Starting phenix.real_space_refine
on Mon Jan 20 13:29:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xei_38290/01_2025/8xei_38290_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xei_38290/01_2025/8xei_38290.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xei_38290/01_2025/8xei_38290.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xei_38290/01_2025/8xei_38290.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xei_38290/01_2025/8xei_38290_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xei_38290/01_2025/8xei_38290_neut.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S     104      5.16       5
     C    7744      2.51       5
     N    2107      2.21       5
     O    2436      1.98       5
     H    2751      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 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: 15142
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 916, 8704
          Classifications: {'peptide': 916}
          Link IDs: {'PCIS': 3, 'PTRANS': 41, 'TRANS': 871}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 6438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 684, 6438
          Classifications: {'peptide': 684}
          Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 651}
  Time building chain proxies: 10.00, per 1000 atoms: 0.66
  Number of scatterers: 15142
  At special positions: 0
  Unit cell: (98.34, 119.46, 133.98, 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     104     16.00
     O    2436      8.00
     N    2107      7.00
     C    7744      6.00
     H    2751      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=36, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  89 " - pdb=" SG  CYS A  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 138 " - pdb=" SG  CYS A 158 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 172 " - pdb=" SG  CYS A 185 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 491 " - pdb=" SG  CYS A 502 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 508 " - pdb=" SG  CYS A 565 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 626 " - pdb=" SG  CYS A 632 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 698 " - pdb=" SG  CYS A 711 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 852 " - pdb=" SG  CYS A 914 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 904 " - pdb=" SG  CYS A 909 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  31 " - pdb=" SG  CYS B  49 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  39 " - pdb=" SG  CYS B 461 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  42 " - pdb=" SG  CYS B  64 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  52 " - pdb=" SG  CYS B  75 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 203 " - pdb=" SG  CYS B 210 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 258 " - pdb=" SG  CYS B 299 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 400 " - pdb=" SG  CYS B 412 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 432 " - pdb=" SG  CYS B 459 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 463 " - pdb=" SG  CYS B 483 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 474 " - pdb=" SG  CYS B 486 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 488 " - pdb=" SG  CYS B 497 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 499 " - pdb=" SG  CYS B 529 " 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
    Simple disulfide: pdb=" SG  CYS B 627 " - pdb=" SG  CYS B 630 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 634 " - pdb=" SG  CYS B 681 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 640 " - pdb=" SG  CYS B 661 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 643 " - pdb=" SG  CYS B 657 " 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: 3.75
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2956

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 30 sheets defined
      15.3% alpha, 29.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 205 through 210
    Processing helix  chain 'A' and resid 218 through 224
    Processing helix  chain 'A' and resid 244 through 248
    Processing helix  chain 'A' and resid 275 through 280
    Processing helix  chain 'A' and resid 335 through 337
      No H-bonds generated for 'chain 'A' and resid 335 through 337'
    Processing helix  chain 'A' and resid 574 through 578
      removed outlier: 3.730A  pdb=" N   PHE A 578 " --> pdb=" O   GLU A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 599
      removed outlier: 3.764A  pdb=" N   ALA A 598 " --> pdb=" O   ASP A 594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 798 through 803
      removed outlier: 3.542A  pdb=" N   VAL A 802 " --> pdb=" O   THR A 798 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 934 through 945
    Processing helix  chain 'B' and resid 30 through 35
      removed outlier: 3.516A  pdb=" N   ARG B  34 " --> pdb=" O   ILE B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 44
    Processing helix  chain 'B' and resid 66 through 71
    Processing helix  chain 'B' and resid 72 through 74
      No H-bonds generated for 'chain 'B' and resid 72 through 74'
    Processing helix  chain 'B' and resid 76 through 78
      No H-bonds generated for 'chain 'B' and resid 76 through 78'
    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
      removed outlier: 3.664A  pdb=" N   TRP B 155 " --> pdb=" O   LYS B 151 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   SER B 156 " --> pdb=" O   ASP B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 169
    Processing helix  chain 'B' and resid 195 through 201
      removed outlier: 3.861A  pdb=" N   LEU B 199 " --> pdb=" O   PRO B 195 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   GLU B 200 " --> pdb=" O   PRO B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 205
      removed outlier: 4.455A  pdb=" N   ASP B 205 " --> pdb=" O   PRO B 202 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 202 through 205'
    Processing helix  chain 'B' and resid 226 through 235
      removed outlier: 3.900A  pdb=" N   ASN B 230 " --> pdb=" O   VAL B 226 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LYS B 235 " --> pdb=" O   GLU B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 258
      removed outlier: 3.546A  pdb=" N   ALA B 251 " --> pdb=" O   GLY B 247 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   GLN B 254 " --> pdb=" O   ASP B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 263
    Processing helix  chain 'B' and resid 285 through 290
    Processing helix  chain 'B' and resid 307 through 312
      removed outlier: 4.344A  pdb=" N   THR B 311 " --> pdb=" O   SER B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 329
    Processing helix  chain 'B' and resid 340 through 350
      removed outlier: 3.782A  pdb=" N   LEU B 350 " --> pdb=" O   ASN B 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 379
    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 467
    Processing helix  chain 'B' and resid 494 through 498
    Processing helix  chain 'B' and resid 590 through 594
    Processing helix  chain 'B' and resid 599 through 603
      removed outlier: 3.515A  pdb=" N   SER B 602 " --> pdb=" O   LEU B 599 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 632 through 646
      removed outlier: 3.890A  pdb=" N   PHE B 636 " --> pdb=" O   ASP B 632 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LYS B 637 " --> pdb=" O   ALA B 633 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLU B 639 " --> pdb=" O   THR B 635 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   CYS B 640 " --> pdb=" O   PHE B 636 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 649 through 654
    Processing helix  chain 'B' and resid 656 through 661
      removed outlier: 3.673A  pdb=" N   TYR B 660 " --> pdb=" O   THR B 656 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 42
      removed outlier: 6.142A  pdb=" N   ASP A 451 " --> pdb=" O   ALA A 441 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ALA A 441 " --> pdb=" O   ASP A 451 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56
    Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 111
      removed outlier: 6.929A  pdb=" N   ASP A 114 " --> pdb=" O   TYR A 110 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 118
      removed outlier: 3.709A  pdb=" N   HIS A 143 " --> pdb=" O   PHE A 118 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 131
    Processing sheet with id=AA6, first strand: chain 'A' and resid 190 through 193
      removed outlier: 3.695A  pdb=" N   SER A 190 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 256 through 259
      removed outlier: 6.401A  pdb=" N   VAL A 283 " --> pdb=" O   ASN A 296 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   ASN A 296 " --> pdb=" O   VAL A 283 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   ILE A 285 " --> pdb=" O   LEU A 294 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 310 through 313
    Processing sheet with id=AA9, first strand: chain 'A' and resid 331 through 333
    Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 378
      removed outlier: 6.587A  pdb=" N   ILE A 374 " --> pdb=" O   ALA A 391 " (cutoff:3.500A)
      removed outlier: 7.560A  pdb=" N   ALA A 391 " --> pdb=" O   ILE A 374 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   ALA A 389 " --> pdb=" O   PRO A 376 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   GLY A 378 " --> pdb=" O   ASP A 387 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   GLN A 419 " --> pdb=" O   ILE A 405 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 408 through 409
    Processing sheet with id=AB3, first strand: chain 'A' and resid 541 through 543
    Processing sheet with id=AB4, first strand: chain 'A' and resid 483 through 484
    Processing sheet with id=AB5, first strand: chain 'A' and resid 491 through 492
    Processing sheet with id=AB6, first strand: chain 'A' and resid 636 through 641
      removed outlier: 7.381A  pdb=" N   GLY A 726 " --> pdb=" O   VAL A 686 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   VAL A 686 " --> pdb=" O   GLY A 726 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   ARG A 728 " --> pdb=" O   ILE A 684 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 646 through 648
      removed outlier: 3.635A  pdb=" N   VAL A 760 " --> pdb=" O   LEU A 745 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   ALA A 671 " --> pdb=" O   LEU A 713 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 772 through 779
      removed outlier: 3.627A  pdb=" N   LYS A 930 " --> pdb=" O   HIS A 843 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   HIS A 843 " --> pdb=" O   LYS A 930 " (cutoff:3.500A)
      removed outlier: 5.685A  pdb=" N   LEU A 932 " --> pdb=" O   ILE A 841 " (cutoff:3.500A)
      removed outlier: 5.524A  pdb=" N   ILE A 841 " --> pdb=" O   LEU A 932 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 782 through 784
      removed outlier: 3.965A  pdb=" N   ASN A 973 " --> pdb=" O   PHE A 956 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LEU A 950 " --> pdb=" O   THR A 979 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   TYR A 948 " --> pdb=" O   VAL A 981 " (cutoff:3.500A)
      removed outlier: 13.133A  pdb=" N   SER A 949 " --> pdb=" O   LYS A 832 " (cutoff:3.500A)
      removed outlier: 12.767A  pdb=" N   LYS A 832 " --> pdb=" O   SER A 949 " (cutoff:3.500A)
      removed outlier: 7.883A  pdb=" N   LYS A 951 " --> pdb=" O   PRO A 830 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   LYS A 822 " --> pdb=" O   ILE A 959 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   GLN A 908 " --> pdb=" O   TYR A 831 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 64 through 65
    Processing sheet with id=AC2, first strand: chain 'B' and resid 86 through 91
      removed outlier: 6.565A  pdb=" N   ARG B 113 " --> pdb=" O   LEU B  90 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 109 through 110
    Processing sheet with id=AC4, first strand: chain 'B' and resid 216 through 223
      removed outlier: 7.070A  pdb=" N   VAL B 219 " --> pdb=" O   ALA B 181 " (cutoff:3.500A)
      removed outlier: 8.628A  pdb=" N   ALA B 181 " --> pdb=" O   VAL B 219 " (cutoff:3.500A)
      removed outlier: 5.381A  pdb=" N   THR B 221 " --> pdb=" O   PHE B 179 " (cutoff:3.500A)
      removed outlier: 5.821A  pdb=" N   PHE B 179 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   HIS B 270 " --> pdb=" O   ASN B 331 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   ILE B 333 " --> pdb=" O   HIS B 270 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   LEU B 272 " --> pdb=" O   ILE B 333 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   ALA B 335 " --> pdb=" O   LEU B 272 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   PHE B 274 " --> pdb=" O   ALA B 335 " (cutoff:3.500A)
      removed outlier: 7.770A  pdb=" N   THR B 337 " --> pdb=" O   PHE B 274 " (cutoff:3.500A)
      removed outlier: 8.119A  pdb=" N   THR B 276 " --> pdb=" O   THR B 337 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 468 through 469
    Processing sheet with id=AC6, first strand: chain 'B' and resid 492 through 493
    Processing sheet with id=AC7, first strand: chain 'B' and resid 525 through 528
    Processing sheet with id=AC8, first strand: chain 'B' and resid 542 through 543
    Processing sheet with id=AC9, first strand: chain 'B' and resid 566 through 569
    Processing sheet with id=AD1, first strand: chain 'B' and resid 605 through 606
    Processing sheet with id=AD2, first strand: chain 'B' and resid 664 through 668
    Processing sheet with id=AD3, first strand: chain 'B' and resid 681 through 684

    418 hydrogen bonds defined for protein.
    1101 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 6.32

  Time building geometry restraints manager: 4.37 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 2751
        1.03 -     1.23: 55
        1.23 -     1.42: 5254
        1.42 -     1.62: 7196
        1.62 -     1.82: 135
  Bond restraints: 15391
  Sorted by residual:
  bond pdb=" NZ  LYS A 399 "
       pdb=" HZ1 LYS A 399 "
    ideal  model  delta    sigma   weight residual
    0.890  0.960 -0.070 2.00e-02 2.50e+03 1.24e+01
  bond pdb=" NZ  LYS A 399 "
       pdb=" HZ3 LYS A 399 "
    ideal  model  delta    sigma   weight residual
    0.890  0.960 -0.070 2.00e-02 2.50e+03 1.22e+01
  bond pdb=" NZ  LYS A 399 "
       pdb=" HZ2 LYS A 399 "
    ideal  model  delta    sigma   weight residual
    0.890  0.959 -0.069 2.00e-02 2.50e+03 1.20e+01
  bond pdb=" N   ASN B  29 "
       pdb=" CA  ASN B  29 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.24e+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 2.70e+00
  ... (remaining 15386 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.78: 21936
        2.78 -     5.56: 110
        5.56 -     8.34: 3
        8.34 -    11.13: 2
       11.13 -    13.91: 1
  Bond angle restraints: 22052
  Sorted by residual:
  angle pdb=" CA  PRO B 189 "
        pdb=" N   PRO B 189 "
        pdb=" CD  PRO B 189 "
      ideal   model   delta    sigma   weight residual
     112.00  107.07    4.93 1.40e+00 5.10e-01 1.24e+01
  angle pdb=" C   SER B 188 "
        pdb=" N   PRO B 189 "
        pdb=" CD  PRO B 189 "
      ideal   model   delta    sigma   weight residual
     125.00  111.09   13.91 4.10e+00 5.95e-02 1.15e+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  122.07   -9.37 3.00e+00 1.11e-01 9.75e+00
  angle pdb=" CB  MET A 824 "
        pdb=" CG  MET A 824 "
        pdb=" SD  MET A 824 "
      ideal   model   delta    sigma   weight residual
     112.70  121.27   -8.57 3.00e+00 1.11e-01 8.17e+00
  angle pdb=" N   HIS B 565 "
        pdb=" CA  HIS B 565 "
        pdb=" C   HIS B 565 "
      ideal   model   delta    sigma   weight residual
     112.97  109.99    2.98 1.06e+00 8.90e-01 7.91e+00
  ... (remaining 22047 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 9093
       17.95 -    35.90: 573
       35.90 -    53.85: 171
       53.85 -    71.80: 40
       71.80 -    89.75: 20
  Dihedral angle restraints: 9897
    sinusoidal: 5246
      harmonic: 4651
  Sorted by residual:
  dihedral pdb=" CB  CYS A 491 "
           pdb=" SG  CYS A 491 "
           pdb=" SG  CYS A 502 "
           pdb=" CB  CYS A 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -173.91   87.91     1      1.00e+01 1.00e-02 9.25e+01
  dihedral pdb=" CB  CYS B  39 "
           pdb=" SG  CYS B  39 "
           pdb=" SG  CYS B 461 "
           pdb=" CB  CYS B 461 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  162.72  -69.72     1      1.00e+01 1.00e-02 6.27e+01
  dihedral pdb=" CA  SER B 188 "
           pdb=" C   SER B 188 "
           pdb=" N   PRO B 189 "
           pdb=" CA  PRO B 189 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -145.67  -34.33     0      5.00e+00 4.00e-02 4.71e+01
  ... (remaining 9894 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1305
       0.037 -    0.074: 386
       0.074 -    0.111: 129
       0.111 -    0.148: 54
       0.148 -    0.185: 1
  Chirality restraints: 1875
  Sorted by residual:
  chirality pdb=" CA  PRO B 189 "
            pdb=" N   PRO B 189 "
            pdb=" C   PRO B 189 "
            pdb=" CB  PRO B 189 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 8.59e-01
  chirality pdb=" CA  ILE A 587 "
            pdb=" N   ILE A 587 "
            pdb=" C   ILE A 587 "
            pdb=" CB  ILE A 587 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.75e-01
  chirality pdb=" CA  ILE B 351 "
            pdb=" N   ILE B 351 "
            pdb=" C   ILE B 351 "
            pdb=" CB  ILE B 351 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.73e-01
  ... (remaining 1872 not shown)

