipping.
Residue ILE  191 is missing expected H atoms. Skipping.
Residue THR  194 is missing expected H atoms. Skipping.
Residue ALA  196 is missing expected H atoms. Skipping.
Residue VAL  199 is missing expected H atoms. Skipping.
Residue LEU  200 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LEU  213 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue ALA  219 is missing expected H atoms. Skipping.
Residue ILE  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Residue VAL  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LEU  238 is missing expected H atoms. Skipping.
Residue ALA  239 is missing expected H atoms. Skipping.
Residue THR  240 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue ALA  243 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue ILE  246 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue VAL  256 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  258 is missing expected H atoms. Skipping.
Residue ILE  266 is missing expected H atoms. Skipping.
Residue VAL  270 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue ALA  276 is missing expected H atoms. Skipping.
Residue ALA  277 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue LEU  280 is missing expected H atoms. Skipping.
Residue MET  282 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  285 is missing expected H atoms. Skipping.
Residue MET  291 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue THR  298 is missing expected H atoms. Skipping.
Residue MET  302 is missing expected H atoms. Skipping.
Residue ALA  303 is missing expected H atoms. Skipping.
Residue ALA  304 is missing expected H atoms. Skipping.
Residue VAL  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue ALA  312 is missing expected H atoms. Skipping.
Residue THR  313 is missing expected H atoms. Skipping.
Residue ILE  315 is missing expected H atoms. Skipping.
Residue ALA  321 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue ILE  325 is missing expected H atoms. Skipping.
Residue ALA  327 is missing expected H atoms. Skipping.
Residue LEU  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU  339 is missing expected H atoms. Skipping.
Residue VAL  342 is missing expected H atoms. Skipping.
Residue VAL  345 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  349 is missing expected H atoms. Skipping.
Residue ALA  352 is missing expected H atoms. Skipping.
Residue THR  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LEU  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue ALA  368 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  374 is missing expected H atoms. Skipping.
Residue ALA  375 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue LEU  380 is missing expected H atoms. Skipping.
Residue ILE  388 is missing expected H atoms. Skipping.
Residue ALA  389 is missing expected H atoms. Skipping.
Residue ILE  390 is missing expected H atoms. Skipping.
Residue ALA  391 is missing expected H atoms. Skipping.
Residue ALA  392 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue VAL  403 is missing expected H atoms. Skipping.
Residue ILE  405 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Residue ALA  415 is missing expected H atoms. Skipping.
Residue VAL  416 is missing expected H atoms. Skipping.
Residue ILE  420 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue ALA  426 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue MET  438 is missing expected H atoms. Skipping.
Residue ALA  441 is missing expected H atoms. Skipping.
Residue THR  442 is missing expected H atoms. Skipping.
Residue ILE  444 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue ILE  453 is missing expected H atoms. Skipping.
Residue VAL  454 is missing expected H atoms. Skipping.
Residue ALA  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue VAL  470 is missing expected H atoms. Skipping.
Residue ILE  471 is missing expected H atoms. Skipping.
Residue THR  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ALA  475 is missing expected H atoms. Skipping.
Residue LEU  477 is missing expected H atoms. Skipping.
Residue VAL  479 is missing expected H atoms. Skipping.
Residue ILE  483 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue THR  490 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue THR  496 is missing expected H atoms. Skipping.
Residue ALA  497 is missing expected H atoms. Skipping.
Residue LEU  498 is missing expected H atoms. Skipping.
Residue VAL  500 is missing expected H atoms. Skipping.
Residue VAL  505 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue ALA  511 is missing expected H atoms. Skipping.
Residue VAL  516 is missing expected H atoms. Skipping.
Residue LEU  517 is missing expected H atoms. Skipping.
Residue LEU  521 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  532 is missing expected H atoms. Skipping.
Residue ALA  537 is missing expected H atoms. Skipping.
Residue ILE  538 is missing expected H atoms. Skipping.
Residue ALA  541 is missing expected H atoms. Skipping.
Residue LEU  542 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue THR  556 is missing expected H atoms. Skipping.
Residue ILE  557 is missing expected H atoms. Skipping.
Residue LEU  562 is missing expected H atoms. Skipping.
Residue MET  563 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue ALA  570 is missing expected H atoms. Skipping.
Residue LEU  572 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue THR  583 is missing expected H atoms. Skipping.
Residue ILE  585 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue ILE  587 is missing expected H atoms. Skipping.
Residue MET  589 is missing expected H atoms. Skipping.
Residue LEU  593 is missing expected H atoms. Skipping.
Residue THR  597 is missing expected H atoms. Skipping.
Residue ALA  598 is missing expected H atoms. Skipping.
Residue ALA  599 is missing expected H atoms. Skipping.
Residue THR  601 is missing expected H atoms. Skipping.
Residue THR  602 is missing expected H atoms. Skipping.
Residue LEU  604 is missing expected H atoms. Skipping.
Residue ILE  607 is missing expected H atoms. Skipping.
Residue LEU  608 is missing expected H atoms. Skipping.
Residue THR  612 is missing expected H atoms. Skipping.
Residue ALA  614 is missing expected H atoms. Skipping.
Residue ILE  616 is missing expected H atoms. Skipping.
Residue ALA  620 is missing expected H atoms. Skipping.
Residue ILE  622 is missing expected H atoms. Skipping.
Residue LEU  623 is missing expected H atoms. Skipping.
Residue LEU  624 is missing expected H atoms. Skipping.
Residue VAL  631 is missing expected H atoms. Skipping.
Residue LEU  636 is missing expected H atoms. Skipping.
Residue VAL  638 is missing expected H atoms. Skipping.
Residue VAL  640 is missing expected H atoms. Skipping.
Residue ILE  647 is missing expected H atoms. Skipping.
Residue ILE  649 is missing expected H atoms. Skipping.
Residue LEU  655 is missing expected H atoms. Skipping.
Residue THR  656 is missing expected H atoms. Skipping.
Residue LEU  657 is missing expected H atoms. Skipping.
Residue ILE  658 is missing expected H atoms. Skipping.
Residue VAL  659 is missing expected H atoms. Skipping.
Residue ALA  661 is missing expected H atoms. Skipping.
Residue ALA  668 is missing expected H atoms. Skipping.
Residue ALA  671 is missing expected H atoms. Skipping.
Residue LEU  673 is missing expected H atoms. Skipping.
Residue ILE  674 is missing expected H atoms. Skipping.
Residue VAL  675 is missing expected H atoms. Skipping.
