Starting phenix.real_space_refine
on Sun Jan 19 23:17:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xen_38294/01_2025/8xen_38294_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xen_38294/01_2025/8xen_38294.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xen_38294/01_2025/8xen_38294.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xen_38294/01_2025/8xen_38294.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xen_38294/01_2025/8xen_38294_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xen_38294/01_2025/8xen_38294_neut.cif"
  }
  resolution = 3.2
  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      94      5.16       5
     C    7356      2.51       5
     N    2003      2.21       5
     O    2300      1.98       5
     H    2606      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 14359
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8804
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 928, 8804
          Classifications: {'peptide': 928}
          Link IDs: {'PCIS': 4, 'PTRANS': 42, 'TRANS': 881}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 5555
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 593, 5555
          Classifications: {'peptide': 593}
          Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 564}
          Chain breaks: 2
  Time building chain proxies: 4.93, per 1000 atoms: 0.34
  Number of scatterers: 14359
  At special positions: 0
  Unit cell: (67.32, 102.3, 232.32, 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      94     16.00
     O    2300      8.00
     N    2003      7.00
     C    7356      6.00
     H    2606      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=30, 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=2.02
    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=2.03
    Simple disulfide: pdb=" SG  CYS B  52 " - pdb=" SG  CYS B  75 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 203 " - pdb=" SG  CYS B 210 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 258 " - pdb=" SG  CYS B 299 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 400 " - pdb=" SG  CYS B 412 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 432 " - pdb=" SG  CYS B 459 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 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: 3.42
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3022 Ramachandran restraints generated.
    1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2802