  Planarity restraints: 3786
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 188 "   -0.109 5.00e-02 4.00e+02   1.64e-01 4.33e+01
        pdb=" N   PRO B 189 "    0.284 5.00e-02 4.00e+02
        pdb=" CA  PRO B 189 "   -0.094 5.00e-02 4.00e+02
        pdb=" CD  PRO B 189 "   -0.082 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 556 "    0.201 9.50e-02 1.11e+02   6.73e-02 5.59e+00
        pdb=" NE  ARG B 556 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 556 "    0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 556 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 556 "    0.000 2.00e-02 2.50e+03
        pdb="HH11 ARG B 556 "   -0.002 2.00e-02 2.50e+03
        pdb="HH12 ARG B 556 "   -0.000 2.00e-02 2.50e+03
        pdb="HH21 ARG B 556 "   -0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG B 556 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 816 "   -0.022 5.00e-02 4.00e+02   3.36e-02 1.80e+00
        pdb=" N   PRO A 817 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 817 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 817 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 3783 not shown)

  Histogram of nonbonded interaction distances:
        1.52 -     2.14: 401
        2.14 -     2.75: 9085
        2.75 -     3.37: 25008
        3.37 -     3.98: 34986
        3.98 -     4.60: 50245
  Nonbonded interactions: 119725
  Sorted by model distance:
  nonbonded pdb=" O   ARG B 265 "
            pdb=" HE2 HIS B 270 "
     model   vdw
     1.520 2.450
  nonbonded pdb=" OE1 GLU A 799 "
            pdb=" H   GLU A 799 "
     model   vdw
     1.552 2.450
  nonbonded pdb=" H   ASP A 287 "
            pdb=" O   SER A 292 "
     model   vdw
     1.613 2.450
  nonbonded pdb=" O   LYS A 633 "
            pdb=" H   GLU A 666 "
     model   vdw
     1.614 2.450
  nonbonded pdb=" OD1 ASP B 698 "
            pdb=" HG  SER B 700 "
     model   vdw
     1.615 2.450
  ... (remaining 119720 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:             8.760
  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:             0.400
  Extract box with map and model:          0.710
  Check model and map are aligned:         0.120
  Set scattering table:                    0.150
  Process input model:                     37.170
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   59.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8745
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      :  0.003   0.062  12640  Z= 0.206
  Angle     :  0.594  13.908  17117  Z= 0.330
  Chirality :  0.043   0.185   1875
  Planarity :  0.005   0.164   2265
  Dihedral  : 14.194  89.749   4690
  Min Nonbonded Distance : 1.860

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.14 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 13.36 %
    Favored  : 85.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.58 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.32 %
    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: -0.16 (0.21), residues: 1594
  helix: -0.46 (0.45), residues: 127
  sheet:  0.44 (0.22), residues: 519
  loop : -0.32 (0.21), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 264 
 HIS   0.003   0.001   HIS A 946 
 PHE   0.016   0.001   PHE A 956 
 TYR   0.015   0.001   TYR A 928 
 ARG   0.015   0.000   ARG B 556 

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 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 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   30 is missing expected H atoms. Skipping.
Residue THR   32 is missing expected H atoms. Skipping.
Residue THR   33 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LEU   43 is missing expected H atoms. Skipping.
Residue ALA   44 is missing expected H atoms. Skipping.
Residue VAL   45 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue ALA   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue LEU   59 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ALA   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   84 is missing expected H atoms. Skipping.
Residue ALA   87 is missing expected H atoms. Skipping.
Residue VAL   89 is missing expected H atoms. Skipping.
Residue LEU   90 is missing expected H atoms. Skipping.
Residue LEU   95 is missing expected H atoms. Skipping.
Residue VAL  106 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue VAL  109 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue ALA  115 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue VAL  133 is missing expected H atoms. Skipping.
Residue VAL  138 is missing expected H atoms. Skipping.
Residue ILE  140 is missing expected H atoms. Skipping.
Residue LEU  143 is missing expected H atoms. Skipping.
Residue MET  144 is missing expected H atoms. Skipping.
Residue LEU  146 is missing expected H atoms. Skipping.
Residue MET  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue ILE  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  162 is missing expected H atoms. Skipping.
Residue LEU  164 is missing expected H atoms. Skipping.
Residue ALA  165 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue MET  168 is missing expected H atoms. Skipping.
Residue LEU  171 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  181 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue MET  191 is missing expected H atoms. Skipping.
Residue ILE  193 is missing expected H atoms. Skipping.
Residue ALA  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  206 is missing expected H atoms. Skipping.
Residue THR  208 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue MET  213 is missing expected H atoms. Skipping.
Residue VAL  219 is missing expected H atoms. Skipping.
Residue LEU  220 is missing expected H atoms. Skipping.
Residue THR  221 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue THR  223 is missing expected H atoms. Skipping.
Residue VAL  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue ALA  244 is missing expected H atoms. Skipping.
Residue ALA  251 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue MET  253 is missing expected H atoms. Skipping.
Residue ALA  255 is missing expected H atoms. Skipping.
Residue THR  256 is missing expected H atoms. Skipping.
Residue VAL  257 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ALA  268 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue THR  275 is missing expected H atoms. Skipping.
Residue THR  276 is missing expected H atoms. Skipping.
Residue ALA  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue ILE  282 is missing expected H atoms. Skipping.
Residue ALA  283 is missing expected H atoms. Skipping.
Residue LEU  284 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue ALA  289 is missing expected H atoms. Skipping.
Residue ILE  291 is missing expected H atoms. Skipping.
Residue VAL  292 is missing expected H atoms. Skipping.
Residue VAL  301 is missing expected H atoms. Skipping.
Residue ALA  309 is missing expected H atoms. Skipping.
Residue THR  311 is missing expected H atoms. Skipping.
Residue THR  312 is missing expected H atoms. Skipping.
Residue MET  313 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue LEU  320 is missing expected H atoms. Skipping.
Residue MET  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  325 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue ILE  333 is missing expected H atoms. Skipping.
Residue ALA  335 is missing expected H atoms. Skipping.
Residue VAL  336 is missing expected H atoms. Skipping.
Residue THR  337 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue VAL  341 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  350 is missing expected H atoms. Skipping.
Residue ILE  351 is missing expected H atoms. Skipping.
Residue THR  354 is missing expected H atoms. Skipping.
Residue THR  355 is missing expected H atoms. Skipping.
Residue VAL  356 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue LEU  359 is missing expected H atoms. Skipping.
Residue MET  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue LEU  367 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue VAL  371 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  377 is missing expected H atoms. Skipping.
Residue VAL  381 is missing expected H atoms. Skipping.
Residue LEU  383 is missing expected H atoms. Skipping.
Residue VAL  385 is missing expected H atoms. Skipping.
Residue LEU  388 is missing expected H atoms. Skipping.
Residue LEU  392 is missing expected H atoms. Skipping.
Residue LEU  394 is missing expected H atoms. Skipping.
Residue ALA  398 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue LEU  401 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue ILE  406 is missing expected H atoms. Skipping.
Residue LEU  409 is missing expected H atoms. Skipping.
Residue MET  413 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue ILE  417 is missing expected H atoms. Skipping.
Residue THR  420 is missing expected H atoms. Skipping.
Residue VAL  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  441 is missing expected H atoms. Skipping.
Residue ILE  442 is missing expected H atoms. Skipping.
Residue VAL  445 is missing expected H atoms. Skipping.
Residue LEU  451 is missing expected H atoms. Skipping.
Residue ILE  452 is missing expected H atoms. Skipping.
Residue VAL  453 is missing expected H atoms. Skipping.
Residue VAL  455 is missing expected H atoms. Skipping.
Residue THR  456 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ALA  465 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue THR  480 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue VAL  520 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  542 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Residue VAL  555 is missing expected H atoms. Skipping.
Residue MET  561 is missing expected H atoms. Skipping.
Residue LEU  574 is missing expected H atoms. Skipping.
Residue THR  580 is missing expected H atoms. Skipping.
Residue THR  587 is missing expected H atoms. Skipping.
Residue THR  588 is missing expected H atoms. Skipping.
Residue THR  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue LEU  599 is missing expected H atoms. Skipping.
Residue LEU  600 is missing expected H atoms. Skipping.
Residue VAL  613 is missing expected H atoms. Skipping.
Residue ILE  615 is missing expected H atoms. Skipping.
Residue THR  623 is missing expected H atoms. Skipping.
Residue THR  629 is missing expected H atoms. Skipping.
Residue ALA  633 is missing expected H atoms. Skipping.
Residue THR  635 is missing expected H atoms. Skipping.
Residue VAL  641 is missing expected H atoms. Skipping.
Residue ALA  650 is missing expected H atoms. Skipping.
Residue LEU  651 is missing expected H atoms. Skipping.
Residue THR  656 is missing expected H atoms. Skipping.
Residue ILE  665 is missing expected H atoms. Skipping.
Residue VAL  668 is missing expected H atoms. Skipping.
Residue LEU  671 is missing expected H atoms. Skipping.
Residue THR  674 is missing expected H atoms. Skipping.
Residue ALA  678 is missing expected H atoms. Skipping.
Residue VAL  679 is missing expected H atoms. Skipping.
Residue THR  682 is missing expected H atoms. Skipping.
Residue VAL  690 is missing expected H atoms. Skipping.
Residue VAL  691 is missing expected H atoms. Skipping.
Residue ILE  704 is missing expected H atoms. Skipping.
Residue LEU  705 is missing expected H atoms. Skipping.
Residue VAL  707 is missing expected H atoms. Skipping.
Residue VAL  708 is missing expected H atoms. Skipping.
Evaluate side-chains
  85 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 1.809 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  305 TYR cc_start: 0.9575 (OUTLIER) cc_final: 0.9122 (t80)
REVERT: B  413 MET cc_start: 0.8406 (ptm) cc_final: 0.8127 (ptm)
REVERT: B  434 GLN cc_start: 0.8808 (mp10) cc_final: 0.8556 (mp10)
  outliers start: 9
  outliers final: 6
  residues processed: 84
  average time/residue: 1.2360
  time to fit residues: 117.1321
Evaluate side-chains
  81 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 2.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 TYR
Chi-restraints excluded: chain A residue  338 LYS
Chi-restraints excluded: chain A residue  480 TYR
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  606 LYS
Chi-restraints excluded: chain B residue  619 SER
Chi-restraints excluded: chain B residue  704 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 134 optimal weight:    6.9990
   chunk 120 optimal weight:    1.9990
   chunk 66 optimal weight:    8.9990
   chunk 41 optimal weight:    2.9990
   chunk 81 optimal weight:   10.0000
   chunk 64 optimal weight:    8.9990
   chunk 124 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 75 optimal weight:    6.9990
   chunk 92 optimal weight:    0.8980
   chunk 144 optimal weight:    9.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 652 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 = 0.3802 r_free = 0.3802 target = 0.111945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.066596 restraints weight = 37788.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.2918 rms_B_bonded: 2.53
r_work: 0.2793 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2675 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8794
moved from start:          0.1254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.048  12640  Z= 0.451
  Angle     :  0.586  18.008  17117  Z= 0.310
  Chirality :  0.046   0.191   1875
  Planarity :  0.005   0.173   2265
  Dihedral  :  5.416  56.859   1743
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 14.67
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.71 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 12.56 %
    Favored  : 85.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.58 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.32 %
    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: -0.39 (0.21), residues: 1594
  helix: -0.07 (0.45), residues: 131
  sheet:  0.35 (0.22), residues: 509
  loop : -0.60 (0.20), residues: 954