Residue ILE  677 is missing expected H atoms. Skipping.
Residue LEU  679 is missing expected H atoms. Skipping.
Residue ALA  681 is missing expected H atoms. Skipping.
Residue ILE  684 is missing expected H atoms. Skipping.
Residue VAL  686 is missing expected H atoms. Skipping.
Residue VAL  687 is missing expected H atoms. Skipping.
Residue ALA  692 is missing expected H atoms. Skipping.
Residue LEU  693 is missing expected H atoms. Skipping.
Residue ALA  694 is missing expected H atoms. Skipping.
Residue LEU  696 is missing expected H atoms. Skipping.
Residue ALA  699 is missing expected H atoms. Skipping.
Residue THR  702 is missing expected H atoms. Skipping.
Residue THR  706 is missing expected H atoms. Skipping.
Residue VAL  709 is missing expected H atoms. Skipping.
Residue VAL  710 is missing expected H atoms. Skipping.
Residue LEU  713 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue ALA  719 is missing expected H atoms. Skipping.
Residue THR  721 is missing expected H atoms. Skipping.
Residue LEU  723 is missing expected H atoms. Skipping.
Residue LEU  724 is missing expected H atoms. Skipping.
Residue ALA  725 is missing expected H atoms. Skipping.
Residue LEU  727 is missing expected H atoms. Skipping.
Residue VAL  731 is missing expected H atoms. Skipping.
Residue MET  737 is missing expected H atoms. Skipping.
Residue THR  739 is missing expected H atoms. Skipping.
Residue VAL  741 is missing expected H atoms. Skipping.
Residue LEU  745 is missing expected H atoms. Skipping.
Residue ILE  747 is missing expected H atoms. Skipping.
Residue LEU  752 is missing expected H atoms. Skipping.
Residue VAL  756 is missing expected H atoms. Skipping.
Residue VAL  759 is missing expected H atoms. Skipping.
Residue VAL  760 is missing expected H atoms. Skipping.
Residue VAL  764 is missing expected H atoms. Skipping.
Residue LEU  766 is missing expected H atoms. Skipping.
Residue ALA  767 is missing expected H atoms. Skipping.
Residue VAL  768 is missing expected H atoms. Skipping.
Residue LEU  769 is missing expected H atoms. Skipping.
Residue ALA  770 is missing expected H atoms. Skipping.
Residue ALA  771 is missing expected H atoms. Skipping.
Residue VAL  772 is missing expected H atoms. Skipping.
Residue ILE  774 is missing expected H atoms. Skipping.
Residue VAL  777 is missing expected H atoms. Skipping.
Residue VAL  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue THR  798 is missing expected H atoms. Skipping.
Residue VAL  802 is missing expected H atoms. Skipping.
Residue VAL  805 is missing expected H atoms. Skipping.
Residue VAL  806 is missing expected H atoms. Skipping.
Residue ILE  809 is missing expected H atoms. Skipping.
Residue LEU  812 is missing expected H atoms. Skipping.
Residue ALA  823 is missing expected H atoms. Skipping.
Residue MET  824 is missing expected H atoms. Skipping.
Residue LEU  825 is missing expected H atoms. Skipping.
Residue LEU  827 is missing expected H atoms. Skipping.
Residue THR  837 is missing expected H atoms. Skipping.
Residue LEU  838 is missing expected H atoms. Skipping.
Residue LEU  839 is missing expected H atoms. Skipping.
Residue ILE  841 is missing expected H atoms. Skipping.
Residue LEU  842 is missing expected H atoms. Skipping.
Residue ILE  846 is missing expected H atoms. Skipping.
Residue MET  850 is missing expected H atoms. Skipping.
Residue THR  853 is missing expected H atoms. Skipping.
Residue MET  856 is missing expected H atoms. Skipping.
Residue ILE  858 is missing expected H atoms. Skipping.
Residue LEU  861 is missing expected H atoms. Skipping.
Residue ILE  863 is missing expected H atoms. Skipping.
Residue ILE  865 is missing expected H atoms. Skipping.
Residue ILE  899 is missing expected H atoms. Skipping.
Residue THR  901 is missing expected H atoms. Skipping.
Residue LEU  902 is missing expected H atoms. Skipping.
Residue VAL  906 is missing expected H atoms. Skipping.
Residue ALA  907 is missing expected H atoms. Skipping.
Residue LEU  910 is missing expected H atoms. Skipping.
Residue ILE  912 is missing expected H atoms. Skipping.
Residue VAL  913 is missing expected H atoms. Skipping.
Residue VAL  916 is missing expected H atoms. Skipping.
Residue LEU  919 is missing expected H atoms. Skipping.
Residue ALA  925 is missing expected H atoms. Skipping.
Residue ILE  926 is missing expected H atoms. Skipping.
Residue LEU  927 is missing expected H atoms. Skipping.
Residue VAL  929 is missing expected H atoms. Skipping.
Residue LEU  932 is missing expected H atoms. Skipping.
Residue LEU  933 is missing expected H atoms. Skipping.
Residue THR  935 is missing expected H atoms. Skipping.
Residue THR  937 is missing expected H atoms. Skipping.
Residue MET  939 is missing expected H atoms. Skipping.
Residue LEU  950 is missing expected H atoms. Skipping.
Residue ALA  954 is missing expected H atoms. Skipping.
Residue VAL  958 is missing expected H atoms. Skipping.
Residue ILE  959 is missing expected H atoms. Skipping.
Residue LEU  966 is missing expected H atoms. Skipping.
Residue ILE  968 is missing expected H atoms. Skipping.
Residue ILE  971 is missing expected H atoms. Skipping.
Residue THR  972 is missing expected H atoms. Skipping.
Residue THR  975 is missing expected H atoms. Skipping.
Residue LEU  976 is missing expected H atoms. Skipping.
Residue VAL  977 is missing expected H atoms. Skipping.
Residue THR  978 is missing expected H atoms. Skipping.
Residue THR  979 is missing expected H atoms. Skipping.
Residue VAL  981 is missing expected H atoms. Skipping.
Residue THR  982 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue ALA  988 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.
Residue VAL  520 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  542 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Residue VAL  555 is missing expected H atoms. Skipping.
Residue MET  561 is missing expected H atoms. Skipping.
Residue LEU  574 is missing expected H atoms. Skipping.
Residue THR  580 is missing expected H atoms. Skipping.
Residue THR  587 is missing expected H atoms. Skipping.
Residue THR  588 is missing expected H atoms. Skipping.
Residue THR  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue LEU  599 is missing expected H atoms. Skipping.