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 27 sheets defined
      14.3% alpha, 33.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 205 through 210
    Processing helix  chain 'A' and resid 218 through 224
    Processing helix  chain 'A' and resid 244 through 248
      removed outlier: 3.697A  pdb=" N   PHE A 247 " --> pdb=" O   GLN A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 400
    Processing helix  chain 'A' and resid 457 through 459
      No H-bonds generated for 'chain 'A' and resid 457 through 459'
    Processing helix  chain 'A' and resid 530 through 534
    Processing helix  chain 'A' and resid 574 through 578
    Processing helix  chain 'A' and resid 594 through 599
    Processing helix  chain 'A' and resid 798 through 802
    Processing helix  chain 'A' and resid 935 through 940
    Processing helix  chain 'A' and resid 941 through 944
    Processing helix  chain 'B' and resid 30 through 34
    Processing helix  chain 'B' and resid 39 through 46
      removed outlier: 4.157A  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 76 through 80
      removed outlier: 3.626A  pdb=" N   ILE B  80 " --> pdb=" O   PRO B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 106
    Processing helix  chain 'B' and resid 147 through 149
      No H-bonds generated for 'chain 'B' and resid 147 through 149'
    Processing helix  chain 'B' and resid 150 through 157
    Processing helix  chain 'B' and resid 159 through 169
    Processing helix  chain 'B' and resid 197 through 205
      Proline residue:  B 202  - end of helix
      removed outlier: 4.338A  pdb=" N   ASP B 205 " --> pdb=" O   PRO B 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 235
      removed outlier: 3.934A  pdb=" N   PHE B 229 " --> pdb=" O   GLN B 225 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   ASN B 230 " --> pdb=" O   VAL B 226 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LYS B 235 " --> pdb=" O   GLU B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 258
      removed outlier: 3.730A  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 284 through 288
      removed outlier: 3.699A  pdb=" N   ARG B 287 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 312
      removed outlier: 3.665A  pdb=" N   SER B 310 " --> pdb=" O   TYR B 307 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   THR B 311 " --> pdb=" O   SER B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 328
    Processing helix  chain 'B' and resid 340 through 349
    Processing helix  chain 'B' and resid 365 through 378
    Processing helix  chain 'B' and resid 401 through 403
      No H-bonds generated for 'chain 'B' and resid 401 through 403'
    Processing helix  chain 'B' and resid 461 through 465
    Processing helix  chain 'B' and resid 474 through 478
    Processing helix  chain 'B' and resid 519 through 523
      removed outlier: 3.519A  pdb=" N   SER B 522 " --> pdb=" O   PRO B 519 " (cutoff:3.500A)
    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 128 through 131
    Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 193
      removed outlier: 3.880A  pdb=" N   SER A 190 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 255 through 259
      removed outlier: 4.166A  pdb=" N   SER A 255 " --> pdb=" O   GLY A 272 " (cutoff:3.500A)
      removed outlier: 6.069A  pdb=" N   VAL A 283 " --> pdb=" O   ASN A 296 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   ASN A 296 " --> pdb=" O   VAL A 283 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   ILE A 285 " --> pdb=" O   LEU A 294 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 310 through 313
    Processing sheet with id=AA7, first strand: chain 'A' and resid 331 through 333
    Processing sheet with id=AA8, first strand: chain 'A' and resid 374 through 378
      removed outlier: 6.540A  pdb=" N   ILE A 374 " --> pdb=" O   ALA A 391 " (cutoff:3.500A)
      removed outlier: 7.535A  pdb=" N   ALA A 391 " --> pdb=" O   ILE A 374 " (cutoff:3.500A)
      removed outlier: 6.024A  pdb=" N   ALA A 389 " --> pdb=" O   PRO A 376 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   GLY A 378 " --> pdb=" O   ASP A 387 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 378
      removed outlier: 6.540A  pdb=" N   ILE A 374 " --> pdb=" O   ALA A 391 " (cutoff:3.500A)
      removed outlier: 7.535A  pdb=" N   ALA A 391 " --> pdb=" O   ILE A 374 " (cutoff:3.500A)
      removed outlier: 6.024A  pdb=" N   ALA A 389 " --> pdb=" O   PRO A 376 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   GLY A 378 " --> pdb=" O   ASP A 387 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   GLN A 419 " --> pdb=" O   ILE A 405 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 489 through 492
      removed outlier: 6.854A  pdb=" N   LYS A 489 " --> pdb=" O   CYS A 502 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   CYS A 502 " --> pdb=" O   LYS A 489 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 489 through 492
      removed outlier: 6.854A  pdb=" N   LYS A 489 " --> pdb=" O   CYS A 502 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   CYS A 502 " --> pdb=" O   LYS A 489 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 483 through 484
      removed outlier: 3.553A  pdb=" N   ILE A 585 " --> pdb=" O   ALA A 620 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 636 through 642
      removed outlier: 7.544A  pdb=" N   GLY A 726 " --> pdb=" O   VAL A 686 " (cutoff:3.500A)
      removed outlier: 5.035A  pdb=" N   VAL A 686 " --> pdb=" O   GLY A 726 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   ARG A 728 " --> pdb=" O   ILE A 684 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 646 through 648
      removed outlier: 6.256A  pdb=" N   ILE A 647 " --> pdb=" O   ALA A 767 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   ARG A 707 " --> pdb=" O   ILE A 677 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 772 through 779
      removed outlier: 6.847A  pdb=" N   ILE A 926 " --> pdb=" O   ILE A 846 " (cutoff:3.500A)
      removed outlier: 4.772A  pdb=" N   ILE A 846 " --> pdb=" O   ILE A 926 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   TYR A 928 " --> pdb=" O   TYR A 844 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   TYR A 844 " --> pdb=" O   TYR A 928 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   LYS A 930 " --> pdb=" O   LEU A 842 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 782 through 785
      removed outlier: 4.162A  pdb=" N   ILE A 971 " --> pdb=" O   VAL A 958 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ASN A 973 " --> pdb=" O   PHE A 956 " (cutoff:3.500A)
      removed outlier: 13.510A  pdb=" N   SER A 949 " --> pdb=" O   LYS A 832 " (cutoff:3.500A)
      removed outlier: 12.702A  pdb=" N   LYS A 832 " --> pdb=" O   SER A 949 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   LYS A 951 " --> pdb=" O   PRO A 830 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   SER A 953 " --> pdb=" O   GLN A 828 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   LYS A 822 " --> pdb=" O   ILE A 959 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   GLN A 908 " --> pdb=" O   TYR A 831 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 836 through 837
      removed outlier: 6.567A  pdb=" N   LYS A 822 " --> pdb=" O   ILE A 959 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   SER A 953 " --> pdb=" O   GLN A 828 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   LYS A 951 " --> pdb=" O   PRO A 830 " (cutoff:3.500A)
      removed outlier: 12.702A  pdb=" N   LYS A 832 " --> pdb=" O   SER A 949 " (cutoff:3.500A)
      removed outlier: 13.510A  pdb=" N   SER A 949 " --> pdb=" O   LYS A 832 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   HIS A 900 " --> pdb=" O   SER A 949 " (cutoff:3.500A)
      removed outlier: 7.375A  pdb=" N   LYS A 951 " --> pdb=" O   HIS A 900 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   LEU A 902 " --> pdb=" O   LYS A 951 " (cutoff:3.500A)
      removed outlier: 8.417A  pdb=" N   SER A 953 " --> pdb=" O   LEU A 902 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 49 through 51
    Processing sheet with id=AC1, first strand: chain 'B' and resid 86 through 87
    Processing sheet with id=AC2, first strand: chain 'B' and resid 109 through 110
      removed outlier: 3.866A  pdb=" N   SER B 422 " --> pdb=" O   THR B 399 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 216 through 223
      removed outlier: 6.636A  pdb=" N   PHE B 179 " --> pdb=" O   VAL B 219 " (cutoff:3.500A)
      removed outlier: 6.049A  pdb=" N   THR B 221 " --> pdb=" O   ILE B 177 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   ILE B 177 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   THR B 223 " --> pdb=" O   LEU B 175 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   LEU B 175 " --> pdb=" O   THR B 223 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   ASP B 139 " --> pdb=" O   LEU B 271 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   VAL B 273 " --> pdb=" O   ASP B 139 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   TYR B 141 " --> pdb=" O   VAL B 273 " (cutoff:3.500A)
      removed outlier: 7.488A  pdb=" N   THR B 275 " --> pdb=" O   TYR B 141 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   LEU B 143 " --> pdb=" O   THR B 275 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   HIS B 270 " --> pdb=" O   ASN B 331 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   ILE B 333 " --> pdb=" O   HIS B 270 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   LEU B 272 " --> pdb=" O   ILE B 333 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   ALA B 335 " --> pdb=" O   LEU B 272 " (cutoff:3.500A)
      removed outlier: 5.730A  pdb=" N   PHE B 274 " --> pdb=" O   ALA B 335 " (cutoff:3.500A)
      removed outlier: 7.716A  pdb=" N   THR B 337 " --> pdb=" O   PHE B 274 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   THR B 276 " --> pdb=" O   THR B 337 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   LEU B 332 " --> pdb=" O   THR B 355 " (cutoff:3.500A)
      removed outlier: 8.418A  pdb=" N   GLY B 357 " --> pdb=" O   LEU B 332 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   PHE B 334 " --> pdb=" O   GLY B 357 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   LEU B 359 " --> pdb=" O   PHE B 334 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   VAL B 336 " --> pdb=" O   LEU B 359 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 525 through 528
      removed outlier: 3.675A  pdb=" N   GLU B 526 " --> pdb=" O   VAL B 533 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 536 through 537
    Processing sheet with id=AC6, first strand: chain 'B' and resid 556 through 557
    Processing sheet with id=AC7, first strand: chain 'B' and resid 566 through 569
    Processing sheet with id=AC8, first strand: chain 'B' and resid 579 through 580
    Processing sheet with id=AC9, first strand: chain 'B' and resid 605 through 608