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 934 
 HIS   0.007   0.001   HIS B 652 
 PHE   0.017   0.002   PHE A 193 
 TYR   0.018   0.002   TYR A 545 
 ARG   0.005   0.000   ARG B 556 

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 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 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   30 is missing expected H atoms. Skipping.
Residue THR   32 is missing expected H atoms. Skipping.
Residue THR   33 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LEU   43 is missing expected H atoms. Skipping.
Residue ALA   44 is missing expected H atoms. Skipping.
Residue VAL   45 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue ALA   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue LEU   59 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ALA   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   84 is missing expected H atoms. Skipping.
Residue ALA   87 is missing expected H atoms. Skipping.
Residue VAL   89 is missing expected H atoms. Skipping.
Residue LEU   90 is missing expected H atoms. Skipping.
Residue LEU   95 is missing expected H atoms. Skipping.
Residue VAL  106 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue VAL  109 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue ALA  115 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue VAL  133 is missing expected H atoms. Skipping.
Residue VAL  138 is missing expected H atoms. Skipping.
Residue ILE  140 is missing expected H atoms. Skipping.
Residue LEU  143 is missing expected H atoms. Skipping.
Residue MET  144 is missing expected H atoms. Skipping.
Residue LEU  146 is missing expected H atoms. Skipping.
Residue MET  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue ILE  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  162 is missing expected H atoms. Skipping.
Residue LEU  164 is missing expected H atoms. Skipping.
Residue ALA  165 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue MET  168 is missing expected H atoms. Skipping.
Residue LEU  171 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  181 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue MET  191 is missing expected H atoms. Skipping.
Residue ILE  193 is missing expected H atoms. Skipping.
Residue ALA  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  206 is missing expected H atoms. Skipping.
Residue THR  208 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue MET  213 is missing expected H atoms. Skipping.
Residue VAL  219 is missing expected H atoms. Skipping.
Residue LEU  220 is missing expected H atoms. Skipping.
Residue THR  221 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue THR  223 is missing expected H atoms. Skipping.
Residue VAL  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue ALA  244 is missing expected H atoms. Skipping.
Residue ALA  251 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue MET  253 is missing expected H atoms. Skipping.
Residue ALA  255 is missing expected H atoms. Skipping.
Residue THR  256 is missing expected H atoms. Skipping.
Residue VAL  257 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ALA  268 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue THR  275 is missing expected H atoms. Skipping.
Residue THR  276 is missing expected H atoms. Skipping.
Residue ALA  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue ILE  282 is missing expected H atoms. Skipping.
Residue ALA  283 is missing expected H atoms. Skipping.
Residue LEU  284 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue ALA  289 is missing expected H atoms. Skipping.
Residue ILE  291 is missing expected H atoms. Skipping.
Residue VAL  292 is missing expected H atoms. Skipping.
Residue VAL  301 is missing expected H atoms. Skipping.
Residue ALA  309 is missing expected H atoms. Skipping.
Residue THR  311 is missing expected H atoms. Skipping.
Residue THR  312 is missing expected H atoms. Skipping.
Residue MET  313 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue LEU  320 is missing expected H atoms. Skipping.
Residue MET  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  325 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue ILE  333 is missing expected H atoms. Skipping.
Residue ALA  335 is missing expected H atoms. Skipping.
Residue VAL  336 is missing expected H atoms. Skipping.
Residue THR  337 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue VAL  341 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  350 is missing expected H atoms. Skipping.
Residue ILE  351 is missing expected H atoms. Skipping.
Residue THR  354 is missing expected H atoms. Skipping.
Residue THR  355 is missing expected H atoms. Skipping.
Residue VAL  356 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue LEU  359 is missing expected H atoms. Skipping.
Residue MET  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue LEU  367 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue VAL  371 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  377 is missing expected H atoms. Skipping.
Residue VAL  381 is missing expected H atoms. Skipping.
Residue LEU  383 is missing expected H atoms. Skipping.
Residue VAL  385 is missing expected H atoms. Skipping.
Residue LEU  388 is missing expected H atoms. Skipping.
Residue LEU  392 is missing expected H atoms. Skipping.
Residue LEU  394 is missing expected H atoms. Skipping.
Residue ALA  398 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue LEU  401 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue ILE  406 is missing expected H atoms. Skipping.
Residue LEU  409 is missing expected H atoms. Skipping.
Residue MET  413 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue ILE  417 is missing expected H atoms. Skipping.
Residue THR  420 is missing expected H atoms. Skipping.
Residue VAL  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  441 is missing expected H atoms. Skipping.
Residue ILE  442 is missing expected H atoms. Skipping.
Residue VAL  445 is missing expected H atoms. Skipping.
Residue LEU  451 is missing expected H atoms. Skipping.
Residue ILE  452 is missing expected H atoms. Skipping.
Residue VAL  453 is missing expected H atoms. Skipping.
Residue VAL  455 is missing expected H atoms. Skipping.
Residue THR  456 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ALA  465 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue THR  480 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue VAL  520 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  542 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Residue VAL  555 is missing expected H atoms. Skipping.
Residue MET  561 is missing expected H atoms. Skipping.
Residue LEU  574 is missing expected H atoms. Skipping.
Residue THR  580 is missing expected H atoms. Skipping.
Residue THR  587 is missing expected H atoms. Skipping.
Residue THR  588 is missing expected H atoms. Skipping.
Residue THR  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue LEU  599 is missing expected H atoms. Skipping.
Residue LEU  600 is missing expected H atoms. Skipping.
Residue VAL  613 is missing expected H atoms. Skipping.
Residue ILE  615 is missing expected H atoms. Skipping.
Residue THR  623 is missing expected H atoms. Skipping.
Residue THR  629 is missing expected H atoms. Skipping.
Residue ALA  633 is missing expected H atoms. Skipping.
Residue THR  635 is missing expected H atoms. Skipping.
Residue VAL  641 is missing expected H atoms. Skipping.
Residue ALA  650 is missing expected H atoms. Skipping.
Residue LEU  651 is missing expected H atoms. Skipping.
Residue THR  656 is missing expected H atoms. Skipping.
Residue ILE  665 is missing expected H atoms. Skipping.
Residue VAL  668 is missing expected H atoms. Skipping.
Residue LEU  671 is missing expected H atoms. Skipping.
Residue THR  674 is missing expected H atoms. Skipping.
Residue ALA  678 is missing expected H atoms. Skipping.
Residue VAL  679 is missing expected H atoms. Skipping.
Residue THR  682 is missing expected H atoms. Skipping.
Residue VAL  690 is missing expected H atoms. Skipping.
Residue VAL  691 is missing expected H atoms. Skipping.
Residue ILE  704 is missing expected H atoms. Skipping.
Residue LEU  705 is missing expected H atoms. Skipping.
Residue VAL  707 is missing expected H atoms. Skipping.
Residue VAL  708 is missing expected H atoms. Skipping.
Evaluate side-chains
  115 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 90
  time to evaluate  : 1.617 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  534 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8335 (mt0)
REVERT: A  775 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7463 (ptm-80)
REVERT: A  825 LEU cc_start: 0.8932 (pp) cc_final: 0.8727 (pp)
REVERT: A  939 MET cc_start: 0.8407 (mmt) cc_final: 0.7212 (tmm)
REVERT: B  338 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8813 (pm20)
REVERT: B  413 MET cc_start: 0.8767 (ptm) cc_final: 0.8477 (ptm)
REVERT: B  436 LYS cc_start: 0.8742 (mmtm) cc_final: 0.8366 (mmpt)
REVERT: B  659 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7989 (tpp80)
REVERT: B  692 ARG cc_start: 0.8482 (mmm-85) cc_final: 0.7999 (mmt180)
  outliers start: 25
  outliers final: 8
  residues processed: 104
  average time/residue: 1.3811
  time to fit residues: 160.2841
Evaluate side-chains
  94 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 1.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  534 GLN
Chi-restraints excluded: chain A residue  641 ASP
Chi-restraints excluded: chain A residue  741 VAL
Chi-restraints excluded: chain A residue  775 ARG
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain B residue  338 GLU
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  561 MET
Chi-restraints excluded: chain B residue  606 LYS
Chi-restraints excluded: chain B residue  657 CYS
Chi-restraints excluded: chain B residue  659 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 155 optimal weight:   10.0000
   chunk 74 optimal weight:    9.9990
   chunk 53 optimal weight:    0.6980
   chunk 110 optimal weight:    1.9990
   chunk 117 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 146 optimal weight:    5.9990
   chunk 63 optimal weight:    7.9990
   chunk 27 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 134 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 652 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 = 0.3794 r_free = 0.3794 target = 0.112660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.067197 restraints weight = 37953.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.2928 rms_B_bonded: 2.57
r_work: 0.2800 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2680 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8771
moved from start:          0.1518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.079  12640  Z= 0.188
  Angle     :  0.472  15.903  17117  Z= 0.249
  Chirality :  0.042   0.212   1875
  Planarity :  0.005   0.167   2265
  Dihedral  :  4.503  37.967   1731
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 15.94
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.08 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 13.07 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.58 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.32 %
    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: -0.21 (0.21), residues: 1594
  helix:  0.24 (0.46), residues: 136
  sheet:  0.42 (0.22), residues: 522
  loop : -0.48 (0.21), residues: 936

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 264 
 HIS   0.007   0.001   HIS B 652 
 PHE   0.012   0.001   PHE A 700 
 TYR   0.010   0.001   TYR B 683 
 ARG   0.003   0.000   ARG B 556 