Residue LEU  600 is missing expected H atoms. Skipping.
Residue VAL  613 is missing expected H atoms. Skipping.
Residue ILE  615 is missing expected H atoms. Skipping.
Residue THR  623 is missing expected H atoms. Skipping.
Evaluate side-chains
  90 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 55
  time to evaluate  : 1.512 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 TRP cc_start: 0.8550 (OUTLIER) cc_final: 0.7935 (t-100)
REVERT: A  145 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7394 (tmt170)
REVERT: A  305 TYR cc_start: 0.8888 (OUTLIER) cc_final: 0.8644 (t80)
REVERT: A  507 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.7137 (p90)
REVERT: A  939 MET cc_start: 0.1933 (mmm) cc_final: 0.0950 (ptp)
REVERT: B  135 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7145 (t0)
REVERT: B  204 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.7261 (p90)
REVERT: B  608 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8287 (pm20)
  outliers start: 35
  outliers final: 25
  residues processed: 83
  average time/residue: 0.2797
  time to fit residues: 35.9689
Evaluate side-chains
  84 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 53
  time to evaluate  : 1.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 TRP
Chi-restraints excluded: chain A residue  145 ARG
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  185 CYS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  305 TYR
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  451 ASP
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  471 ILE
Chi-restraints excluded: chain A residue  503 PHE
Chi-restraints excluded: chain A residue  507 PHE
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain A residue  712 ASP
Chi-restraints excluded: chain A residue  747 ILE
Chi-restraints excluded: chain A residue  772 VAL
Chi-restraints excluded: chain A residue  826 HIS
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  135 ASP
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  204 TYR
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  321 MET
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  451 LEU
Chi-restraints excluded: chain B residue  474 CYS
Chi-restraints excluded: chain B residue  493 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    4.9990
   chunk 136 optimal weight:   10.0000
   chunk 140 optimal weight:    8.9990
   chunk 82 optimal weight:   50.0000
   chunk 59 optimal weight:   10.0000
   chunk 107 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 123 optimal weight:    0.4980
   chunk 129 optimal weight:    3.9990
   chunk 89 optimal weight:   10.0000
   chunk 144 optimal weight:    0.8980
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.3053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12032  Z= 0.236
  Angle     :  0.475   8.335  16302  Z= 0.254
  Chirality :  0.043   0.138   1790
  Planarity :  0.003   0.034   2157
  Dihedral  :  4.403  18.938   1646
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 30.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 11.86 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.58 %
    Cis-general     : 0.07 %
    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: -0.92 (0.22), residues: 1522
  helix: -0.69 (0.44), residues: 140
  sheet: -0.30 (0.24), residues: 472
  loop : -0.72 (0.21), residues: 910

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 144 
 HIS   0.003   0.001   HIS A 121 
 PHE   0.013   0.001   PHE A 306 
 TYR   0.017   0.001   TYR A 305 
 ARG   0.002   0.000   ARG A 728 

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   33 is missing expected H atoms. Skipping.
Residue VAL   35 is missing expected H atoms. Skipping.
Residue ALA   39 is missing expected H atoms. Skipping.
Residue ALA   52 is missing expected H atoms. Skipping.
Residue VAL   53 is missing expected H atoms. Skipping.
Residue VAL   57 is missing expected H atoms. Skipping.
Residue ALA   60 is missing expected H atoms. Skipping.
Residue MET   64 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue VAL   68 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue THR   75 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   86 is missing expected H atoms. Skipping.
Residue LEU   87 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ILE  100 is missing expected H atoms. Skipping.
Residue ALA  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue ALA  111 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue ALA  126 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue ALA  137 is missing expected H atoms. Skipping.
Residue ALA  139 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  146 is missing expected H atoms. Skipping.
Residue MET  148 is missing expected H atoms. Skipping.
Residue VAL  155 is missing expected H atoms. Skipping.
Residue THR  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  164 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue VAL  167 is missing expected H atoms. Skipping.
Residue ALA  170 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  179 is missing expected H atoms. Skipping.
Residue ILE  191 is missing expected H atoms. Skipping.
Residue THR  194 is missing expected H atoms. Skipping.
Residue ALA  196 is missing expected H atoms. Skipping.
Residue VAL  199 is missing expected H atoms. Skipping.
Residue LEU  200 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LEU  213 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue ALA  219 is missing expected H atoms. Skipping.
Residue ILE  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Residue VAL  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LEU  238 is missing expected H atoms. Skipping.
Residue ALA  239 is missing expected H atoms. Skipping.
Residue THR  240 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue ALA  243 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue ILE  246 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue VAL  256 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  258 is missing expected H atoms. Skipping.
Residue ILE  266 is missing expected H atoms. Skipping.
Residue VAL  270 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue ALA  276 is missing expected H atoms. Skipping.
Residue ALA  277 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue LEU  280 is missing expected H atoms. Skipping.
Residue MET  282 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  285 is missing expected H atoms. Skipping.
Residue MET  291 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue THR  298 is missing expected H atoms. Skipping.
Residue MET  302 is missing expected H atoms. Skipping.
Residue ALA  303 is missing expected H atoms. Skipping.
Residue ALA  304 is missing expected H atoms. Skipping.
Residue VAL  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue ALA  312 is missing expected H atoms. Skipping.
Residue THR  313 is missing expected H atoms. Skipping.
Residue ILE  315 is missing expected H atoms. Skipping.
Residue ALA  321 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue ILE  325 is missing expected H atoms. Skipping.
Residue ALA  327 is missing expected H atoms. Skipping.
Residue LEU  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU  339 is missing expected H atoms. Skipping.
Residue VAL  342 is missing expected H atoms. Skipping.
Residue VAL  345 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  349 is missing expected H atoms. Skipping.
Residue ALA  352 is missing expected H atoms. Skipping.
Residue THR  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LEU  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue ALA  368 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  374 is missing expected H atoms. Skipping.
Residue ALA  375 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue LEU  380 is missing expected H atoms. Skipping.
Residue ILE  388 is missing expected H atoms. Skipping.
Residue ALA  389 is missing expected H atoms. Skipping.
Residue ILE  390 is missing expected H atoms. Skipping.
Residue ALA  391 is missing expected H atoms. Skipping.
Residue ALA  392 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue VAL  403 is missing expected H atoms. Skipping.
Residue ILE  405 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Residue ALA  415 is missing expected H atoms. Skipping.
Residue VAL  416 is missing expected H atoms. Skipping.