    395 hydrogen bonds defined for protein.
    1008 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: 5.92

  Time building geometry restraints manager: 4.07 seconds

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

  Histogram of bond lengths:
        0.82 -     1.02: 2606
        1.02 -     1.22: 0
        1.22 -     1.42: 5031
        1.42 -     1.62: 6834
        1.62 -     1.82: 125
  Bond restraints: 14596
  Sorted by residual:
  bond pdb=" NE  ARG B 505 "
       pdb=" HE  ARG B 505 "
    ideal  model  delta    sigma   weight residual
    0.860  0.969 -0.109 2.00e-02 2.50e+03 2.97e+01
  bond pdb=" CB  PRO B 490 "
       pdb=" CG  PRO B 490 "
    ideal  model  delta    sigma   weight residual
    1.492  1.585 -0.093 5.00e-02 4.00e+02 3.45e+00
  bond pdb=" N   ASN B  29 "
       pdb=" CA  ASN B  29 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.05e+00
  bond pdb=" N   PHE A  31 "
       pdb=" CA  PHE A  31 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.60e+00
  bond pdb=" CB  PRO A 549 "
       pdb=" CG  PRO A 549 "
    ideal  model  delta    sigma   weight residual
    1.492  1.568 -0.076 5.00e-02 4.00e+02 2.33e+00
  ... (remaining 14591 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.26: 20711
        2.26 -     4.52: 181
        4.52 -     6.77: 15
        6.77 -     9.03: 0
        9.03 -    11.29: 1
  Bond angle restraints: 20908
  Sorted by residual:
  angle pdb=" CA  PRO B 490 "
        pdb=" N   PRO B 490 "
        pdb=" CD  PRO B 490 "
      ideal   model   delta    sigma   weight residual
     112.00  106.63    5.37 1.40e+00 5.10e-01 1.47e+01
  angle pdb=" N   GLN B 508 "
        pdb=" CA  GLN B 508 "
        pdb=" C   GLN B 508 "
      ideal   model   delta    sigma   weight residual
     113.18  108.57    4.61 1.21e+00 6.83e-01 1.45e+01
  angle pdb=" CB  MET B 594 "
        pdb=" CG  MET B 594 "
        pdb=" SD  MET B 594 "
      ideal   model   delta    sigma   weight residual
     112.70  123.99  -11.29 3.00e+00 1.11e-01 1.42e+01
  angle pdb=" N   ALA A 907 "
        pdb=" CA  ALA A 907 "
        pdb=" C   ALA A 907 "
      ideal   model   delta    sigma   weight residual
     109.24  114.47   -5.23 1.51e+00 4.39e-01 1.20e+01
  angle pdb=" N   ASP A 178 "
        pdb=" CA  ASP A 178 "
        pdb=" C   ASP A 178 "
      ideal   model   delta    sigma   weight residual
     108.34  112.77   -4.43 1.31e+00 5.83e-01 1.14e+01
  ... (remaining 20903 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.75: 8612
       17.75 -    35.50: 568
       35.50 -    53.26: 131
       53.26 -    71.01: 40
       71.01 -    88.76: 13
  Dihedral angle restraints: 9364
    sinusoidal: 4953
      harmonic: 4411
  Sorted by residual:
  dihedral pdb=" CB  CYS B 400 "
           pdb=" SG  CYS B 400 "
           pdb=" SG  CYS B 412 "
           pdb=" CB  CYS B 412 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -153.80   67.80     1      1.00e+01 1.00e-02 5.97e+01
  dihedral pdb=" CA  ASP A 176 "
           pdb=" C   ASP A 176 "
           pdb=" N   ILE A 177 "
           pdb=" CA  ILE A 177 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.46  -27.54     0      5.00e+00 4.00e-02 3.03e+01
  dihedral pdb=" CA  HIS A 143 "
           pdb=" C   HIS A 143 "
           pdb=" N   TRP A 144 "
           pdb=" CA  TRP A 144 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.94  -26.06     0      5.00e+00 4.00e-02 2.72e+01
  ... (remaining 9361 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1142
       0.034 -    0.069: 449
       0.069 -    0.103: 106
       0.103 -    0.138: 82
       0.138 -    0.172: 5
  Chirality restraints: 1784
  Sorted by residual:
  chirality pdb=" CA  PRO A 549 "
            pdb=" N   PRO A 549 "
            pdb=" C   PRO A 549 "
            pdb=" CB  PRO A 549 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 7.42e-01
  chirality pdb=" CB  ILE B 417 "
            pdb=" CA  ILE B 417 "
            pdb=" CG1 ILE B 417 "
            pdb=" CG2 ILE B 417 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.79   -0.15 2.00e-01 2.50e+01 5.62e-01
  chirality pdb=" CA  ILE B 291 "
            pdb=" N   ILE B 291 "
            pdb=" C   ILE B 291 "
            pdb=" CB  ILE B 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.95e-01
  ... (remaining 1781 not shown)