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 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 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   30 is missing expected H atoms. Skipping.
Residue THR   32 is missing expected H atoms. Skipping.
Residue THR   33 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LEU   43 is missing expected H atoms. Skipping.
Residue ALA   44 is missing expected H atoms. Skipping.
Residue VAL   45 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue ALA   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue LEU   59 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ALA   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   84 is missing expected H atoms. Skipping.
Residue ALA   87 is missing expected H atoms. Skipping.
Residue VAL   89 is missing expected H atoms. Skipping.
Residue LEU   90 is missing expected H atoms. Skipping.
Residue LEU   95 is missing expected H atoms. Skipping.
Residue VAL  106 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue VAL  109 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue ALA  115 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue VAL  133 is missing expected H atoms. Skipping.
Residue VAL  138 is missing expected H atoms. Skipping.
Residue ILE  140 is missing expected H atoms. Skipping.
Residue LEU  143 is missing expected H atoms. Skipping.
Residue MET  144 is missing expected H atoms. Skipping.
Residue LEU  146 is missing expected H atoms. Skipping.
Residue MET  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue ILE  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  162 is missing expected H atoms. Skipping.
Residue LEU  164 is missing expected H atoms. Skipping.
Residue ALA  165 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue MET  168 is missing expected H atoms. Skipping.
Residue LEU  171 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  181 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue MET  191 is missing expected H atoms. Skipping.
Residue ILE  193 is missing expected H atoms. Skipping.
Residue ALA  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  206 is missing expected H atoms. Skipping.
Residue THR  208 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue MET  213 is missing expected H atoms. Skipping.
Residue VAL  219 is missing expected H atoms. Skipping.
Residue LEU  220 is missing expected H atoms. Skipping.
Residue THR  221 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue THR  223 is missing expected H atoms. Skipping.
Residue VAL  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue ALA  244 is missing expected H atoms. Skipping.
Residue ALA  251 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue MET  253 is missing expected H atoms. Skipping.
Residue ALA  255 is missing expected H atoms. Skipping.
Residue THR  256 is missing expected H atoms. Skipping.
Residue VAL  257 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ALA  268 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue THR  275 is missing expected H atoms. Skipping.
Residue THR  276 is missing expected H atoms. Skipping.
Residue ALA  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue ILE  282 is missing expected H atoms. Skipping.
Residue ALA  283 is missing expected H atoms. Skipping.
Residue LEU  284 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue ALA  289 is missing expected H atoms. Skipping.
Residue ILE  291 is missing expected H atoms. Skipping.
Residue VAL  292 is missing expected H atoms. Skipping.
Residue VAL  301 is missing expected H atoms. Skipping.
Residue ALA  309 is missing expected H atoms. Skipping.
Residue THR  311 is missing expected H atoms. Skipping.
Residue THR  312 is missing expected H atoms. Skipping.
Residue MET  313 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue LEU  320 is missing expected H atoms. Skipping.
Residue MET  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  325 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue ILE  333 is missing expected H atoms. Skipping.
Residue ALA  335 is missing expected H atoms. Skipping.
Residue VAL  336 is missing expected H atoms. Skipping.
Residue THR  337 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue VAL  341 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  350 is missing expected H atoms. Skipping.
Residue ILE  351 is missing expected H atoms. Skipping.
Residue THR  354 is missing expected H atoms. Skipping.
Residue THR  355 is missing expected H atoms. Skipping.
Residue VAL  356 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue LEU  359 is missing expected H atoms. Skipping.
Residue MET  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue LEU  367 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue VAL  371 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  377 is missing expected H atoms. Skipping.
Residue VAL  381 is missing expected H atoms. Skipping.
Residue LEU  383 is missing expected H atoms. Skipping.
Residue VAL  385 is missing expected H atoms. Skipping.
Residue LEU  388 is missing expected H atoms. Skipping.
Residue LEU  392 is missing expected H atoms. Skipping.
Residue LEU  394 is missing expected H atoms. Skipping.
Residue ALA  398 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue LEU  401 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue ILE  406 is missing expected H atoms. Skipping.
Residue LEU  409 is missing expected H atoms. Skipping.
Residue MET  413 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue ILE  417 is missing expected H atoms. Skipping.
Residue THR  420 is missing expected H atoms. Skipping.
Residue VAL  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  441 is missing expected H atoms. Skipping.
Residue ILE  442 is missing expected H atoms. Skipping.
Residue VAL  445 is missing expected H atoms. Skipping.
Residue LEU  451 is missing expected H atoms. Skipping.
Residue ILE  452 is missing expected H atoms. Skipping.
Residue VAL  453 is missing expected H atoms. Skipping.
Residue VAL  455 is missing expected H atoms. Skipping.
Residue THR  456 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ALA  465 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue THR  480 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue VAL  520 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  542 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Residue VAL  555 is missing expected H atoms. Skipping.
Residue MET  561 is missing expected H atoms. Skipping.
Residue LEU  574 is missing expected H atoms. Skipping.
Residue THR  580 is missing expected H atoms. Skipping.
Residue THR  587 is missing expected H atoms. Skipping.
Residue THR  588 is missing expected H atoms. Skipping.
Residue THR  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue LEU  599 is missing expected H atoms. Skipping.
Residue LEU  600 is missing expected H atoms. Skipping.
Residue VAL  613 is missing expected H atoms. Skipping.
Residue ILE  615 is missing expected H atoms. Skipping.
Residue THR  623 is missing expected H atoms. Skipping.
Residue THR  629 is missing expected H atoms. Skipping.
Residue ALA  633 is missing expected H atoms. Skipping.
Residue THR  635 is missing expected H atoms. Skipping.
Residue VAL  641 is missing expected H atoms. Skipping.
Residue ALA  650 is missing expected H atoms. Skipping.
Residue LEU  651 is missing expected H atoms. Skipping.
Residue THR  656 is missing expected H atoms. Skipping.
Residue ILE  665 is missing expected H atoms. Skipping.
Residue VAL  668 is missing expected H atoms. Skipping.
Residue LEU  671 is missing expected H atoms. Skipping.
Residue THR  674 is missing expected H atoms. Skipping.
Residue ALA  678 is missing expected H atoms. Skipping.
Residue VAL  679 is missing expected H atoms. Skipping.
Residue THR  682 is missing expected H atoms. Skipping.
Residue VAL  690 is missing expected H atoms. Skipping.
Residue VAL  691 is missing expected H atoms. Skipping.
Residue ILE  704 is missing expected H atoms. Skipping.
Residue LEU  705 is missing expected H atoms. Skipping.
Residue VAL  707 is missing expected H atoms. Skipping.
Residue VAL  708 is missing expected H atoms. Skipping.
Evaluate side-chains
  109 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 1.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  526 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8251 (mm-30)
REVERT: A  624 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7484 (mm)
REVERT: A  625 ASP cc_start: 0.8596 (m-30) cc_final: 0.8324 (t0)
REVERT: A  939 MET cc_start: 0.8432 (mmt) cc_final: 0.7275 (tmm)
REVERT: B  413 MET cc_start: 0.8722 (ptm) cc_final: 0.8342 (ptm)
REVERT: B  436 LYS cc_start: 0.8735 (mmtm) cc_final: 0.8360 (mmpt)
REVERT: B  659 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7910 (tpp80)
REVERT: B  683 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.7059 (p90)
REVERT: B  692 ARG cc_start: 0.8498 (mmm-85) cc_final: 0.8036 (mmt180)
  outliers start: 22
  outliers final: 6
  residues processed: 101
  average time/residue: 1.4846
  time to fit residues: 165.8024
Evaluate side-chains
  93 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 1.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  561 MET
Chi-restraints excluded: chain B residue  596 SER
Chi-restraints excluded: chain B residue  606 LYS
Chi-restraints excluded: chain B residue  637 LYS
Chi-restraints excluded: chain B residue  659 ARG
Chi-restraints excluded: chain B residue  683 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 104 optimal weight:    2.9990
   chunk 155 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 88 optimal weight:    7.9990
   chunk 149 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   chunk 90 optimal weight:    5.9990
   chunk 140 optimal weight:    9.9990
   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 350 GLN
** A 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.110406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.065598 restraints weight = 37824.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 2.52
r_work: 0.2776 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2658 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8766
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.050  12640  Z= 0.488
  Angle     :  0.579  18.456  17117  Z= 0.301
  Chirality :  0.046   0.187   1875
  Planarity :  0.005   0.175   2265
  Dihedral  :  4.916  38.079   1731
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 19.84
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.90 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 12.85 %
    Favored  : 84.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.58 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.32 %
    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: -0.43 (0.21), residues: 1594
  helix:  0.15 (0.45), residues: 139
  sheet:  0.28 (0.22), residues: 520
  loop : -0.66 (0.20), residues: 935

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 264 
 HIS   0.007   0.001   HIS B 652 
 PHE   0.019   0.002   PHE A 306 
 TYR   0.015   0.002   TYR A 545 
 ARG   0.006   0.000   ARG A 813 

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 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 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   30 is missing expected H atoms. Skipping.
Residue THR   32 is missing expected H atoms. Skipping.
Residue THR   33 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LEU   43 is missing expected H atoms. Skipping.
Residue ALA   44 is missing expected H atoms. Skipping.
Residue VAL   45 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue ALA   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue LEU   59 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ALA   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   84 is missing expected H atoms. Skipping.
Residue ALA   87 is missing expected H atoms. Skipping.
Residue VAL   89 is missing expected H atoms. Skipping.
Residue LEU   90 is missing expected H atoms. Skipping.
Residue LEU   95 is missing expected H atoms. Skipping.
Residue VAL  106 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue VAL  109 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue ALA  115 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue VAL  133 is missing expected H atoms. Skipping.
Residue VAL  138 is missing expected H atoms. Skipping.
Residue ILE  140 is missing expected H atoms. Skipping.
Residue LEU  143 is missing expected H atoms. Skipping.
Residue MET  144 is missing expected H atoms. Skipping.
Residue LEU  146 is missing expected H atoms. Skipping.
Residue MET  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue ILE  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  162 is missing expected H atoms. Skipping.
Residue LEU  164 is missing expected H atoms. Skipping.
Residue ALA  165 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue MET  168 is missing expected H atoms. Skipping.
Residue LEU  171 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  181 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue MET  191 is missing expected H atoms. Skipping.
Residue ILE  193 is missing expected H atoms. Skipping.
Residue ALA  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  206 is missing expected H atoms. Skipping.
Residue THR  208 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue MET  213 is missing expected H atoms. Skipping.
Residue VAL  219 is missing expected H atoms. Skipping.
Residue LEU  220 is missing expected H atoms. Skipping.
Residue THR  221 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue THR  223 is missing expected H atoms. Skipping.
Residue VAL  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue ALA  244 is missing expected H atoms. Skipping.
Residue ALA  251 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue MET  253 is missing expected H atoms. Skipping.
Residue ALA  255 is missing expected H atoms. Skipping.
Residue THR  256 is missing expected H atoms. Skipping.
Residue VAL  257 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ALA  268 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue THR  275 is missing expected H atoms. Skipping.
Residue THR  276 is missing expected H atoms. Skipping.
Residue ALA  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue ILE  282 is missing expected H atoms. Skipping.
Residue ALA  283 is missing expected H atoms. Skipping.
Residue LEU  284 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue ALA  289 is missing expected H atoms. Skipping.
Residue ILE  291 is missing expected H atoms. Skipping.
Residue VAL  292 is missing expected H atoms. Skipping.
Residue VAL  301 is missing expected H atoms. Skipping.
Residue ALA  309 is missing expected H atoms. Skipping.
Residue THR  311 is missing expected H atoms. Skipping.
Residue THR  312 is missing expected H atoms. Skipping.
Residue MET  313 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue LEU  320 is missing expected H atoms. Skipping.
Residue MET  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  325 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue ILE  333 is missing expected H atoms. Skipping.
Residue ALA  335 is missing expected H atoms. Skipping.
Residue VAL  336 is missing expected H atoms. Skipping.
Residue THR  337 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue VAL  341 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  350 is missing expected H atoms. Skipping.
Residue ILE  351 is missing expected H atoms. Skipping.
Residue THR  354 is missing expected H atoms. Skipping.
Residue THR  355 is missing expected H atoms. Skipping.
Residue VAL  356 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue LEU  359 is missing expected H atoms. Skipping.
Residue MET  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue LEU  367 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue VAL  371 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  377 is missing expected H atoms. Skipping.
Residue VAL  381 is missing expected H atoms. Skipping.
Residue LEU  383 is missing expected H atoms. Skipping.
Residue VAL  385 is missing expected H atoms. Skipping.
Residue LEU  388 is missing expected H atoms. Skipping.
Residue LEU  392 is missing expected H atoms. Skipping.
Residue LEU  394 is missing expected H atoms. Skipping.
Residue ALA  398 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue LEU  401 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue ILE  406 is missing expected H atoms. Skipping.
Residue LEU  409 is missing expected H atoms. Skipping.
Residue MET  413 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue ILE  417 is missing expected H atoms. Skipping.
Residue THR  420 is missing expected H atoms. Skipping.
Residue VAL  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  441 is missing expected H atoms. Skipping.
Residue ILE  442 is missing expected H atoms. Skipping.
Residue VAL  445 is missing expected H atoms. Skipping.
Residue LEU  451 is missing expected H atoms. Skipping.
Residue ILE  452 is missing expected H atoms. Skipping.
Residue VAL  453 is missing expected H atoms. Skipping.
Residue VAL  455 is missing expected H atoms. Skipping.
Residue THR  456 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ALA  465 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue THR  480 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue VAL  520 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  542 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Residue VAL  555 is missing expected H atoms. Skipping.
Residue MET  561 is missing expected H atoms. Skipping.
Residue LEU  574 is missing expected H atoms. Skipping.
Residue THR  580 is missing expected H atoms. Skipping.
Residue THR  587 is missing expected H atoms. Skipping.
Residue THR  588 is missing expected H atoms. Skipping.
Residue THR  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue LEU  599 is missing expected H atoms. Skipping.
Residue LEU  600 is missing expected H atoms. Skipping.
Residue VAL  613 is missing expected H atoms. Skipping.
Residue ILE  615 is missing expected H atoms. Skipping.
Residue THR  623 is missing expected H atoms. Skipping.
Residue THR  629 is missing expected H atoms. Skipping.
Residue ALA  633 is missing expected H atoms. Skipping.
Residue THR  635 is missing expected H atoms. Skipping.
Residue VAL  641 is missing expected H atoms. Skipping.
Residue ALA  650 is missing expected H atoms. Skipping.
Residue LEU  651 is missing expected H atoms. Skipping.
Residue THR  656 is missing expected H atoms. Skipping.
Residue ILE  665 is missing expected H atoms. Skipping.
Residue VAL  668 is missing expected H atoms. Skipping.
Residue LEU  671 is missing expected H atoms. Skipping.
Residue THR  674 is missing expected H atoms. Skipping.
Residue ALA  678 is missing expected H atoms. Skipping.
Residue VAL  679 is missing expected H atoms. Skipping.
Residue THR  682 is missing expected H atoms. Skipping.
Residue VAL  690 is missing expected H atoms. Skipping.
Residue VAL  691 is missing expected H atoms. Skipping.
Residue ILE  704 is missing expected H atoms. Skipping.
Residue LEU  705 is missing expected H atoms. Skipping.
Residue VAL  707 is missing expected H atoms. Skipping.
Residue VAL  708 is missing expected H atoms. Skipping.
Evaluate side-chains
  115 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 83
  time to evaluate  : 1.494 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  939 MET cc_start: 0.8437 (mmt) cc_final: 0.7359 (tmm)
REVERT: B  338 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8720 (tm-30)
REVERT: B  413 MET cc_start: 0.8785 (ptm) cc_final: 0.8387 (ptm)
REVERT: B  637 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8782 (mmtp)
REVERT: B  657 CYS cc_start: 0.5577 (OUTLIER) cc_final: 0.5321 (p)
  outliers start: 32
  outliers final: 8
  residues processed: 106
  average time/residue: 1.2449
  time to fit residues: 148.0373
Evaluate side-chains
  90 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 1.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  641 ASP
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  338 GLU
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  596 SER
Chi-restraints excluded: chain B residue  637 LYS
Chi-restraints excluded: chain B residue  638 LYS
Chi-restraints excluded: chain B residue  657 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 30 optimal weight:    0.1980
   chunk 24 optimal weight:    0.9990
   chunk 155 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   chunk 144 optimal weight:    8.9990
   chunk 80 optimal weight:    9.9990
   chunk 133 optimal weight:    2.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** A 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 652 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 = 0.3789 r_free = 0.3789 target = 0.112448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.067089 restraints weight = 38308.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 2.58
r_work: 0.2807 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2687 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8759
moved from start:          0.1996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.086  12640  Z= 0.158
  Angle     :  0.466  15.858  17117  Z= 0.243
  Chirality :  0.042   0.213   1875
  Planarity :  0.005   0.168   2265
  Dihedral  :  4.225  30.670   1727
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 19.06
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.33 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 14.30 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.58 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.32 %
    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: -0.21 (0.21), residues: 1594
  helix:  0.43 (0.47), residues: 135
  sheet:  0.45 (0.22), residues: 521
  loop : -0.53 (0.21), residues: 938

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 264 
 HIS   0.006   0.001   HIS B 652 
 PHE   0.013   0.001   PHE A 683 
 TYR   0.009   0.001   TYR B 344 
 ARG   0.007   0.000   ARG B 556 