Residue ILE  420 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue ALA  426 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue MET  438 is missing expected H atoms. Skipping.
Residue ALA  441 is missing expected H atoms. Skipping.
Residue THR  442 is missing expected H atoms. Skipping.
Residue ILE  444 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue ILE  453 is missing expected H atoms. Skipping.
Residue VAL  454 is missing expected H atoms. Skipping.
Residue ALA  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue VAL  470 is missing expected H atoms. Skipping.
Residue ILE  471 is missing expected H atoms. Skipping.
Residue THR  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ALA  475 is missing expected H atoms. Skipping.
Residue LEU  477 is missing expected H atoms. Skipping.
Residue VAL  479 is missing expected H atoms. Skipping.
Residue ILE  483 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue THR  490 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue THR  496 is missing expected H atoms. Skipping.
Residue ALA  497 is missing expected H atoms. Skipping.
Residue LEU  498 is missing expected H atoms. Skipping.
Residue VAL  500 is missing expected H atoms. Skipping.
Residue VAL  505 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue ALA  511 is missing expected H atoms. Skipping.
Residue VAL  516 is missing expected H atoms. Skipping.
Residue LEU  517 is missing expected H atoms. Skipping.
Residue LEU  521 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  532 is missing expected H atoms. Skipping.
Residue ALA  537 is missing expected H atoms. Skipping.
Residue ILE  538 is missing expected H atoms. Skipping.
Residue ALA  541 is missing expected H atoms. Skipping.
Residue LEU  542 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue THR  556 is missing expected H atoms. Skipping.
Residue ILE  557 is missing expected H atoms. Skipping.
Residue LEU  562 is missing expected H atoms. Skipping.
Residue MET  563 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue ALA  570 is missing expected H atoms. Skipping.
Residue LEU  572 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue THR  583 is missing expected H atoms. Skipping.
Residue ILE  585 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue ILE  587 is missing expected H atoms. Skipping.
Residue MET  589 is missing expected H atoms. Skipping.
Residue LEU  593 is missing expected H atoms. Skipping.
Residue THR  597 is missing expected H atoms. Skipping.
Residue ALA  598 is missing expected H atoms. Skipping.
Residue ALA  599 is missing expected H atoms. Skipping.
Residue THR  601 is missing expected H atoms. Skipping.
Residue THR  602 is missing expected H atoms. Skipping.
Residue LEU  604 is missing expected H atoms. Skipping.
Residue ILE  607 is missing expected H atoms. Skipping.
Residue LEU  608 is missing expected H atoms. Skipping.
Residue THR  612 is missing expected H atoms. Skipping.
Residue ALA  614 is missing expected H atoms. Skipping.
Residue ILE  616 is missing expected H atoms. Skipping.
Residue ALA  620 is missing expected H atoms. Skipping.
Residue ILE  622 is missing expected H atoms. Skipping.
Residue LEU  623 is missing expected H atoms. Skipping.
Residue LEU  624 is missing expected H atoms. Skipping.
Residue VAL  631 is missing expected H atoms. Skipping.
Residue LEU  636 is missing expected H atoms. Skipping.
Residue VAL  638 is missing expected H atoms. Skipping.
Residue VAL  640 is missing expected H atoms. Skipping.
Residue ILE  647 is missing expected H atoms. Skipping.
Residue ILE  649 is missing expected H atoms. Skipping.
Residue LEU  655 is missing expected H atoms. Skipping.
Residue THR  656 is missing expected H atoms. Skipping.
Residue LEU  657 is missing expected H atoms. Skipping.
Residue ILE  658 is missing expected H atoms. Skipping.
Residue VAL  659 is missing expected H atoms. Skipping.
Residue ALA  661 is missing expected H atoms. Skipping.
Residue ALA  668 is missing expected H atoms. Skipping.
Residue ALA  671 is missing expected H atoms. Skipping.
Residue LEU  673 is missing expected H atoms. Skipping.
Residue ILE  674 is missing expected H atoms. Skipping.
Residue VAL  675 is missing expected H atoms. Skipping.
Residue ILE  677 is missing expected H atoms. Skipping.
Residue LEU  679 is missing expected H atoms. Skipping.
Residue ALA  681 is missing expected H atoms. Skipping.
Residue ILE  684 is missing expected H atoms. Skipping.
Residue VAL  686 is missing expected H atoms. Skipping.
Residue VAL  687 is missing expected H atoms. Skipping.
Residue ALA  692 is missing expected H atoms. Skipping.
Residue LEU  693 is missing expected H atoms. Skipping.
Residue ALA  694 is missing expected H atoms. Skipping.
Residue LEU  696 is missing expected H atoms. Skipping.
Residue ALA  699 is missing expected H atoms. Skipping.
Residue THR  702 is missing expected H atoms. Skipping.
Residue THR  706 is missing expected H atoms. Skipping.
Residue VAL  709 is missing expected H atoms. Skipping.
Residue VAL  710 is missing expected H atoms. Skipping.
Residue LEU  713 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue ALA  719 is missing expected H atoms. Skipping.
Residue THR  721 is missing expected H atoms. Skipping.
Residue LEU  723 is missing expected H atoms. Skipping.
Residue LEU  724 is missing expected H atoms. Skipping.
Residue ALA  725 is missing expected H atoms. Skipping.
Residue LEU  727 is missing expected H atoms. Skipping.
Residue VAL  731 is missing expected H atoms. Skipping.
Residue MET  737 is missing expected H atoms. Skipping.
Residue THR  739 is missing expected H atoms. Skipping.
Residue VAL  741 is missing expected H atoms. Skipping.
Residue LEU  745 is missing expected H atoms. Skipping.
Residue ILE  747 is missing expected H atoms. Skipping.
Residue LEU  752 is missing expected H atoms. Skipping.
Residue VAL  756 is missing expected H atoms. Skipping.
Residue VAL  759 is missing expected H atoms. Skipping.
Residue VAL  760 is missing expected H atoms. Skipping.
Residue VAL  764 is missing expected H atoms. Skipping.
Residue LEU  766 is missing expected H atoms. Skipping.
Residue ALA  767 is missing expected H atoms. Skipping.
Residue VAL  768 is missing expected H atoms. Skipping.
Residue LEU  769 is missing expected H atoms. Skipping.
Residue ALA  770 is missing expected H atoms. Skipping.
Residue ALA  771 is missing expected H atoms. Skipping.
Residue VAL  772 is missing expected H atoms. Skipping.
Residue ILE  774 is missing expected H atoms. Skipping.