  Planarity restraints: 3588
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B 509 "    0.238 2.00e-02 2.50e+03   3.50e-01 1.84e+03
        pdb=" CD  GLN B 509 "   -0.019 2.00e-02 2.50e+03
        pdb=" OE1 GLN B 509 "   -0.228 2.00e-02 2.50e+03
        pdb=" NE2 GLN B 509 "   -0.003 2.00e-02 2.50e+03
        pdb="HE21 GLN B 509 "   -0.554 2.00e-02 2.50e+03
        pdb="HE22 GLN B 509 "    0.566 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 548 "    0.076 5.00e-02 4.00e+02   1.14e-01 2.09e+01
        pdb=" N   PRO A 549 "   -0.198 5.00e-02 4.00e+02
        pdb=" CA  PRO A 549 "    0.061 5.00e-02 4.00e+02
        pdb=" CD  PRO A 549 "    0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B 508 "    0.033 2.00e-02 2.50e+03   3.66e-02 2.01e+01
        pdb=" CD  GLN B 508 "    0.002 2.00e-02 2.50e+03
        pdb=" OE1 GLN B 508 "   -0.034 2.00e-02 2.50e+03
        pdb=" NE2 GLN B 508 "    0.002 2.00e-02 2.50e+03
        pdb="HE21 GLN B 508 "    0.053 2.00e-02 2.50e+03
        pdb="HE22 GLN B 508 "   -0.055 2.00e-02 2.50e+03
  ... (remaining 3585 not shown)

  Histogram of nonbonded interaction distances:
        1.43 -     2.06: 303
        2.06 -     2.70: 7074
        2.70 -     3.33: 24132
        3.33 -     3.97: 33231
        3.97 -     4.60: 48534
  Nonbonded interactions: 113274
  Sorted by model distance:
  nonbonded pdb=" O   ARG A 579 "
            pdb=" HE  ARG A 579 "
     model   vdw
     1.428 2.450
  nonbonded pdb=" O   ASP A 178 "
            pdb=" H   GLY A 181 "
     model   vdw
     1.468 2.450
  nonbonded pdb=" OE2 GLU B 435 "
            pdb=" H   GLU B 437 "
     model   vdw
     1.496 2.450
  nonbonded pdb=" OD2 ASP A 114 "
            pdb="HH21 ARG A 145 "
     model   vdw
     1.555 2.450
  nonbonded pdb=" O   VAL A 802 "
            pdb=" HG1 THR A 935 "
     model   vdw
     1.569 2.450
  ... (remaining 113269 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:             15.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     35.280
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   53.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
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   0.093  11990  Z= 0.289
  Angle     :  0.632  11.288  16240  Z= 0.363
  Chirality :  0.044   0.172   1784
  Planarity :  0.005   0.114   2146
  Dihedral  : 13.686  88.759   4436
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.29 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  6.56 %
    Favored  : 93.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.46 %
    Cis-general     : 0.00 %
    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: 1511
  helix: -1.40 (0.45), residues: 129
  sheet:  0.17 (0.23), residues: 507
  loop : -0.62 (0.21), residues: 875

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 144 
 HIS   0.004   0.001   HIS A 143 
 PHE   0.013   0.001   PHE A 184 
 TYR   0.013   0.001   TYR B 142 
 ARG   0.006   0.001   ARG B  34 

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

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

  3022 Ramachandran restraints generated.
    1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3022 Ramachandran restraints generated.
    1511 Oldfield, 0 Emsley, 1511 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 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
  58 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 54
  time to evaluate  : 1.571 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  555 MET cc_start: 0.6092 (mtp) cc_final: 0.5713 (mtt)
REVERT: A  762 HIS cc_start: 0.4069 (t70) cc_final: 0.3061 (t-90)
REVERT: B  505 ARG cc_start: 0.6178 (OUTLIER) cc_final: 0.5143 (ptm160)
REVERT: B  594 MET cc_start: 0.4902 (ppp) cc_final: 0.4665 (ppp)
  outliers start: 4
  outliers final: 2
  residues processed: 57
  average time/residue: 0.3867
  time to fit residues: 31.8114
Evaluate side-chains
  52 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 49
  time to evaluate  : 1.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain B residue  505 ARG
Chi-restraints excluded: chain B residue  546 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 127 optimal weight:    5.9990
   chunk 114 optimal weight:    2.9990
   chunk 63 optimal weight:   30.0000
   chunk 39 optimal weight:    4.9990
   chunk 77 optimal weight:   40.0000
   chunk 61 optimal weight:    5.9990
   chunk 118 optimal weight:    2.9990
   chunk 45 optimal weight:    6.9990
   chunk 71 optimal weight:   20.0000
   chunk 88 optimal weight:    6.9990
   chunk 137 optimal weight:    0.2980
   overall best weight:    3.4588