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 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 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   30 is missing expected H atoms. Skipping.
Residue THR   32 is missing expected H atoms. Skipping.
Residue THR   33 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LEU   43 is missing expected H atoms. Skipping.
Residue ALA   44 is missing expected H atoms. Skipping.
Residue VAL   45 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue ALA   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue LEU   59 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ALA   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   84 is missing expected H atoms. Skipping.
Residue ALA   87 is missing expected H atoms. Skipping.
Residue VAL   89 is missing expected H atoms. Skipping.
Residue LEU   90 is missing expected H atoms. Skipping.
Residue LEU   95 is missing expected H atoms. Skipping.
Residue VAL  106 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue VAL  109 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue ALA  115 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue VAL  133 is missing expected H atoms. Skipping.
Residue VAL  138 is missing expected H atoms. Skipping.
Residue ILE  140 is missing expected H atoms. Skipping.
Residue LEU  143 is missing expected H atoms. Skipping.
Residue MET  144 is missing expected H atoms. Skipping.
Residue LEU  146 is missing expected H atoms. Skipping.
Residue MET  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue ILE  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  162 is missing expected H atoms. Skipping.
Residue LEU  164 is missing expected H atoms. Skipping.
Residue ALA  165 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue MET  168 is missing expected H atoms. Skipping.
Residue LEU  171 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  181 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue MET  191 is missing expected H atoms. Skipping.
Residue ILE  193 is missing expected H atoms. Skipping.
Residue ALA  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  206 is missing expected H atoms. Skipping.
Residue THR  208 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue MET  213 is missing expected H atoms. Skipping.
Residue VAL  219 is missing expected H atoms. Skipping.
Residue LEU  220 is missing expected H atoms. Skipping.
Residue THR  221 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue THR  223 is missing expected H atoms. Skipping.
Residue VAL  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue ALA  244 is missing expected H atoms. Skipping.
Residue ALA  251 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue MET  253 is missing expected H atoms. Skipping.
Residue ALA  255 is missing expected H atoms. Skipping.
Residue THR  256 is missing expected H atoms. Skipping.
Residue VAL  257 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ALA  268 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue THR  275 is missing expected H atoms. Skipping.
Residue THR  276 is missing expected H atoms. Skipping.
Residue ALA  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue ILE  282 is missing expected H atoms. Skipping.
Residue ALA  283 is missing expected H atoms. Skipping.
Residue LEU  284 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue ALA  289 is missing expected H atoms. Skipping.
Residue ILE  291 is missing expected H atoms. Skipping.
Residue VAL  292 is missing expected H atoms. Skipping.
Residue VAL  301 is missing expected H atoms. Skipping.
Residue ALA  309 is missing expected H atoms. Skipping.
Residue THR  311 is missing expected H atoms. Skipping.
Residue THR  312 is missing expected H atoms. Skipping.
Residue MET  313 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue LEU  320 is missing expected H atoms. Skipping.
Residue MET  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  325 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue ILE  333 is missing expected H atoms. Skipping.
Residue ALA  335 is missing expected H atoms. Skipping.
Residue VAL  336 is missing expected H atoms. Skipping.
Residue THR  337 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue VAL  341 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  350 is missing expected H atoms. Skipping.
Residue ILE  351 is missing expected H atoms. Skipping.
Residue THR  354 is missing expected H atoms. Skipping.
Residue THR  355 is missing expected H atoms. Skipping.
Residue VAL  356 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue LEU  359 is missing expected H atoms. Skipping.
Residue MET  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue LEU  367 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue VAL  371 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  377 is missing expected H atoms. Skipping.
Residue VAL  381 is missing expected H atoms. Skipping.
Residue LEU  383 is missing expected H atoms. Skipping.
Residue VAL  385 is missing expected H atoms. Skipping.
Residue LEU  388 is missing expected H atoms. Skipping.
Residue LEU  392 is missing expected H atoms. Skipping.
Residue LEU  394 is missing expected H atoms. Skipping.
Residue ALA  398 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue LEU  401 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue ILE  406 is missing expected H atoms. Skipping.
Residue LEU  409 is missing expected H atoms. Skipping.
Residue MET  413 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue ILE  417 is missing expected H atoms. Skipping.
Residue THR  420 is missing expected H atoms. Skipping.
Residue VAL  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  441 is missing expected H atoms. Skipping.
Residue ILE  442 is missing expected H atoms. Skipping.
Residue VAL  445 is missing expected H atoms. Skipping.
Residue LEU  451 is missing expected H atoms. Skipping.
Residue ILE  452 is missing expected H atoms. Skipping.
Residue VAL  453 is missing expected H atoms. Skipping.
Residue VAL  455 is missing expected H atoms. Skipping.
Residue THR  456 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ALA  465 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue THR  480 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue VAL  520 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  542 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Residue VAL  555 is missing expected H atoms. Skipping.
Residue MET  561 is missing expected H atoms. Skipping.
Residue LEU  574 is missing expected H atoms. Skipping.
Residue THR  580 is missing expected H atoms. Skipping.
Residue THR  587 is missing expected H atoms. Skipping.
Residue THR  588 is missing expected H atoms. Skipping.
Residue THR  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue LEU  599 is missing expected H atoms. Skipping.
Residue LEU  600 is missing expected H atoms. Skipping.
Residue VAL  613 is missing expected H atoms. Skipping.
Residue ILE  615 is missing expected H atoms. Skipping.
Residue THR  623 is missing expected H atoms. Skipping.
Residue THR  629 is missing expected H atoms. Skipping.
Residue ALA  633 is missing expected H atoms. Skipping.
Residue THR  635 is missing expected H atoms. Skipping.
Residue VAL  641 is missing expected H atoms. Skipping.
Residue ALA  650 is missing expected H atoms. Skipping.
Residue LEU  651 is missing expected H atoms. Skipping.
Residue THR  656 is missing expected H atoms. Skipping.
Residue ILE  665 is missing expected H atoms. Skipping.
Residue VAL  668 is missing expected H atoms. Skipping.
Residue LEU  671 is missing expected H atoms. Skipping.
Residue THR  674 is missing expected H atoms. Skipping.
Residue ALA  678 is missing expected H atoms. Skipping.
Residue VAL  679 is missing expected H atoms. Skipping.
Residue THR  682 is missing expected H atoms. Skipping.
Residue VAL  690 is missing expected H atoms. Skipping.
Residue VAL  691 is missing expected H atoms. Skipping.
Residue ILE  704 is missing expected H atoms. Skipping.
Residue LEU  705 is missing expected H atoms. Skipping.
Residue VAL  707 is missing expected H atoms. Skipping.
Residue VAL  708 is missing expected H atoms. Skipping.
Evaluate side-chains
  107 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 84
  time to evaluate  : 1.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  526 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8102 (mm-30)
REVERT: A  625 ASP cc_start: 0.8661 (m-30) cc_final: 0.8340 (t0)
REVERT: A  939 MET cc_start: 0.8474 (mmt) cc_final: 0.7281 (tmm)
REVERT: B  413 MET cc_start: 0.8744 (ptm) cc_final: 0.8386 (ptm)
  outliers start: 23
  outliers final: 11
  residues processed: 100
  average time/residue: 1.2873
  time to fit residues: 145.1185
Evaluate side-chains
  94 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 1.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 TRP
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  589 MET
Chi-restraints excluded: chain A residue  641 ASP
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  637 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 60 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 76 optimal weight:   10.0000
   chunk 19 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 61 optimal weight:    7.9990
   chunk 118 optimal weight:    0.8980
   chunk 77 optimal weight:    8.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 652 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 = 0.3789 r_free = 0.3789 target = 0.111562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.066839 restraints weight = 38043.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 2.53
r_work: 0.2800 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2682 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8744
moved from start:          0.2099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066  12640  Z= 0.306
  Angle     :  0.509  16.552  17117  Z= 0.264
  Chirality :  0.043   0.198   1875
  Planarity :  0.005   0.170   2265
  Dihedral  :  4.351  32.860   1727
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 20.75
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.65 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 14.80 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.58 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.32 %
    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: -0.25 (0.21), residues: 1594
  helix:  0.35 (0.47), residues: 134
  sheet:  0.41 (0.22), residues: 520
  loop : -0.54 (0.21), residues: 940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 264 
 HIS   0.007   0.001   HIS B 652 
 PHE   0.015   0.001   PHE A 306 
 TYR   0.010   0.001   TYR A 545 
 ARG   0.008   0.000   ARG B 556 

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 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 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   30 is missing expected H atoms. Skipping.
Residue THR   32 is missing expected H atoms. Skipping.
Residue THR   33 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LEU   43 is missing expected H atoms. Skipping.
Residue ALA   44 is missing expected H atoms. Skipping.
Residue VAL   45 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue ALA   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue LEU   59 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ALA   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   84 is missing expected H atoms. Skipping.
Residue ALA   87 is missing expected H atoms. Skipping.
Residue VAL   89 is missing expected H atoms. Skipping.
Residue LEU   90 is missing expected H atoms. Skipping.
Residue LEU   95 is missing expected H atoms. Skipping.
Residue VAL  106 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue VAL  109 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue ALA  115 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue VAL  133 is missing expected H atoms. Skipping.
Residue VAL  138 is missing expected H atoms. Skipping.
Residue ILE  140 is missing expected H atoms. Skipping.
Residue LEU  143 is missing expected H atoms. Skipping.
Residue MET  144 is missing expected H atoms. Skipping.
Residue LEU  146 is missing expected H atoms. Skipping.
Residue MET  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue ILE  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  162 is missing expected H atoms. Skipping.
Residue LEU  164 is missing expected H atoms. Skipping.
Residue ALA  165 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue MET  168 is missing expected H atoms. Skipping.
Residue LEU  171 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  181 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue MET  191 is missing expected H atoms. Skipping.
Residue ILE  193 is missing expected H atoms. Skipping.
Residue ALA  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  206 is missing expected H atoms. Skipping.
Residue THR  208 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue MET  213 is missing expected H atoms. Skipping.
Residue VAL  219 is missing expected H atoms. Skipping.
Residue LEU  220 is missing expected H atoms. Skipping.
Residue THR  221 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue THR  223 is missing expected H atoms. Skipping.
Residue VAL  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue ALA  244 is missing expected H atoms. Skipping.
Residue ALA  251 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue MET  253 is missing expected H atoms. Skipping.
Residue ALA  255 is missing expected H atoms. Skipping.
Residue THR  256 is missing expected H atoms. Skipping.
Residue VAL  257 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ALA  268 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue THR  275 is missing expected H atoms. Skipping.
Residue THR  276 is missing expected H atoms. Skipping.
Residue ALA  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue ILE  282 is missing expected H atoms. Skipping.
Residue ALA  283 is missing expected H atoms. Skipping.
Residue LEU  284 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue ALA  289 is missing expected H atoms. Skipping.
Residue ILE  291 is missing expected H atoms. Skipping.
Residue VAL  292 is missing expected H atoms. Skipping.
Residue VAL  301 is missing expected H atoms. Skipping.
Residue ALA  309 is missing expected H atoms. Skipping.
Residue THR  311 is missing expected H atoms. Skipping.
Residue THR  312 is missing expected H atoms. Skipping.
Residue MET  313 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue LEU  320 is missing expected H atoms. Skipping.
Residue MET  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  325 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue ILE  333 is missing expected H atoms. Skipping.
Residue ALA  335 is missing expected H atoms. Skipping.
Residue VAL  336 is missing expected H atoms. Skipping.
Residue THR  337 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue VAL  341 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  350 is missing expected H atoms. Skipping.
Residue ILE  351 is missing expected H atoms. Skipping.
Residue THR  354 is missing expected H atoms. Skipping.
Residue THR  355 is missing expected H atoms. Skipping.
Residue VAL  356 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue LEU  359 is missing expected H atoms. Skipping.
Residue MET  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue LEU  367 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue VAL  371 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  377 is missing expected H atoms. Skipping.
Residue VAL  381 is missing expected H atoms. Skipping.
Residue LEU  383 is missing expected H atoms. Skipping.
Residue VAL  385 is missing expected H atoms. Skipping.
Residue LEU  388 is missing expected H atoms. Skipping.
Residue LEU  392 is missing expected H atoms. Skipping.
Residue LEU  394 is missing expected H atoms. Skipping.
Residue ALA  398 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue LEU  401 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue ILE  406 is missing expected H atoms. Skipping.
Residue LEU  409 is missing expected H atoms. Skipping.
Residue MET  413 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue ILE  417 is missing expected H atoms. Skipping.
Residue THR  420 is missing expected H atoms. Skipping.
Residue VAL  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  441 is missing expected H atoms. Skipping.
Residue ILE  442 is missing expected H atoms. Skipping.
Residue VAL  445 is missing expected H atoms. Skipping.
Residue LEU  451 is missing expected H atoms. Skipping.
Residue ILE  452 is missing expected H atoms. Skipping.
Residue VAL  453 is missing expected H atoms. Skipping.
Residue VAL  455 is missing expected H atoms. Skipping.
Residue THR  456 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ALA  465 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue THR  480 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue VAL  520 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  542 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Residue VAL  555 is missing expected H atoms. Skipping.
Residue MET  561 is missing expected H atoms. Skipping.
Residue LEU  574 is missing expected H atoms. Skipping.
Residue THR  580 is missing expected H atoms. Skipping.
Residue THR  587 is missing expected H atoms. Skipping.
Residue THR  588 is missing expected H atoms. Skipping.
Residue THR  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue LEU  599 is missing expected H atoms. Skipping.
Residue LEU  600 is missing expected H atoms. Skipping.
Residue VAL  613 is missing expected H atoms. Skipping.
Residue ILE  615 is missing expected H atoms. Skipping.
Residue THR  623 is missing expected H atoms. Skipping.
Residue THR  629 is missing expected H atoms. Skipping.
Residue ALA  633 is missing expected H atoms. Skipping.
Residue THR  635 is missing expected H atoms. Skipping.
Residue VAL  641 is missing expected H atoms. Skipping.
Residue ALA  650 is missing expected H atoms. Skipping.
Residue LEU  651 is missing expected H atoms. Skipping.
Residue THR  656 is missing expected H atoms. Skipping.
Residue ILE  665 is missing expected H atoms. Skipping.
Residue VAL  668 is missing expected H atoms. Skipping.
Residue LEU  671 is missing expected H atoms. Skipping.
Residue THR  674 is missing expected H atoms. Skipping.
Residue ALA  678 is missing expected H atoms. Skipping.
Residue VAL  679 is missing expected H atoms. Skipping.
Residue THR  682 is missing expected H atoms. Skipping.
Residue VAL  690 is missing expected H atoms. Skipping.
Residue VAL  691 is missing expected H atoms. Skipping.
Residue ILE  704 is missing expected H atoms. Skipping.
Residue LEU  705 is missing expected H atoms. Skipping.
Residue VAL  707 is missing expected H atoms. Skipping.
Residue VAL  708 is missing expected H atoms. Skipping.
Evaluate side-chains
  110 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 85
  time to evaluate  : 1.611 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  526 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8143 (mm-30)
REVERT: A  939 MET cc_start: 0.8490 (mmt) cc_final: 0.7296 (tmm)
REVERT: B  338 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8787 (pm20)
REVERT: B  413 MET cc_start: 0.8768 (ptm) cc_final: 0.8383 (ptm)
  outliers start: 25
  outliers final: 11
  residues processed: 102
  average time/residue: 1.2746
  time to fit residues: 146.0110
Evaluate side-chains
  94 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 1.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  589 MET
Chi-restraints excluded: chain A residue  641 ASP
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  338 GLU
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  596 SER
Chi-restraints excluded: chain B residue  637 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 104 optimal weight:    1.9990
   chunk 87 optimal weight:   10.0000
   chunk 66 optimal weight:    6.9990
   chunk 140 optimal weight:    8.9990
   chunk 15 optimal weight:    0.4980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 652 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 = 0.3788 r_free = 0.3788 target = 0.112051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.066916 restraints weight = 38197.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.2909 rms_B_bonded: 2.56
r_work: 0.2781 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2661 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8754
moved from start:          0.2213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  12640  Z= 0.253
  Angle     :  0.490  16.240  17117  Z= 0.253
  Chirality :  0.043   0.203   1875
  Planarity :  0.005   0.169   2265
  Dihedral  :  4.228  31.727   1727
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 21.12
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.08 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 15.09 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.58 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.32 %
    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: -0.21 (0.21), residues: 1594
  helix:  0.35 (0.47), residues: 135
  sheet:  0.48 (0.22), residues: 519
  loop : -0.54 (0.21), residues: 940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 264 
 HIS   0.007   0.001   HIS B 652 
 PHE   0.011   0.001   PHE A 193 
 TYR   0.012   0.001   TYR B 683 
 ARG   0.007   0.000   ARG B 556 