Residue VAL  777 is missing expected H atoms. Skipping.
Residue VAL  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue THR  798 is missing expected H atoms. Skipping.
Residue VAL  802 is missing expected H atoms. Skipping.
Residue VAL  805 is missing expected H atoms. Skipping.
Residue VAL  806 is missing expected H atoms. Skipping.
Residue ILE  809 is missing expected H atoms. Skipping.
Residue LEU  812 is missing expected H atoms. Skipping.
Residue ALA  823 is missing expected H atoms. Skipping.
Residue MET  824 is missing expected H atoms. Skipping.
Residue LEU  825 is missing expected H atoms. Skipping.
Residue LEU  827 is missing expected H atoms. Skipping.
Residue THR  837 is missing expected H atoms. Skipping.
Residue LEU  838 is missing expected H atoms. Skipping.
Residue LEU  839 is missing expected H atoms. Skipping.
Residue ILE  841 is missing expected H atoms. Skipping.
Residue LEU  842 is missing expected H atoms. Skipping.
Residue ILE  846 is missing expected H atoms. Skipping.
Residue MET  850 is missing expected H atoms. Skipping.
Residue THR  853 is missing expected H atoms. Skipping.
Residue MET  856 is missing expected H atoms. Skipping.
Residue ILE  858 is missing expected H atoms. Skipping.
Residue LEU  861 is missing expected H atoms. Skipping.
Residue ILE  863 is missing expected H atoms. Skipping.
Residue ILE  865 is missing expected H atoms. Skipping.
Residue ILE  899 is missing expected H atoms. Skipping.
Residue THR  901 is missing expected H atoms. Skipping.
Residue LEU  902 is missing expected H atoms. Skipping.
Residue VAL  906 is missing expected H atoms. Skipping.
Residue ALA  907 is missing expected H atoms. Skipping.
Residue LEU  910 is missing expected H atoms. Skipping.
Residue ILE  912 is missing expected H atoms. Skipping.
Residue VAL  913 is missing expected H atoms. Skipping.
Residue VAL  916 is missing expected H atoms. Skipping.
Residue LEU  919 is missing expected H atoms. Skipping.
Residue ALA  925 is missing expected H atoms. Skipping.
Residue ILE  926 is missing expected H atoms. Skipping.
Residue LEU  927 is missing expected H atoms. Skipping.
Residue VAL  929 is missing expected H atoms. Skipping.
Residue LEU  932 is missing expected H atoms. Skipping.
Residue LEU  933 is missing expected H atoms. Skipping.
Residue THR  935 is missing expected H atoms. Skipping.
Residue THR  937 is missing expected H atoms. Skipping.
Residue MET  939 is missing expected H atoms. Skipping.
Residue LEU  950 is missing expected H atoms. Skipping.
Residue ALA  954 is missing expected H atoms. Skipping.
Residue VAL  958 is missing expected H atoms. Skipping.
Residue ILE  959 is missing expected H atoms. Skipping.
Residue LEU  966 is missing expected H atoms. Skipping.
Residue ILE  968 is missing expected H atoms. Skipping.
Residue ILE  971 is missing expected H atoms. Skipping.
Residue THR  972 is missing expected H atoms. Skipping.
Residue THR  975 is missing expected H atoms. Skipping.
Residue LEU  976 is missing expected H atoms. Skipping.
Residue VAL  977 is missing expected H atoms. Skipping.
Residue THR  978 is missing expected H atoms. Skipping.
Residue THR  979 is missing expected H atoms. Skipping.
Residue VAL  981 is missing expected H atoms. Skipping.
Residue THR  982 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue ALA  988 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.
Residue VAL  520 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  542 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Residue VAL  555 is missing expected H atoms. Skipping.
Residue MET  561 is missing expected H atoms. Skipping.
Residue LEU  574 is missing expected H atoms. Skipping.
Residue THR  580 is missing expected H atoms. Skipping.
Residue THR  587 is missing expected H atoms. Skipping.
Residue THR  588 is missing expected H atoms. Skipping.
Residue THR  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue LEU  599 is missing expected H atoms. Skipping.
Residue LEU  600 is missing expected H atoms. Skipping.
Residue VAL  613 is missing expected H atoms. Skipping.
Residue ILE  615 is missing expected H atoms. Skipping.
Residue THR  623 is missing expected H atoms. Skipping.
Evaluate side-chains
  78 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 52
  time to evaluate  : 1.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 TRP cc_start: 0.8502 (OUTLIER) cc_final: 0.8154 (t-100)
REVERT: A  145 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7287 (tmt170)
REVERT: A  507 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.7027 (p90)
REVERT: A  939 MET cc_start: 0.1833 (mmm) cc_final: 0.0828 (ptp)
REVERT: B  204 TYR cc_start: 0.7725 (OUTLIER) cc_final: 0.7172 (p90)
  outliers start: 26
  outliers final: 20
  residues processed: 72
  average time/residue: 0.2813
  time to fit residues: 31.5762
Evaluate side-chains
  74 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 50
  time to evaluate  : 1.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 TRP
Chi-restraints excluded: chain A residue  145 ARG
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  322 ASP
Chi-restraints excluded: chain A residue  451 ASP
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  503 PHE
Chi-restraints excluded: chain A residue  507 PHE
Chi-restraints excluded: chain A residue  578 PHE
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain A residue  747 ILE
Chi-restraints excluded: chain A residue  772 VAL
Chi-restraints excluded: chain A residue  826 HIS
Chi-restraints excluded: chain B residue  135 ASP
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  204 TYR
Chi-restraints excluded: chain B residue  321 MET
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  451 LEU
Chi-restraints excluded: chain B residue  474 CYS
Chi-restraints excluded: chain B residue  493 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 88 optimal weight:   20.0000
   chunk 68 optimal weight:    0.0020
   chunk 100 optimal weight:    3.9990
   chunk 151 optimal weight:    8.9990
   chunk 139 optimal weight:    0.7980
   chunk 120 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 93 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   chunk 95 optimal weight:    9.9990
   chunk 128 optimal weight:    5.9990
   overall best weight:    1.5392

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

Flipped N/Q/H residues before XYZ refinement:
** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.3138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  12032  Z= 0.258
  Angle     :  0.479   8.461  16302  Z= 0.255
  Chirality :  0.043   0.143   1790
  Planarity :  0.003   0.031   2157
  Dihedral  :  4.353  18.944   1646
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 31.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 12.02 %
    Favored  : 86.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.58 %
    Cis-general     : 0.07 %
    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: -0.86 (0.22), residues: 1522
  helix: -0.60 (0.44), residues: 140
  sheet: -0.27 (0.24), residues: 485
  loop : -0.69 (0.21), residues: 897

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 144 
 HIS   0.003   0.001   HIS A 121 
 PHE   0.015   0.001   PHE A 306 
 TYR   0.019   0.001   TYR A 305 
 ARG   0.002   0.000   ARG A 519 

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   33 is missing expected H atoms. Skipping.