-------------------------------------------------------------------------------
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**
A 733 GLN
** A 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.126450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.081381 restraints weight = 46873.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 3.21
r_work: 0.3081 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.1549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.074  11990  Z= 0.552
  Angle     :  0.698   7.442  16240  Z= 0.368
  Chirality :  0.049   0.200   1784
  Planarity :  0.006   0.118   2146
  Dihedral  :  5.889  39.179   1644
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 21.15
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.49 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  :  7.94 %
    Favored  : 90.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.46 %
    Cis-general     : 0.00 %
    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: -1.15 (0.21), residues: 1511
  helix: -1.48 (0.43), residues: 115
  sheet: -0.31 (0.22), residues: 531
  loop : -0.91 (0.21), residues: 865

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 144 
 HIS   0.006   0.001   HIS B 270 
 PHE   0.025   0.002   PHE A  49 
 TYR   0.020   0.002   TYR B 136 
 ARG   0.004   0.001   ARG B 242 

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

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

  3022 Ramachandran restraints generated.
    1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3022 Ramachandran restraints generated.
    1511 Oldfield, 0 Emsley, 1511 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 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
  74 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 54
  time to evaluate  : 1.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  305 TYR cc_start: 0.8991 (OUTLIER) cc_final: 0.8592 (t80)
REVERT: A  539 ARG cc_start: 0.7918 (mpp-170) cc_final: 0.6472 (mtp85)
REVERT: A  762 HIS cc_start: 0.2876 (t70) cc_final: 0.2636 (t-90)
  outliers start: 20
  outliers final: 10
  residues processed: 68
  average time/residue: 0.3162
  time to fit residues: 32.1725
Evaluate side-chains
  62 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 51
  time to evaluate  : 1.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  305 TYR
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain A residue  730 SER
Chi-restraints excluded: chain A residue  826 HIS
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  400 CYS
Chi-restraints excluded: chain B residue  546 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 16 optimal weight:    0.3980
   chunk 117 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 95 optimal weight:    9.9990
   chunk 15 optimal weight:    0.7980
   chunk 4 optimal weight:    0.5980
   chunk 136 optimal weight:    3.9990
   chunk 145 optimal weight:    9.9990
   chunk 135 optimal weight:    0.9990
   chunk 120 optimal weight:    0.9990
   chunk 59 optimal weight:   20.0000
   overall best weight:    0.7584

-------------------------------------------------------------------------------
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**
** A 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 454 GLN
B 508 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.129139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.082069 restraints weight = 47094.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 3.38
r_work: 0.3177 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.1691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.084  11990  Z= 0.161
  Angle     :  0.464   6.648  16240  Z= 0.251
  Chirality :  0.043   0.199   1784
  Planarity :  0.004   0.116   2146
  Dihedral  :  4.811  40.069   1640
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 18.86
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.24 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  :  8.93 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.46 %
    Cis-general     : 0.00 %
    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: -0.72 (0.22), residues: 1511
  helix: -0.57 (0.48), residues: 117
  sheet: -0.06 (0.23), residues: 529
  loop : -0.68 (0.22), residues: 865

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 144 
 HIS   0.002   0.001   HIS A 143 
 PHE   0.010   0.001   PHE B 274 
 TYR   0.008   0.001   TYR B 344 
 ARG   0.002   0.000   ARG B 119 

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

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

  3022 Ramachandran restraints generated.
    1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3022 Ramachandran restraints generated.
    1511 Oldfield, 0 Emsley, 1511 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 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
  69 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 1.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  445 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.6687 (m-30)
REVERT: A  539 ARG cc_start: 0.7923 (mpp-170) cc_final: 0.6352 (mtp85)
REVERT: A  555 MET cc_start: 0.6540 (mtp) cc_final: 0.6129 (mtt)
REVERT: B  487 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7618 (mmt180)
  outliers start: 14
  outliers final: 7
  residues processed: 65
  average time/residue: 0.3651
  time to fit residues: 34.2113
Evaluate side-chains
  60 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 1.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  445 ASP
Chi-restraints excluded: chain A residue  730 SER
Chi-restraints excluded: chain A residue  826 HIS
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain B residue  400 CYS
Chi-restraints excluded: chain B residue  487 ARG
Chi-restraints excluded: chain B residue  546 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 140 optimal weight:    8.9990
   chunk 59 optimal weight:    9.9990
   chunk 64 optimal weight:   30.0000
   chunk 124 optimal weight:    4.9990
   chunk 96 optimal weight:    8.9990
   chunk 3 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 74 optimal weight:   10.0000
   chunk 136 optimal weight:    5.9990
   chunk 88 optimal weight:   50.0000
   chunk 90 optimal weight:    8.9990
   overall best weight:    5.5990

-------------------------------------------------------------------------------
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**
A 630 ASN
** A 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.123624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.079224 restraints weight = 47467.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.3209 rms_B_bonded: 3.19
r_work: 0.3041 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.2568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.013   0.091  11990  Z= 0.870
  Angle     :  0.880  10.432  16240  Z= 0.456
  Chirality :  0.055   0.210   1784
  Planarity :  0.006   0.127   2146
  Dihedral  :  6.201  39.726   1639
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 35.51
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  9.40 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 11.53 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.46 %
    Cis-general     : 0.00 %
    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: -1.81 (0.21), residues: 1511
  helix: -1.81 (0.42), residues: 116
  sheet: -0.68 (0.22), residues: 531
  loop : -1.45 (0.20), residues: 864

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP A 144 
 HIS   0.010   0.002   HIS A 762 
 PHE   0.032   0.003   PHE A  49 
 TYR   0.025   0.003   TYR A 142 
 ARG   0.005   0.001   ARG B  93 