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 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 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   30 is missing expected H atoms. Skipping.
Residue THR   32 is missing expected H atoms. Skipping.
Residue THR   33 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LEU   43 is missing expected H atoms. Skipping.
Residue ALA   44 is missing expected H atoms. Skipping.
Residue VAL   45 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue ALA   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue LEU   59 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ALA   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   84 is missing expected H atoms. Skipping.
Residue ALA   87 is missing expected H atoms. Skipping.
Residue VAL   89 is missing expected H atoms. Skipping.
Residue LEU   90 is missing expected H atoms. Skipping.
Residue LEU   95 is missing expected H atoms. Skipping.
Residue VAL  106 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue VAL  109 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue ALA  115 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue VAL  133 is missing expected H atoms. Skipping.
Residue VAL  138 is missing expected H atoms. Skipping.
Residue ILE  140 is missing expected H atoms. Skipping.
Residue LEU  143 is missing expected H atoms. Skipping.
Residue MET  144 is missing expected H atoms. Skipping.
Residue LEU  146 is missing expected H atoms. Skipping.
Residue MET  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue ILE  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  162 is missing expected H atoms. Skipping.
Residue LEU  164 is missing expected H atoms. Skipping.
Residue ALA  165 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue MET  168 is missing expected H atoms. Skipping.
Residue LEU  171 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  181 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue MET  191 is missing expected H atoms. Skipping.
Residue ILE  193 is missing expected H atoms. Skipping.
Residue ALA  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  206 is missing expected H atoms. Skipping.
Residue THR  208 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue MET  213 is missing expected H atoms. Skipping.
Residue VAL  219 is missing expected H atoms. Skipping.
Residue LEU  220 is missing expected H atoms. Skipping.
Residue THR  221 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue THR  223 is missing expected H atoms. Skipping.
Residue VAL  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue ALA  244 is missing expected H atoms. Skipping.
Residue ALA  251 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue MET  253 is missing expected H atoms. Skipping.
Residue ALA  255 is missing expected H atoms. Skipping.
Residue THR  256 is missing expected H atoms. Skipping.
Residue VAL  257 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ALA  268 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue THR  275 is missing expected H atoms. Skipping.
Residue THR  276 is missing expected H atoms. Skipping.
Residue ALA  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue ILE  282 is missing expected H atoms. Skipping.
Residue ALA  283 is missing expected H atoms. Skipping.
Residue LEU  284 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue ALA  289 is missing expected H atoms. Skipping.
Residue ILE  291 is missing expected H atoms. Skipping.
Residue VAL  292 is missing expected H atoms. Skipping.
Residue VAL  301 is missing expected H atoms. Skipping.
Residue ALA  309 is missing expected H atoms. Skipping.
Residue THR  311 is missing expected H atoms. Skipping.
Residue THR  312 is missing expected H atoms. Skipping.
Residue MET  313 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue LEU  320 is missing expected H atoms. Skipping.
Residue MET  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  325 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue ILE  333 is missing expected H atoms. Skipping.
Residue ALA  335 is missing expected H atoms. Skipping.
Residue VAL  336 is missing expected H atoms. Skipping.
Residue THR  337 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue VAL  341 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  350 is missing expected H atoms. Skipping.
Residue ILE  351 is missing expected H atoms. Skipping.
Residue THR  354 is missing expected H atoms. Skipping.
Residue THR  355 is missing expected H atoms. Skipping.
Residue VAL  356 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue LEU  359 is missing expected H atoms. Skipping.
Residue MET  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue LEU  367 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue VAL  371 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  377 is missing expected H atoms. Skipping.
Residue VAL  381 is missing expected H atoms. Skipping.
Residue LEU  383 is missing expected H atoms. Skipping.
Residue VAL  385 is missing expected H atoms. Skipping.
Residue LEU  388 is missing expected H atoms. Skipping.
Residue LEU  392 is missing expected H atoms. Skipping.
Residue LEU  394 is missing expected H atoms. Skipping.
Residue ALA  398 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue LEU  401 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue ILE  406 is missing expected H atoms. Skipping.
Residue LEU  409 is missing expected H atoms. Skipping.
Residue MET  413 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue ILE  417 is missing expected H atoms. Skipping.
Residue THR  420 is missing expected H atoms. Skipping.
Residue VAL  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  441 is missing expected H atoms. Skipping.
Residue ILE  442 is missing expected H atoms. Skipping.
Residue VAL  445 is missing expected H atoms. Skipping.
Residue LEU  451 is missing expected H atoms. Skipping.
Residue ILE  452 is missing expected H atoms. Skipping.
Residue VAL  453 is missing expected H atoms. Skipping.
Residue VAL  455 is missing expected H atoms. Skipping.
Residue THR  456 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ALA  465 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue THR  480 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue VAL  520 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  542 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Residue VAL  555 is missing expected H atoms. Skipping.
Residue MET  561 is missing expected H atoms. Skipping.
Residue LEU  574 is missing expected H atoms. Skipping.
Residue THR  580 is missing expected H atoms. Skipping.
Residue THR  587 is missing expected H atoms. Skipping.
Residue THR  588 is missing expected H atoms. Skipping.
Residue THR  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue LEU  599 is missing expected H atoms. Skipping.
Residue LEU  600 is missing expected H atoms. Skipping.
Residue VAL  613 is missing expected H atoms. Skipping.
Residue ILE  615 is missing expected H atoms. Skipping.
Residue THR  623 is missing expected H atoms. Skipping.
Residue THR  629 is missing expected H atoms. Skipping.
Residue ALA  633 is missing expected H atoms. Skipping.
Residue THR  635 is missing expected H atoms. Skipping.
Residue VAL  641 is missing expected H atoms. Skipping.
Residue ALA  650 is missing expected H atoms. Skipping.
Residue LEU  651 is missing expected H atoms. Skipping.
Residue THR  656 is missing expected H atoms. Skipping.
Residue ILE  665 is missing expected H atoms. Skipping.
Residue VAL  668 is missing expected H atoms. Skipping.
Residue LEU  671 is missing expected H atoms. Skipping.
Residue THR  674 is missing expected H atoms. Skipping.
Residue ALA  678 is missing expected H atoms. Skipping.
Residue VAL  679 is missing expected H atoms. Skipping.
Residue THR  682 is missing expected H atoms. Skipping.
Residue VAL  690 is missing expected H atoms. Skipping.
Residue VAL  691 is missing expected H atoms. Skipping.
Residue ILE  704 is missing expected H atoms. Skipping.
Residue LEU  705 is missing expected H atoms. Skipping.
Residue VAL  707 is missing expected H atoms. Skipping.
Residue VAL  708 is missing expected H atoms. Skipping.
Evaluate side-chains
  108 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 84
  time to evaluate  : 1.565 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  305 TYR cc_start: 0.9578 (OUTLIER) cc_final: 0.9314 (t80)
REVERT: A  526 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8180 (mm-30)
REVERT: A  625 ASP cc_start: 0.8665 (m-30) cc_final: 0.8339 (t0)
REVERT: A  939 MET cc_start: 0.8496 (mmt) cc_final: 0.7303 (tmm)
REVERT: B  413 MET cc_start: 0.8756 (ptm) cc_final: 0.8383 (ptm)
REVERT: B  659 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7442 (ttp80)
  outliers start: 24
  outliers final: 12
  residues processed: 101
  average time/residue: 1.2060
  time to fit residues: 137.2287
Evaluate side-chains
  99 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 1.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 TYR
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  589 MET
Chi-restraints excluded: chain A residue  641 ASP
Chi-restraints excluded: chain A residue  754 ASP
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  561 MET
Chi-restraints excluded: chain B residue  596 SER
Chi-restraints excluded: chain B residue  659 ARG
Chi-restraints excluded: chain B residue  683 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 61 optimal weight:    8.9990
   chunk 133 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 86 optimal weight:    8.9990
   chunk 58 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 93 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9980
   chunk 76 optimal weight:    0.1980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** A 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 475 ASN
** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.112150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.067016 restraints weight = 38002.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.2909 rms_B_bonded: 2.55
r_work: 0.2781 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2661 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8757
moved from start:          0.2306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074  12640  Z= 0.249
  Angle     :  0.487  15.929  17117  Z= 0.251
  Chirality :  0.043   0.199   1875
  Planarity :  0.005   0.168   2265
  Dihedral  :  4.187  31.462   1727
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 21.08
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.40 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 15.31 %
    Favored  : 83.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.58 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.32 %
    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: -0.20 (0.21), residues: 1594
  helix:  0.39 (0.48), residues: 135
  sheet:  0.47 (0.22), residues: 519
  loop : -0.53 (0.21), residues: 940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 264 
 HIS   0.008   0.001   HIS B 652 
 PHE   0.011   0.001   PHE A 306 
 TYR   0.017   0.001   TYR B 695 
 ARG   0.010   0.000   ARG B 556 