Residue VAL   35 is missing expected H atoms. Skipping.
Residue ALA   39 is missing expected H atoms. Skipping.
Residue ALA   52 is missing expected H atoms. Skipping.
Residue VAL   53 is missing expected H atoms. Skipping.
Residue VAL   57 is missing expected H atoms. Skipping.
Residue ALA   60 is missing expected H atoms. Skipping.
Residue MET   64 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   67 is missing expected H atoms. Skipping.
Residue VAL   68 is missing expected H atoms. Skipping.
Residue ALA   70 is missing expected H atoms. Skipping.
Residue ALA   73 is missing expected H atoms. Skipping.
Residue THR   75 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   81 is missing expected H atoms. Skipping.
Residue VAL   86 is missing expected H atoms. Skipping.
Residue LEU   87 is missing expected H atoms. Skipping.
Residue THR   94 is missing expected H atoms. Skipping.
Residue ILE  100 is missing expected H atoms. Skipping.
Residue ALA  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue ALA  111 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue ALA  126 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue ALA  137 is missing expected H atoms. Skipping.
Residue ALA  139 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  146 is missing expected H atoms. Skipping.
Residue MET  148 is missing expected H atoms. Skipping.
Residue VAL  155 is missing expected H atoms. Skipping.
Residue THR  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  164 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue VAL  167 is missing expected H atoms. Skipping.
Residue ALA  170 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  179 is missing expected H atoms. Skipping.
Residue ILE  191 is missing expected H atoms. Skipping.
Residue THR  194 is missing expected H atoms. Skipping.
Residue ALA  196 is missing expected H atoms. Skipping.
Residue VAL  199 is missing expected H atoms. Skipping.
Residue LEU  200 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LEU  213 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue VAL  218 is missing expected H atoms. Skipping.
Residue ALA  219 is missing expected H atoms. Skipping.
Residue ILE  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Residue VAL  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LEU  238 is missing expected H atoms. Skipping.
Residue ALA  239 is missing expected H atoms. Skipping.
Residue THR  240 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue ALA  243 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue ILE  246 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue VAL  256 is missing expected H atoms. Skipping.
Residue ALA  257 is missing expected H atoms. Skipping.
Residue VAL  258 is missing expected H atoms. Skipping.
Residue ILE  266 is missing expected H atoms. Skipping.
Residue VAL  270 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue ALA  276 is missing expected H atoms. Skipping.
Residue ALA  277 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue LEU  280 is missing expected H atoms. Skipping.
Residue MET  282 is missing expected H atoms. Skipping.
Residue VAL  283 is missing expected H atoms. Skipping.
Residue ILE  285 is missing expected H atoms. Skipping.
Residue MET  291 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue THR  298 is missing expected H atoms. Skipping.
Residue MET  302 is missing expected H atoms. Skipping.
Residue ALA  303 is missing expected H atoms. Skipping.
Residue ALA  304 is missing expected H atoms. Skipping.
Residue VAL  310 is missing expected H atoms. Skipping.
Residue ALA  311 is missing expected H atoms. Skipping.
Residue ALA  312 is missing expected H atoms. Skipping.
Residue THR  313 is missing expected H atoms. Skipping.
Residue ILE  315 is missing expected H atoms. Skipping.
Residue ALA  321 is missing expected H atoms. Skipping.
Residue VAL  323 is missing expected H atoms. Skipping.
Residue ILE  325 is missing expected H atoms. Skipping.
Residue ALA  327 is missing expected H atoms. Skipping.
Residue LEU  329 is missing expected H atoms. Skipping.
Residue MET  331 is missing expected H atoms. Skipping.
Residue LEU  339 is missing expected H atoms. Skipping.
Residue VAL  342 is missing expected H atoms. Skipping.
Residue VAL  345 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  349 is missing expected H atoms. Skipping.
Residue ALA  352 is missing expected H atoms. Skipping.
Residue THR  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LEU  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue ALA  368 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  374 is missing expected H atoms. Skipping.
Residue ALA  375 is missing expected H atoms. Skipping.
Residue LEU  377 is missing expected H atoms. Skipping.
Residue LEU  380 is missing expected H atoms. Skipping.
Residue ILE  388 is missing expected H atoms. Skipping.
Residue ALA  389 is missing expected H atoms. Skipping.
Residue ILE  390 is missing expected H atoms. Skipping.
Residue ALA  391 is missing expected H atoms. Skipping.
Residue ALA  392 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue VAL  403 is missing expected H atoms. Skipping.
Residue ILE  405 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue LEU  413 is missing expected H atoms. Skipping.
Residue ALA  415 is missing expected H atoms. Skipping.
Residue VAL  416 is missing expected H atoms. Skipping.
Residue ILE  420 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue ALA  426 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue MET  430 is missing expected H atoms. Skipping.
Residue MET  438 is missing expected H atoms. Skipping.
Residue ALA  441 is missing expected H atoms. Skipping.
Residue THR  442 is missing expected H atoms. Skipping.
Residue ILE  444 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue ILE  453 is missing expected H atoms. Skipping.
Residue VAL  454 is missing expected H atoms. Skipping.
Residue ALA  456 is missing expected H atoms. Skipping.
Residue VAL  459 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue LEU  464 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue VAL  470 is missing expected H atoms. Skipping.
Residue ILE  471 is missing expected H atoms. Skipping.
Residue THR  472 is missing expected H atoms. Skipping.
Residue VAL  473 is missing expected H atoms. Skipping.
Residue ALA  475 is missing expected H atoms. Skipping.
Residue LEU  477 is missing expected H atoms. Skipping.
Residue VAL  479 is missing expected H atoms. Skipping.
Residue ILE  483 is missing expected H atoms. Skipping.
Residue LEU  484 is missing expected H atoms. Skipping.
Residue THR  490 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue THR  496 is missing expected H atoms. Skipping.
Residue ALA  497 is missing expected H atoms. Skipping.
Residue LEU  498 is missing expected H atoms. Skipping.
Residue VAL  500 is missing expected H atoms. Skipping.
Residue VAL  505 is missing expected H atoms. Skipping.