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

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

  3022 Ramachandran restraints generated.
    1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3022 Ramachandran restraints generated.
    1511 Oldfield, 0 Emsley, 1511 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 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
  93 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 55
  time to evaluate  : 1.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  285 ILE cc_start: 0.9605 (OUTLIER) cc_final: 0.9313 (mm)
REVERT: A  305 TYR cc_start: 0.9044 (OUTLIER) cc_final: 0.8583 (t80)
REVERT: A  445 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7663 (m-30)
REVERT: A  539 ARG cc_start: 0.7938 (mpp-170) cc_final: 0.6732 (mtp85)
  outliers start: 38
  outliers final: 25
  residues processed: 87
  average time/residue: 0.3189
  time to fit residues: 40.6494
Evaluate side-chains
  79 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 51
  time to evaluate  : 1.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  305 TYR
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  445 ASP
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  730 SER
Chi-restraints excluded: chain A residue  826 HIS
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  230 ASN
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain B residue  348 SER
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  400 CYS
Chi-restraints excluded: chain B residue  421 VAL
Chi-restraints excluded: chain B residue  487 ARG
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  546 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 139 optimal weight:    9.9990
   chunk 33 optimal weight:    0.7980
   chunk 116 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 143 optimal weight:    2.9990
   chunk 68 optimal weight:   10.0000
   chunk 126 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 34 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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**
** A 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.127668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.079435 restraints weight = 46648.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 3.14
r_work: 0.3066 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.2435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.081  11990  Z= 0.166
  Angle     :  0.488   7.013  16240  Z= 0.263
  Chirality :  0.043   0.181   1784
  Planarity :  0.004   0.118   2146
  Dihedral  :  4.987  40.078   1639
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 26.99
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.36 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 13.13 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.46 %
    Cis-general     : 0.00 %
    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: -1.18 (0.22), residues: 1511
  helix: -0.84 (0.46), residues: 123
  sheet: -0.35 (0.23), residues: 524
  loop : -1.02 (0.21), residues: 864

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 144 
 HIS   0.003   0.001   HIS A 762 
 PHE   0.009   0.001   PHE B 274 
 TYR   0.009   0.001   TYR B 583 
 ARG   0.002   0.000   ARG A 145 

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

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

  3022 Ramachandran restraints generated.
    1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3022 Ramachandran restraints generated.
    1511 Oldfield, 0 Emsley, 1511 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 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
  66 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 49
  time to evaluate  : 1.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  305 TYR cc_start: 0.8810 (OUTLIER) cc_final: 0.8418 (t80)
REVERT: A  445 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.6917 (m-30)
REVERT: A  539 ARG cc_start: 0.7794 (mpp-170) cc_final: 0.6284 (mtp85)
REVERT: A  555 MET cc_start: 0.6560 (mtp) cc_final: 0.6201 (mtt)
REVERT: B  213 MET cc_start: 0.8750 (tpt) cc_final: 0.8276 (tpt)
REVERT: B  487 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7867 (mmt180)
  outliers start: 17
  outliers final: 10
  residues processed: 62
  average time/residue: 0.3611
  time to fit residues: 32.4329
Evaluate side-chains
  61 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 1.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 TYR
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  305 TYR
Chi-restraints excluded: chain A residue  445 ASP
Chi-restraints excluded: chain A residue  730 SER
Chi-restraints excluded: chain A residue  826 HIS
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain B residue  400 CYS
Chi-restraints excluded: chain B residue  487 ARG
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  546 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 116 optimal weight:    3.9990
   chunk 90 optimal weight:   20.0000
   chunk 9 optimal weight:    2.9990
   chunk 135 optimal weight:    2.9990
   chunk 71 optimal weight:   20.0000
   chunk 134 optimal weight:    3.9990
   chunk 128 optimal weight:    4.9990
   chunk 76 optimal weight:   50.0000
   chunk 125 optimal weight:    2.9990
   chunk 131 optimal weight:    3.9990
   chunk 101 optimal weight:    0.9980
   overall best weight:    2.7988

-------------------------------------------------------------------------------
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**
** A 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.125272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.076869 restraints weight = 46703.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 3.16
r_work: 0.3009 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.2637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.066  11990  Z= 0.458
  Angle     :  0.606   7.192  16240  Z= 0.319
  Chirality :  0.046   0.167   1784
  Planarity :  0.005   0.119   2146
  Dihedral  :  5.296  40.336   1639
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 30.92
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.60 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 13.74 %
    Favored  : 84.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.46 %
    Cis-general     : 0.00 %
    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: -1.42 (0.22), residues: 1511
  helix: -1.07 (0.45), residues: 123
  sheet: -0.49 (0.23), residues: 527
  loop : -1.19 (0.21), residues: 861

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 144 
 HIS   0.004   0.001   HIS B 472 
 PHE   0.019   0.002   PHE A  49 
 TYR   0.016   0.002   TYR A 142 
 ARG   0.002   0.000   ARG A 540 