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 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 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   30 is missing expected H atoms. Skipping.
Residue THR   32 is missing expected H atoms. Skipping.
Residue THR   33 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LEU   43 is missing expected H atoms. Skipping.
Residue ALA   44 is missing expected H atoms. Skipping.
Residue VAL   45 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue ALA   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue LEU   59 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ALA   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   84 is missing expected H atoms. Skipping.
Residue ALA   87 is missing expected H atoms. Skipping.
Residue VAL   89 is missing expected H atoms. Skipping.
Residue LEU   90 is missing expected H atoms. Skipping.
Residue LEU   95 is missing expected H atoms. Skipping.
Residue VAL  106 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue VAL  109 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue ALA  115 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue VAL  133 is missing expected H atoms. Skipping.
Residue VAL  138 is missing expected H atoms. Skipping.
Residue ILE  140 is missing expected H atoms. Skipping.
Residue LEU  143 is missing expected H atoms. Skipping.
Residue MET  144 is missing expected H atoms. Skipping.
Residue LEU  146 is missing expected H atoms. Skipping.
Residue MET  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue ILE  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  162 is missing expected H atoms. Skipping.
Residue LEU  164 is missing expected H atoms. Skipping.
Residue ALA  165 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue MET  168 is missing expected H atoms. Skipping.
Residue LEU  171 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  181 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue MET  191 is missing expected H atoms. Skipping.
Residue ILE  193 is missing expected H atoms. Skipping.
Residue ALA  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  206 is missing expected H atoms. Skipping.
Residue THR  208 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue MET  213 is missing expected H atoms. Skipping.
Residue VAL  219 is missing expected H atoms. Skipping.
Residue LEU  220 is missing expected H atoms. Skipping.
Residue THR  221 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue THR  223 is missing expected H atoms. Skipping.
Residue VAL  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue ALA  244 is missing expected H atoms. Skipping.
Residue ALA  251 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue MET  253 is missing expected H atoms. Skipping.
Residue ALA  255 is missing expected H atoms. Skipping.
Residue THR  256 is missing expected H atoms. Skipping.
Residue VAL  257 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ALA  268 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue THR  275 is missing expected H atoms. Skipping.
Residue THR  276 is missing expected H atoms. Skipping.
Residue ALA  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue ILE  282 is missing expected H atoms. Skipping.
Residue ALA  283 is missing expected H atoms. Skipping.
Residue LEU  284 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue ALA  289 is missing expected H atoms. Skipping.
Residue ILE  291 is missing expected H atoms. Skipping.
Residue VAL  292 is missing expected H atoms. Skipping.
Residue VAL  301 is missing expected H atoms. Skipping.
Residue ALA  309 is missing expected H atoms. Skipping.
Residue THR  311 is missing expected H atoms. Skipping.
Residue THR  312 is missing expected H atoms. Skipping.
Residue MET  313 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue LEU  320 is missing expected H atoms. Skipping.
Residue MET  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  325 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue ILE  333 is missing expected H atoms. Skipping.
Residue ALA  335 is missing expected H atoms. Skipping.
Residue VAL  336 is missing expected H atoms. Skipping.
Residue THR  337 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue VAL  341 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  350 is missing expected H atoms. Skipping.
Residue ILE  351 is missing expected H atoms. Skipping.
Residue THR  354 is missing expected H atoms. Skipping.
Residue THR  355 is missing expected H atoms. Skipping.
Residue VAL  356 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue LEU  359 is missing expected H atoms. Skipping.
Residue MET  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue LEU  367 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue VAL  371 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  377 is missing expected H atoms. Skipping.
Residue VAL  381 is missing expected H atoms. Skipping.
Residue LEU  383 is missing expected H atoms. Skipping.
Residue VAL  385 is missing expected H atoms. Skipping.
Residue LEU  388 is missing expected H atoms. Skipping.
Residue LEU  392 is missing expected H atoms. Skipping.
Residue LEU  394 is missing expected H atoms. Skipping.
Residue ALA  398 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue LEU  401 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue ILE  406 is missing expected H atoms. Skipping.
Residue LEU  409 is missing expected H atoms. Skipping.
Residue MET  413 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue ILE  417 is missing expected H atoms. Skipping.
Residue THR  420 is missing expected H atoms. Skipping.
Residue VAL  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  441 is missing expected H atoms. Skipping.
Residue ILE  442 is missing expected H atoms. Skipping.
Residue VAL  445 is missing expected H atoms. Skipping.
Residue LEU  451 is missing expected H atoms. Skipping.
Residue ILE  452 is missing expected H atoms. Skipping.
Residue VAL  453 is missing expected H atoms. Skipping.
Residue VAL  455 is missing expected H atoms. Skipping.
Residue THR  456 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ALA  465 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue THR  480 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue VAL  520 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  542 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Residue VAL  555 is missing expected H atoms. Skipping.
Residue MET  561 is missing expected H atoms. Skipping.
Residue LEU  574 is missing expected H atoms. Skipping.
Residue THR  580 is missing expected H atoms. Skipping.
Residue THR  587 is missing expected H atoms. Skipping.
Residue THR  588 is missing expected H atoms. Skipping.
Residue THR  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue LEU  599 is missing expected H atoms. Skipping.
Residue LEU  600 is missing expected H atoms. Skipping.
Residue VAL  613 is missing expected H atoms. Skipping.
Residue ILE  615 is missing expected H atoms. Skipping.
Residue THR  623 is missing expected H atoms. Skipping.
Residue THR  629 is missing expected H atoms. Skipping.
Residue ALA  633 is missing expected H atoms. Skipping.
Residue THR  635 is missing expected H atoms. Skipping.
Residue VAL  641 is missing expected H atoms. Skipping.
Residue ALA  650 is missing expected H atoms. Skipping.
Residue LEU  651 is missing expected H atoms. Skipping.
Residue THR  656 is missing expected H atoms. Skipping.
Residue ILE  665 is missing expected H atoms. Skipping.
Residue VAL  668 is missing expected H atoms. Skipping.
Residue LEU  671 is missing expected H atoms. Skipping.
Residue THR  674 is missing expected H atoms. Skipping.
Residue ALA  678 is missing expected H atoms. Skipping.
Residue VAL  679 is missing expected H atoms. Skipping.
Residue THR  682 is missing expected H atoms. Skipping.
Residue VAL  690 is missing expected H atoms. Skipping.
Residue VAL  691 is missing expected H atoms. Skipping.
Residue ILE  704 is missing expected H atoms. Skipping.
Residue LEU  705 is missing expected H atoms. Skipping.
Residue VAL  707 is missing expected H atoms. Skipping.
Residue VAL  708 is missing expected H atoms. Skipping.
Evaluate side-chains
  109 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 86
  time to evaluate  : 1.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  305 TYR cc_start: 0.9586 (OUTLIER) cc_final: 0.9305 (t80)
REVERT: A  526 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8182 (mm-30)
REVERT: A  624 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7640 (mm)
REVERT: A  625 ASP cc_start: 0.8676 (m-30) cc_final: 0.8327 (t0)
REVERT: A  939 MET cc_start: 0.8496 (mmt) cc_final: 0.7311 (tmm)
REVERT: B  338 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8802 (pm20)
REVERT: B  413 MET cc_start: 0.8778 (ptm) cc_final: 0.8453 (ptm)
REVERT: B  659 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7417 (ttp80)
  outliers start: 23
  outliers final: 16
  residues processed: 101
  average time/residue: 1.2815
  time to fit residues: 145.8549
Evaluate side-chains
  103 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 82
  time to evaluate  : 1.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  305 TYR
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  589 MET
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  641 ASP
Chi-restraints excluded: chain A residue  754 ASP
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  313 MET
Chi-restraints excluded: chain B residue  338 GLU
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  561 MET
Chi-restraints excluded: chain B residue  596 SER
Chi-restraints excluded: chain B residue  658 ASN
Chi-restraints excluded: chain B residue  659 ARG
Chi-restraints excluded: chain B residue  683 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 144 optimal weight:    8.9990
   chunk 43 optimal weight:    1.9990
   chunk 132 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 129 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 843 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 652 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 = 0.3790 r_free = 0.3790 target = 0.112134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.066838 restraints weight = 38068.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.2904 rms_B_bonded: 2.58
r_work: 0.2778 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2657 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8758
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071  12640  Z= 0.265
  Angle     :  0.501  16.019  17117  Z= 0.257
  Chirality :  0.043   0.195   1875
  Planarity :  0.005   0.168   2265
  Dihedral  :  4.258  31.883   1727
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 22.14
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.27 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 15.38 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.58 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.32 %
    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: -0.19 (0.21), residues: 1594
  helix:  0.34 (0.47), residues: 140
  sheet:  0.47 (0.22), residues: 519
  loop : -0.51 (0.21), residues: 935

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 264 
 HIS   0.009   0.001   HIS B 652 
 PHE   0.012   0.001   PHE A 306 
 TYR   0.018   0.001   TYR B 695 
 ARG   0.009   0.000   ARG B 556 

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 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 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   30 is missing expected H atoms. Skipping.
Residue THR   32 is missing expected H atoms. Skipping.
Residue THR   33 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LEU   43 is missing expected H atoms. Skipping.
Residue ALA   44 is missing expected H atoms. Skipping.
Residue VAL   45 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue ALA   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue LEU   59 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ALA   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   84 is missing expected H atoms. Skipping.
Residue ALA   87 is missing expected H atoms. Skipping.
Residue VAL   89 is missing expected H atoms. Skipping.
Residue LEU   90 is missing expected H atoms. Skipping.
Residue LEU   95 is missing expected H atoms. Skipping.
Residue VAL  106 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue VAL  109 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue ALA  115 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue VAL  133 is missing expected H atoms. Skipping.
Residue VAL  138 is missing expected H atoms. Skipping.
Residue ILE  140 is missing expected H atoms. Skipping.
Residue LEU  143 is missing expected H atoms. Skipping.
Residue MET  144 is missing expected H atoms. Skipping.
Residue LEU  146 is missing expected H atoms. Skipping.
Residue MET  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue ILE  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  162 is missing expected H atoms. Skipping.
Residue LEU  164 is missing expected H atoms. Skipping.
Residue ALA  165 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue MET  168 is missing expected H atoms. Skipping.
Residue LEU  171 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  181 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue MET  191 is missing expected H atoms. Skipping.
Residue ILE  193 is missing expected H atoms. Skipping.
Residue ALA  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  206 is missing expected H atoms. Skipping.
Residue THR  208 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue MET  213 is missing expected H atoms. Skipping.
Residue VAL  219 is missing expected H atoms. Skipping.
Residue LEU  220 is missing expected H atoms. Skipping.
Residue THR  221 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue THR  223 is missing expected H atoms. Skipping.
Residue VAL  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue ALA  244 is missing expected H atoms. Skipping.
Residue ALA  251 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue MET  253 is missing expected H atoms. Skipping.
Residue ALA  255 is missing expected H atoms. Skipping.
Residue THR  256 is missing expected H atoms. Skipping.
Residue VAL  257 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ALA  268 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue THR  275 is missing expected H atoms. Skipping.
Residue THR  276 is missing expected H atoms. Skipping.
Residue ALA  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue ILE  282 is missing expected H atoms. Skipping.
Residue ALA  283 is missing expected H atoms. Skipping.
Residue LEU  284 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue ALA  289 is missing expected H atoms. Skipping.
Residue ILE  291 is missing expected H atoms. Skipping.
Residue VAL  292 is missing expected H atoms. Skipping.
Residue VAL  301 is missing expected H atoms. Skipping.
Residue ALA  309 is missing expected H atoms. Skipping.
Residue THR  311 is missing expected H atoms. Skipping.
Residue THR  312 is missing expected H atoms. Skipping.
Residue MET  313 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue LEU  320 is missing expected H atoms. Skipping.
Residue MET  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  325 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue ILE  333 is missing expected H atoms. Skipping.
Residue ALA  335 is missing expected H atoms. Skipping.
Residue VAL  336 is missing expected H atoms. Skipping.
Residue THR  337 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue VAL  341 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  350 is missing expected H atoms. Skipping.
Residue ILE  351 is missing expected H atoms. Skipping.
Residue THR  354 is missing expected H atoms. Skipping.
Residue THR  355 is missing expected H atoms. Skipping.
Residue VAL  356 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue LEU  359 is missing expected H atoms. Skipping.
Residue MET  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue LEU  367 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue VAL  371 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  377 is missing expected H atoms. Skipping.
Residue VAL  381 is missing expected H atoms. Skipping.
Residue LEU  383 is missing expected H atoms. Skipping.
Residue VAL  385 is missing expected H atoms. Skipping.
Residue LEU  388 is missing expected H atoms. Skipping.
Residue LEU  392 is missing expected H atoms. Skipping.
Residue LEU  394 is missing expected H atoms. Skipping.
Residue ALA  398 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue LEU  401 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue ILE  406 is missing expected H atoms. Skipping.
Residue LEU  409 is missing expected H atoms. Skipping.
Residue MET  413 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue ILE  417 is missing expected H atoms. Skipping.
Residue THR  420 is missing expected H atoms. Skipping.
Residue VAL  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  441 is missing expected H atoms. Skipping.
Residue ILE  442 is missing expected H atoms. Skipping.
Residue VAL  445 is missing expected H atoms. Skipping.
Residue LEU  451 is missing expected H atoms. Skipping.
Residue ILE  452 is missing expected H atoms. Skipping.
Residue VAL  453 is missing expected H atoms. Skipping.
Residue VAL  455 is missing expected H atoms. Skipping.
Residue THR  456 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ALA  465 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue THR  480 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue VAL  520 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  542 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Residue VAL  555 is missing expected H atoms. Skipping.
Residue MET  561 is missing expected H atoms. Skipping.
Residue LEU  574 is missing expected H atoms. Skipping.
Residue THR  580 is missing expected H atoms. Skipping.
Residue THR  587 is missing expected H atoms. Skipping.
Residue THR  588 is missing expected H atoms. Skipping.
Residue THR  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue LEU  599 is missing expected H atoms. Skipping.
Residue LEU  600 is missing expected H atoms. Skipping.
Residue VAL  613 is missing expected H atoms. Skipping.
Residue ILE  615 is missing expected H atoms. Skipping.
Residue THR  623 is missing expected H atoms. Skipping.
Residue THR  629 is missing expected H atoms. Skipping.
Residue ALA  633 is missing expected H atoms. Skipping.
Residue THR  635 is missing expected H atoms. Skipping.
Residue VAL  641 is missing expected H atoms. Skipping.
Residue ALA  650 is missing expected H atoms. Skipping.
Residue LEU  651 is missing expected H atoms. Skipping.
Residue THR  656 is missing expected H atoms. Skipping.
Residue ILE  665 is missing expected H atoms. Skipping.
Residue VAL  668 is missing expected H atoms. Skipping.
Residue LEU  671 is missing expected H atoms. Skipping.
Residue THR  674 is missing expected H atoms. Skipping.
Residue ALA  678 is missing expected H atoms. Skipping.
Residue VAL  679 is missing expected H atoms. Skipping.
Residue THR  682 is missing expected H atoms. Skipping.
Residue VAL  690 is missing expected H atoms. Skipping.
Residue VAL  691 is missing expected H atoms. Skipping.
Residue ILE  704 is missing expected H atoms. Skipping.
Residue LEU  705 is missing expected H atoms. Skipping.
Residue VAL  707 is missing expected H atoms. Skipping.
Residue VAL  708 is missing expected H atoms. Skipping.
Evaluate side-chains
  105 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 84
  time to evaluate  : 1.790 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  305 TYR cc_start: 0.9590 (OUTLIER) cc_final: 0.9317 (t80)
REVERT: A  526 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8183 (mm-30)
REVERT: A  624 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7654 (mm)
REVERT: A  625 ASP cc_start: 0.8699 (m-30) cc_final: 0.8340 (t0)
REVERT: A  939 MET cc_start: 0.8477 (mmt) cc_final: 0.7303 (tmm)
REVERT: B  338 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8803 (pm20)
REVERT: B  413 MET cc_start: 0.8770 (ptm) cc_final: 0.8451 (ptm)
REVERT: B  659 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7394 (ttp80)
REVERT: B  695 TYR cc_start: 0.7733 (t80) cc_final: 0.7511 (t80)
  outliers start: 21
  outliers final: 16
  residues processed: 98
  average time/residue: 1.2194
  time to fit residues: 134.7497
Evaluate side-chains
  105 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 84
  time to evaluate  : 1.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  305 TYR
Chi-restraints excluded: chain A residue  338 LYS
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  589 MET
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  641 ASP
Chi-restraints excluded: chain A residue  754 ASP
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  313 MET
Chi-restraints excluded: chain B residue  338 GLU
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  561 MET
Chi-restraints excluded: chain B residue  596 SER
Chi-restraints excluded: chain B residue  659 ARG
Chi-restraints excluded: chain B residue  683 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 129 optimal weight:    0.3980
   chunk 135 optimal weight:    8.9990
   chunk 40 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 93 optimal weight:   10.0000
   chunk 50 optimal weight:    0.0050
   chunk 99 optimal weight:    1.9990
   chunk 123 optimal weight:    0.9990
   chunk 68 optimal weight:    9.9990
   chunk 38 optimal weight:    1.9990
   chunk 102 optimal weight:    1.9990
   overall best weight:    1.0800