Residue LEU  509 is missing expected H atoms. Skipping.
Residue ALA  511 is missing expected H atoms. Skipping.
Residue VAL  516 is missing expected H atoms. Skipping.
Residue LEU  517 is missing expected H atoms. Skipping.
Residue LEU  521 is missing expected H atoms. Skipping.
Residue VAL  525 is missing expected H atoms. Skipping.
Residue LEU  527 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue LEU  529 is missing expected H atoms. Skipping.
Residue LEU  532 is missing expected H atoms. Skipping.
Residue ALA  537 is missing expected H atoms. Skipping.
Residue ILE  538 is missing expected H atoms. Skipping.
Residue ALA  541 is missing expected H atoms. Skipping.
Residue LEU  542 is missing expected H atoms. Skipping.
Residue LEU  544 is missing expected H atoms. Skipping.
Residue MET  555 is missing expected H atoms. Skipping.
Residue THR  556 is missing expected H atoms. Skipping.
Residue ILE  557 is missing expected H atoms. Skipping.
Residue LEU  562 is missing expected H atoms. Skipping.
Residue MET  563 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue ALA  570 is missing expected H atoms. Skipping.
Residue LEU  572 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue THR  583 is missing expected H atoms. Skipping.
Residue ILE  585 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue ILE  587 is missing expected H atoms. Skipping.
Residue MET  589 is missing expected H atoms. Skipping.
Residue LEU  593 is missing expected H atoms. Skipping.
Residue THR  597 is missing expected H atoms. Skipping.
Residue ALA  598 is missing expected H atoms. Skipping.
Residue ALA  599 is missing expected H atoms. Skipping.
Residue THR  601 is missing expected H atoms. Skipping.
Residue THR  602 is missing expected H atoms. Skipping.
Residue LEU  604 is missing expected H atoms. Skipping.
Residue ILE  607 is missing expected H atoms. Skipping.
Residue LEU  608 is missing expected H atoms. Skipping.
Residue THR  612 is missing expected H atoms. Skipping.
Residue ALA  614 is missing expected H atoms. Skipping.
Residue ILE  616 is missing expected H atoms. Skipping.
Residue ALA  620 is missing expected H atoms. Skipping.
Residue ILE  622 is missing expected H atoms. Skipping.
Residue LEU  623 is missing expected H atoms. Skipping.
Residue LEU  624 is missing expected H atoms. Skipping.
Residue VAL  631 is missing expected H atoms. Skipping.
Residue LEU  636 is missing expected H atoms. Skipping.
Residue VAL  638 is missing expected H atoms. Skipping.
Residue VAL  640 is missing expected H atoms. Skipping.
Residue ILE  647 is missing expected H atoms. Skipping.
Residue ILE  649 is missing expected H atoms. Skipping.
Residue LEU  655 is missing expected H atoms. Skipping.
Residue THR  656 is missing expected H atoms. Skipping.
Residue LEU  657 is missing expected H atoms. Skipping.
Residue ILE  658 is missing expected H atoms. Skipping.
Residue VAL  659 is missing expected H atoms. Skipping.
Residue ALA  661 is missing expected H atoms. Skipping.
Residue ALA  668 is missing expected H atoms. Skipping.
Residue ALA  671 is missing expected H atoms. Skipping.
Residue LEU  673 is missing expected H atoms. Skipping.
Residue ILE  674 is missing expected H atoms. Skipping.
Residue VAL  675 is missing expected H atoms. Skipping.
Residue ILE  677 is missing expected H atoms. Skipping.
Residue LEU  679 is missing expected H atoms. Skipping.
Residue ALA  681 is missing expected H atoms. Skipping.
Residue ILE  684 is missing expected H atoms. Skipping.
Residue VAL  686 is missing expected H atoms. Skipping.
Residue VAL  687 is missing expected H atoms. Skipping.
Residue ALA  692 is missing expected H atoms. Skipping.
Residue LEU  693 is missing expected H atoms. Skipping.
Residue ALA  694 is missing expected H atoms. Skipping.
Residue LEU  696 is missing expected H atoms. Skipping.
Residue ALA  699 is missing expected H atoms. Skipping.
Residue THR  702 is missing expected H atoms. Skipping.
Residue THR  706 is missing expected H atoms. Skipping.
Residue VAL  709 is missing expected H atoms. Skipping.
Residue VAL  710 is missing expected H atoms. Skipping.
Residue LEU  713 is missing expected H atoms. Skipping.
Residue MET  717 is missing expected H atoms. Skipping.
Residue ALA  719 is missing expected H atoms. Skipping.
Residue THR  721 is missing expected H atoms. Skipping.
Residue LEU  723 is missing expected H atoms. Skipping.
Residue LEU  724 is missing expected H atoms. Skipping.
Residue ALA  725 is missing expected H atoms. Skipping.
Residue LEU  727 is missing expected H atoms. Skipping.
Residue VAL  731 is missing expected H atoms. Skipping.
Residue MET  737 is missing expected H atoms. Skipping.
Residue THR  739 is missing expected H atoms. Skipping.
Residue VAL  741 is missing expected H atoms. Skipping.
Residue LEU  745 is missing expected H atoms. Skipping.
Residue ILE  747 is missing expected H atoms. Skipping.
Residue LEU  752 is missing expected H atoms. Skipping.
Residue VAL  756 is missing expected H atoms. Skipping.
Residue VAL  759 is missing expected H atoms. Skipping.
Residue VAL  760 is missing expected H atoms. Skipping.
Residue VAL  764 is missing expected H atoms. Skipping.
Residue LEU  766 is missing expected H atoms. Skipping.
Residue ALA  767 is missing expected H atoms. Skipping.
Residue VAL  768 is missing expected H atoms. Skipping.
Residue LEU  769 is missing expected H atoms. Skipping.
Residue ALA  770 is missing expected H atoms. Skipping.
Residue ALA  771 is missing expected H atoms. Skipping.
Residue VAL  772 is missing expected H atoms. Skipping.
Residue ILE  774 is missing expected H atoms. Skipping.
Residue VAL  777 is missing expected H atoms. Skipping.
Residue VAL  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue THR  798 is missing expected H atoms. Skipping.
Residue VAL  802 is missing expected H atoms. Skipping.
Residue VAL  805 is missing expected H atoms. Skipping.
Residue VAL  806 is missing expected H atoms. Skipping.
Residue ILE  809 is missing expected H atoms. Skipping.
Residue LEU  812 is missing expected H atoms. Skipping.