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

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

  3022 Ramachandran restraints generated.
    1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3022 Ramachandran restraints generated.
    1511 Oldfield, 0 Emsley, 1511 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 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 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 50
  time to evaluate  : 1.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  305 TYR cc_start: 0.8932 (OUTLIER) cc_final: 0.8517 (t80)
REVERT: A  445 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7507 (m-30)
REVERT: A  539 ARG cc_start: 0.7820 (mpp-170) cc_final: 0.6405 (mtp85)
REVERT: A  555 MET cc_start: 0.6663 (mtp) cc_final: 0.6268 (mtt)
REVERT: B  487 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7878 (mmt180)
  outliers start: 25
  outliers final: 18
  residues processed: 70
  average time/residue: 0.3427
  time to fit residues: 35.7730
Evaluate side-chains
  68 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 47
  time to evaluate  : 1.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 TYR
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  305 TYR
Chi-restraints excluded: chain A residue  445 ASP
Chi-restraints excluded: chain A residue  509 LEU
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  730 SER
Chi-restraints excluded: chain A residue  825 LEU
Chi-restraints excluded: chain A residue  826 HIS
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain B residue  348 SER
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  382 GLU
Chi-restraints excluded: chain B residue  400 CYS
Chi-restraints excluded: chain B residue  487 ARG
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  546 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 81 optimal weight:   40.0000
   chunk 16 optimal weight:    0.7980
   chunk 134 optimal weight:    3.9990
   chunk 40 optimal weight:    0.6980
   chunk 128 optimal weight:    1.9990
   chunk 67 optimal weight:    9.9990
   chunk 98 optimal weight:    6.9990
   chunk 129 optimal weight:    0.1980
   chunk 44 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0970
   chunk 121 optimal weight:    1.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.127938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.079717 restraints weight = 46504.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 3.16
r_work: 0.3068 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.2710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.081  11990  Z= 0.162
  Angle     :  0.454   6.371  16240  Z= 0.244
  Chirality :  0.043   0.175   1784
  Planarity :  0.004   0.114   2146
  Dihedral  :  4.611  41.120   1639
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 28.20
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.77 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 14.43 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.46 %
    Cis-general     : 0.00 %
    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: -1.04 (0.22), residues: 1511
  helix: -0.58 (0.47), residues: 122
  sheet: -0.25 (0.23), residues: 530
  loop : -0.96 (0.22), residues: 859

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 144 
 HIS   0.002   0.000   HIS B 218 
 PHE   0.007   0.001   PHE B 274 
 TYR   0.008   0.001   TYR B 583 
 ARG   0.002   0.000   ARG B 515 

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

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

  3022 Ramachandran restraints generated.
    1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3022 Ramachandran restraints generated.
    1511 Oldfield, 0 Emsley, 1511 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 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
  65 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 47
  time to evaluate  : 1.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  445 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.6648 (m-30)
REVERT: A  555 MET cc_start: 0.6491 (mtp) cc_final: 0.6139 (mtt)
REVERT: B  213 MET cc_start: 0.8733 (tpt) cc_final: 0.8288 (tpt)
REVERT: B  487 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7751 (mmt180)
  outliers start: 18
  outliers final: 13
  residues processed: 63
  average time/residue: 0.2996
  time to fit residues: 28.9458
Evaluate side-chains
  62 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 47
  time to evaluate  : 1.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 TYR
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  438 MET
Chi-restraints excluded: chain A residue  445 ASP
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  730 SER
Chi-restraints excluded: chain A residue  825 LEU
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain B residue  400 CYS
Chi-restraints excluded: chain B residue  487 ARG
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  546 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 84 optimal weight:    8.9990
   chunk 50 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 147 optimal weight:   30.0000
   chunk 21 optimal weight:    0.3980
   chunk 136 optimal weight:    9.9990
   chunk 96 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.9986

-------------------------------------------------------------------------------
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**
** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.127646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.079348 restraints weight = 46368.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 3.31
r_work: 0.3063 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.2780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076  11990  Z= 0.195
  Angle     :  0.458   6.007  16240  Z= 0.244
  Chirality :  0.043   0.173   1784
  Planarity :  0.004   0.112   2146
  Dihedral  :  4.447  40.819   1639
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 28.16
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.29 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 14.12 %
    Favored  : 84.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.46 %
    Cis-general     : 0.00 %
    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: -0.89 (0.22), residues: 1511
  helix: -0.48 (0.47), residues: 122
  sheet: -0.14 (0.23), residues: 531
  loop : -0.87 (0.22), residues: 858

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 144 
 HIS   0.002   0.000   HIS A 143 
 PHE   0.009   0.001   PHE A  49 
 TYR   0.008   0.001   TYR A 142 
 ARG   0.002   0.000   ARG B 119 

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

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

  3022 Ramachandran restraints generated.
    1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3022 Ramachandran restraints generated.
    1511 Oldfield, 0 Emsley, 1511 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 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
  68 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 47
  time to evaluate  : 1.625 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  445 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7092 (m-30)
REVERT: B  487 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7752 (mmt180)
  outliers start: 21
  outliers final: 16
  residues processed: 65
  average time/residue: 0.2980
  time to fit residues: 29.8372
Evaluate side-chains
  65 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 47
  time to evaluate  : 1.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  438 MET
Chi-restraints excluded: chain A residue  445 ASP
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  612 THR
Chi-restraints excluded: chain A residue  730 SER
Chi-restraints excluded: chain A residue  825 LEU
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  257 VAL
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain B residue  400 CYS
Chi-restraints excluded: chain B residue  487 ARG
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  546 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 59 optimal weight:    5.9990
   chunk 113 optimal weight:    5.9990
   chunk 97 optimal weight:   10.0000
   chunk 87 optimal weight:   30.0000
   chunk 81 optimal weight:    5.9990
   chunk 135 optimal weight:    0.9990
   chunk 78 optimal weight:   20.0000
   chunk 14 optimal weight:    3.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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**
** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.125800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.077348 restraints weight = 46554.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 3.20
r_work: 0.3013 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.2935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  11990  Z= 0.418
  Angle     :  0.579   6.431  16240  Z= 0.305
  Chirality :  0.046   0.167   1784
  Planarity :  0.005   0.112   2146
  Dihedral  :  5.015  40.129   1639
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 32.01
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.27 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.82 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.46 %
    Cis-general     : 0.00 %
    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: -1.17 (0.22), residues: 1511
  helix: -0.96 (0.45), residues: 122
  sheet: -0.31 (0.23), residues: 527
  loop : -1.02 (0.22), residues: 862