Residue ALA  823 is missing expected H atoms. Skipping.
Residue MET  824 is missing expected H atoms. Skipping.
Residue LEU  825 is missing expected H atoms. Skipping.
Residue LEU  827 is missing expected H atoms. Skipping.
Residue THR  837 is missing expected H atoms. Skipping.
Residue LEU  838 is missing expected H atoms. Skipping.
Residue LEU  839 is missing expected H atoms. Skipping.
Residue ILE  841 is missing expected H atoms. Skipping.
Residue LEU  842 is missing expected H atoms. Skipping.
Residue ILE  846 is missing expected H atoms. Skipping.
Residue MET  850 is missing expected H atoms. Skipping.
Residue THR  853 is missing expected H atoms. Skipping.
Residue MET  856 is missing expected H atoms. Skipping.
Residue ILE  858 is missing expected H atoms. Skipping.
Residue LEU  861 is missing expected H atoms. Skipping.
Residue ILE  863 is missing expected H atoms. Skipping.
Residue ILE  865 is missing expected H atoms. Skipping.
Residue ILE  899 is missing expected H atoms. Skipping.
Residue THR  901 is missing expected H atoms. Skipping.
Residue LEU  902 is missing expected H atoms. Skipping.
Residue VAL  906 is missing expected H atoms. Skipping.
Residue ALA  907 is missing expected H atoms. Skipping.
Residue LEU  910 is missing expected H atoms. Skipping.
Residue ILE  912 is missing expected H atoms. Skipping.
Residue VAL  913 is missing expected H atoms. Skipping.
Residue VAL  916 is missing expected H atoms. Skipping.
Residue LEU  919 is missing expected H atoms. Skipping.
Residue ALA  925 is missing expected H atoms. Skipping.
Residue ILE  926 is missing expected H atoms. Skipping.
Residue LEU  927 is missing expected H atoms. Skipping.
Residue VAL  929 is missing expected H atoms. Skipping.
Residue LEU  932 is missing expected H atoms. Skipping.
Residue LEU  933 is missing expected H atoms. Skipping.
Residue THR  935 is missing expected H atoms. Skipping.
Residue THR  937 is missing expected H atoms. Skipping.
Residue MET  939 is missing expected H atoms. Skipping.
Residue LEU  950 is missing expected H atoms. Skipping.
Residue ALA  954 is missing expected H atoms. Skipping.
Residue VAL  958 is missing expected H atoms. Skipping.
Residue ILE  959 is missing expected H atoms. Skipping.
Residue LEU  966 is missing expected H atoms. Skipping.
Residue ILE  968 is missing expected H atoms. Skipping.
Residue ILE  971 is missing expected H atoms. Skipping.
Residue THR  972 is missing expected H atoms. Skipping.
Residue THR  975 is missing expected H atoms. Skipping.
Residue LEU  976 is missing expected H atoms. Skipping.
Residue VAL  977 is missing expected H atoms. Skipping.
Residue THR  978 is missing expected H atoms. Skipping.
Residue THR  979 is missing expected H atoms. Skipping.
Residue VAL  981 is missing expected H atoms. Skipping.
Residue THR  982 is missing expected H atoms. Skipping.
Residue ILE  985 is missing expected H atoms. Skipping.
Residue ALA  988 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.
Residue VAL  520 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  542 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Residue VAL  555 is missing expected H atoms. Skipping.
Residue MET  561 is missing expected H atoms. Skipping.
Residue LEU  574 is missing expected H atoms. Skipping.
Residue THR  580 is missing expected H atoms. Skipping.
Residue THR  587 is missing expected H atoms. Skipping.
Residue THR  588 is missing expected H atoms. Skipping.
Residue THR  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue LEU  599 is missing expected H atoms. Skipping.
Residue LEU  600 is missing expected H atoms. Skipping.
Residue VAL  613 is missing expected H atoms. Skipping.
Residue ILE  615 is missing expected H atoms. Skipping.
Residue THR  623 is missing expected H atoms. Skipping.
Evaluate side-chains
  77 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 51
  time to evaluate  : 1.490 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 TRP cc_start: 0.8513 (OUTLIER) cc_final: 0.8154 (t-100)
REVERT: A  145 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7261 (tmt170)
REVERT: A  507 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.7031 (p90)
REVERT: A  939 MET cc_start: 0.1721 (mmm) cc_final: 0.0756 (ptp)
REVERT: B  204 TYR cc_start: 0.7726 (OUTLIER) cc_final: 0.7174 (p90)
  outliers start: 26
  outliers final: 22
  residues processed: 71
  average time/residue: 0.2727
  time to fit residues: 30.3767
Evaluate side-chains
  77 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 51
  time to evaluate  : 1.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 TRP
Chi-restraints excluded: chain A residue  145 ARG
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  305 TYR
Chi-restraints excluded: chain A residue  322 ASP
Chi-restraints excluded: chain A residue  451 ASP
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  503 PHE
Chi-restraints excluded: chain A residue  507 PHE
Chi-restraints excluded: chain A residue  578 PHE
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain A residue  747 ILE
Chi-restraints excluded: chain A residue  772 VAL
Chi-restraints excluded: chain A residue  826 HIS
Chi-restraints excluded: chain B residue  135 ASP
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  204 TYR
Chi-restraints excluded: chain B residue  321 MET
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  451 LEU
Chi-restraints excluded: chain B residue  459 CYS
Chi-restraints excluded: chain B residue  474 CYS
Chi-restraints excluded: chain B residue  493 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 111 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 120 optimal weight:    0.0980
   chunk 50 optimal weight:    9.9990
   chunk 124 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 814 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.111969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.067509 restraints weight = 51909.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 3.73
r_work: 0.2990 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.3197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  12032  Z= 0.200
  Angle     :  0.449   8.259  16302  Z= 0.239
  Chirality :  0.042   0.139   1790
  Planarity :  0.003   0.032   2157
  Dihedral  :  4.121  17.215   1646
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 31.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 12.32 %
    Favored  : 85.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.58 %
    Cis-general     : 0.07 %
    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: -0.66 (0.22), residues: 1522
  helix: -0.15 (0.47), residues: 134
  sheet: -0.24 (0.24), residues: 484
  loop : -0.54 (0.22), residues: 904

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 144 
 HIS   0.002   0.001   HIS A 121 
 PHE   0.011   0.001   PHE A 306 
 TYR   0.015   0.001   TYR A 305 
 ARG   0.001   0.000   ARG A 728 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3931.18 seconds
wall clock time: 72 minutes 45.21 seconds (4365.21 seconds total)