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 144 
 HIS   0.004   0.001   HIS B 472 
 PHE   0.017   0.002   PHE A  49 
 TYR   0.017   0.001   TYR A 142 
 ARG   0.003   0.000   ARG B 119 

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

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

  3022 Ramachandran restraints generated.
    1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3022 Ramachandran restraints generated.
    1511 Oldfield, 0 Emsley, 1511 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 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
  74 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 48
  time to evaluate  : 1.518 
Fit side-chains
   revert: symmetry clash
REVERT: A  445 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7498 (m-30)
REVERT: B  487 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7802 (mmt180)
  outliers start: 26
  outliers final: 21
  residues processed: 71
  average time/residue: 0.3088
  time to fit residues: 33.8480
Evaluate side-chains
  69 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 46
  time to evaluate  : 1.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  438 MET
Chi-restraints excluded: chain A residue  445 ASP
Chi-restraints excluded: chain A residue  509 LEU
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  612 THR
Chi-restraints excluded: chain A residue  730 SER
Chi-restraints excluded: chain A residue  825 LEU
Chi-restraints excluded: chain A residue  850 MET
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  257 VAL
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  400 CYS
Chi-restraints excluded: chain B residue  487 ARG
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  546 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 99 optimal weight:    4.9990
   chunk 87 optimal weight:   30.0000
   chunk 28 optimal weight:    2.9990
   chunk 131 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 110 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:   10.0000
   overall best weight:    1.5584

-------------------------------------------------------------------------------
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**
** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.126644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.078760 restraints weight = 45937.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 3.00
r_work: 0.3049 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.2993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  11990  Z= 0.267
  Angle     :  0.496   5.724  16240  Z= 0.264
  Chirality :  0.043   0.164   1784
  Planarity :  0.004   0.110   2146
  Dihedral  :  4.713  40.641   1639
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 30.88
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.08 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 14.12 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.46 %
    Cis-general     : 0.00 %
    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: -1.06 (0.22), residues: 1511
  helix: -0.76 (0.46), residues: 122
  sheet: -0.27 (0.23), residues: 529
  loop : -0.94 (0.22), residues: 860

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 144 
 HIS   0.002   0.001   HIS B 472 
 PHE   0.011   0.001   PHE A  49 
 TYR   0.010   0.001   TYR A 142 
 ARG   0.002   0.000   ARG A  95 

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

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

  3022 Ramachandran restraints generated.
    1511 Oldfield, 0 Emsley, 1511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3022 Ramachandran restraints generated.
    1511 Oldfield, 0 Emsley, 1511 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 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
  69 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 47
  time to evaluate  : 1.433 
Fit side-chains
   revert: symmetry clash
REVERT: A  445 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7321 (m-30)
REVERT: B  487 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7828 (mmt180)
  outliers start: 22
  outliers final: 19
  residues processed: 66
  average time/residue: 0.2900
  time to fit residues: 29.2566
Evaluate side-chains
  68 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 47
  time to evaluate  : 1.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  438 MET
Chi-restraints excluded: chain A residue  445 ASP
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  612 THR
Chi-restraints excluded: chain A residue  730 SER
Chi-restraints excluded: chain A residue  825 LEU
Chi-restraints excluded: chain A residue  850 MET
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  257 VAL
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain B residue  400 CYS
Chi-restraints excluded: chain B residue  487 ARG
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  546 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 66 optimal weight:    9.9990
   chunk 42 optimal weight:    2.9990
   chunk 74 optimal weight:    5.9990
   chunk 124 optimal weight:    0.5980
   chunk 70 optimal weight:   10.0000
   chunk 105 optimal weight:    2.9990
   chunk 96 optimal weight:    0.4980
   chunk 55 optimal weight:    0.8980
   chunk 57 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.128212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.080611 restraints weight = 46126.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 3.08
r_work: 0.3087 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.3058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.077  11990  Z= 0.158
  Angle     :  0.434   5.226  16240  Z= 0.232
  Chirality :  0.042   0.172   1784
  Planarity :  0.004   0.106   2146
  Dihedral  :  4.223  41.014   1639
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 29.24
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.56 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 14.27 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.46 %
    Cis-general     : 0.00 %
    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: -0.77 (0.22), residues: 1511
  helix: -0.30 (0.48), residues: 122
  sheet: -0.03 (0.24), residues: 507
  loop : -0.80 (0.22), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 144 
 HIS   0.002   0.000   HIS B 218 
 PHE   0.009   0.001   PHE B 274 
 TYR   0.007   0.001   TYR B 344 
 ARG   0.001   0.000   ARG B 119 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10318.27 seconds
wall clock time: 184 minutes 28.07 seconds (11068.07 seconds total)