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

Flipped N/Q/H residues before XYZ refinement:
** A 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 475 ASN
** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 694 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.112318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.067320 restraints weight = 38193.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.2918 rms_B_bonded: 2.56
r_work: 0.2790 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2671 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8746
moved from start:          0.2447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076  12640  Z= 0.221
  Angle     :  0.487  15.484  17117  Z= 0.251
  Chirality :  0.043   0.199   1875
  Planarity :  0.005   0.166   2265
  Dihedral  :  4.161  30.861   1727
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 22.10
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.27 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 15.67 %
    Favored  : 82.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.58 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.32 %
    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: -0.19 (0.21), residues: 1594
  helix:  0.12 (0.45), residues: 149
  sheet:  0.47 (0.22), residues: 522
  loop : -0.48 (0.21), residues: 923

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 264 
 HIS   0.008   0.001   HIS B 652 
 PHE   0.010   0.001   PHE A 193 
 TYR   0.017   0.001   TYR B 695 
 ARG   0.010   0.000   ARG B 556 

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

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

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3188 Ramachandran restraints generated.
    1594 Oldfield, 0 Emsley, 1594 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 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   30 is missing expected H atoms. Skipping.
Residue THR   32 is missing expected H atoms. Skipping.
Residue THR   33 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue LEU   43 is missing expected H atoms. Skipping.
Residue ALA   44 is missing expected H atoms. Skipping.
Residue VAL   45 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue ALA   56 is missing expected H atoms. Skipping.
Residue LEU   57 is missing expected H atoms. Skipping.
Residue LEU   59 is missing expected H atoms. Skipping.
Residue LEU   66 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ALA   76 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue VAL   84 is missing expected H atoms. Skipping.
Residue ALA   87 is missing expected H atoms. Skipping.
Residue VAL   89 is missing expected H atoms. Skipping.
Residue LEU   90 is missing expected H atoms. Skipping.
Residue LEU   95 is missing expected H atoms. Skipping.
Residue VAL  106 is missing expected H atoms. Skipping.
Residue THR  107 is missing expected H atoms. Skipping.
Residue VAL  109 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue ALA  115 is missing expected H atoms. Skipping.
Residue LEU  116 is missing expected H atoms. Skipping.
Residue LEU  118 is missing expected H atoms. Skipping.
Residue ILE  128 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue VAL  133 is missing expected H atoms. Skipping.
Residue VAL  138 is missing expected H atoms. Skipping.
Residue ILE  140 is missing expected H atoms. Skipping.
Residue LEU  143 is missing expected H atoms. Skipping.
Residue MET  144 is missing expected H atoms. Skipping.
Residue LEU  146 is missing expected H atoms. Skipping.
Residue MET  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue ILE  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue THR  162 is missing expected H atoms. Skipping.
Residue LEU  164 is missing expected H atoms. Skipping.
Residue ALA  165 is missing expected H atoms. Skipping.
Residue THR  166 is missing expected H atoms. Skipping.
Residue MET  168 is missing expected H atoms. Skipping.
Residue LEU  171 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue ILE  177 is missing expected H atoms. Skipping.
Residue ALA  181 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue VAL  187 is missing expected H atoms. Skipping.
Residue MET  191 is missing expected H atoms. Skipping.
Residue ILE  193 is missing expected H atoms. Skipping.
Residue ALA  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  206 is missing expected H atoms. Skipping.
Residue THR  208 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Residue LEU  211 is missing expected H atoms. Skipping.
Residue MET  213 is missing expected H atoms. Skipping.
Residue VAL  219 is missing expected H atoms. Skipping.
Residue LEU  220 is missing expected H atoms. Skipping.
Residue THR  221 is missing expected H atoms. Skipping.
Residue LEU  222 is missing expected H atoms. Skipping.
Residue THR  223 is missing expected H atoms. Skipping.
Residue VAL  226 is missing expected H atoms. Skipping.
Residue THR  227 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue ALA  244 is missing expected H atoms. Skipping.
Residue ALA  251 is missing expected H atoms. Skipping.
Residue ILE  252 is missing expected H atoms. Skipping.
Residue MET  253 is missing expected H atoms. Skipping.
Residue ALA  255 is missing expected H atoms. Skipping.
Residue THR  256 is missing expected H atoms. Skipping.
Residue VAL  257 is missing expected H atoms. Skipping.
Residue ILE  262 is missing expected H atoms. Skipping.
Residue ALA  268 is missing expected H atoms. Skipping.
Residue LEU  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue VAL  273 is missing expected H atoms. Skipping.
Residue THR  275 is missing expected H atoms. Skipping.
Residue THR  276 is missing expected H atoms. Skipping.
Residue ALA  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue ILE  282 is missing expected H atoms. Skipping.
Residue ALA  283 is missing expected H atoms. Skipping.
Residue LEU  284 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue ALA  289 is missing expected H atoms. Skipping.
Residue ILE  291 is missing expected H atoms. Skipping.
Residue VAL  292 is missing expected H atoms. Skipping.
Residue VAL  301 is missing expected H atoms. Skipping.
Residue ALA  309 is missing expected H atoms. Skipping.
Residue THR  311 is missing expected H atoms. Skipping.
Residue THR  312 is missing expected H atoms. Skipping.
Residue MET  313 is missing expected H atoms. Skipping.
Residue LEU  318 is missing expected H atoms. Skipping.
Residue LEU  320 is missing expected H atoms. Skipping.
Residue MET  321 is missing expected H atoms. Skipping.
Residue THR  322 is missing expected H atoms. Skipping.
Residue LEU  325 is missing expected H atoms. Skipping.
Residue ILE  330 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue ILE  333 is missing expected H atoms. Skipping.
Residue ALA  335 is missing expected H atoms. Skipping.
Residue VAL  336 is missing expected H atoms. Skipping.
Residue THR  337 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue VAL  341 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  350 is missing expected H atoms. Skipping.
Residue ILE  351 is missing expected H atoms. Skipping.
Residue THR  354 is missing expected H atoms. Skipping.
Residue THR  355 is missing expected H atoms. Skipping.
Residue VAL  356 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue LEU  359 is missing expected H atoms. Skipping.
Residue MET  361 is missing expected H atoms. Skipping.
Residue VAL  366 is missing expected H atoms. Skipping.
Residue LEU  367 is missing expected H atoms. Skipping.
Residue LEU  369 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue VAL  371 is missing expected H atoms. Skipping.
Residue ALA  373 is missing expected H atoms. Skipping.
Residue ILE  377 is missing expected H atoms. Skipping.
Residue VAL  381 is missing expected H atoms. Skipping.
Residue LEU  383 is missing expected H atoms. Skipping.
Residue VAL  385 is missing expected H atoms. Skipping.
Residue LEU  388 is missing expected H atoms. Skipping.
Residue LEU  392 is missing expected H atoms. Skipping.
Residue LEU  394 is missing expected H atoms. Skipping.
Residue ALA  398 is missing expected H atoms. Skipping.
Residue THR  399 is missing expected H atoms. Skipping.
Residue LEU  401 is missing expected H atoms. Skipping.
Residue VAL  405 is missing expected H atoms. Skipping.
Residue ILE  406 is missing expected H atoms. Skipping.
Residue LEU  409 is missing expected H atoms. Skipping.
Residue MET  413 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue ILE  417 is missing expected H atoms. Skipping.
Residue THR  420 is missing expected H atoms. Skipping.
Residue VAL  421 is missing expected H atoms. Skipping.
Residue ILE  425 is missing expected H atoms. Skipping.
Residue ALA  427 is missing expected H atoms. Skipping.
Residue VAL  429 is missing expected H atoms. Skipping.
Residue THR  441 is missing expected H atoms. Skipping.
Residue ILE  442 is missing expected H atoms. Skipping.
Residue VAL  445 is missing expected H atoms. Skipping.
Residue LEU  451 is missing expected H atoms. Skipping.
Residue ILE  452 is missing expected H atoms. Skipping.
Residue VAL  453 is missing expected H atoms. Skipping.
Residue VAL  455 is missing expected H atoms. Skipping.
Residue THR  456 is missing expected H atoms. Skipping.
Residue ALA  462 is missing expected H atoms. Skipping.
Residue ALA  465 is missing expected H atoms. Skipping.
Residue ALA  467 is missing expected H atoms. Skipping.
Residue THR  480 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue LEU  493 is missing expected H atoms. Skipping.
Residue VAL  520 is missing expected H atoms. Skipping.
Residue LEU  528 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  542 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Residue VAL  555 is missing expected H atoms. Skipping.
Residue MET  561 is missing expected H atoms. Skipping.
Residue LEU  574 is missing expected H atoms. Skipping.
Residue THR  580 is missing expected H atoms. Skipping.
Residue THR  587 is missing expected H atoms. Skipping.
Residue THR  588 is missing expected H atoms. Skipping.
Residue THR  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue MET  594 is missing expected H atoms. Skipping.
Residue LEU  599 is missing expected H atoms. Skipping.
Residue LEU  600 is missing expected H atoms. Skipping.
Residue VAL  613 is missing expected H atoms. Skipping.
Residue ILE  615 is missing expected H atoms. Skipping.
Residue THR  623 is missing expected H atoms. Skipping.
Residue THR  629 is missing expected H atoms. Skipping.
Residue ALA  633 is missing expected H atoms. Skipping.
Residue THR  635 is missing expected H atoms. Skipping.
Residue VAL  641 is missing expected H atoms. Skipping.
Residue ALA  650 is missing expected H atoms. Skipping.
Residue LEU  651 is missing expected H atoms. Skipping.
Residue THR  656 is missing expected H atoms. Skipping.
Residue ILE  665 is missing expected H atoms. Skipping.
Residue VAL  668 is missing expected H atoms. Skipping.
Residue LEU  671 is missing expected H atoms. Skipping.
Residue THR  674 is missing expected H atoms. Skipping.
Residue ALA  678 is missing expected H atoms. Skipping.
Residue VAL  679 is missing expected H atoms. Skipping.
Residue THR  682 is missing expected H atoms. Skipping.
Residue VAL  690 is missing expected H atoms. Skipping.
Residue VAL  691 is missing expected H atoms. Skipping.
Residue ILE  704 is missing expected H atoms. Skipping.
Residue LEU  705 is missing expected H atoms. Skipping.
Residue VAL  707 is missing expected H atoms. Skipping.
Residue VAL  708 is missing expected H atoms. Skipping.
Evaluate side-chains
  107 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 1.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  305 TYR cc_start: 0.9574 (OUTLIER) cc_final: 0.9299 (t80)
REVERT: A  526 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8196 (mm-30)
REVERT: A  530 ASP cc_start: 0.8504 (t0) cc_final: 0.8244 (m-30)
REVERT: A  624 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7577 (mm)
REVERT: A  625 ASP cc_start: 0.8693 (m-30) cc_final: 0.8342 (t0)
REVERT: A  939 MET cc_start: 0.8492 (mmt) cc_final: 0.7271 (tmm)
REVERT: B  338 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8791 (pm20)
REVERT: B  413 MET cc_start: 0.8782 (ptm) cc_final: 0.8458 (ptm)
REVERT: B  659 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7373 (ttp80)
REVERT: B  695 TYR cc_start: 0.7725 (t80) cc_final: 0.7517 (t80)
  outliers start: 21
  outliers final: 16
  residues processed: 100
  average time/residue: 1.2467
  time to fit residues: 140.3246
Evaluate side-chains
  103 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 82
  time to evaluate  : 1.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 TRP
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  305 TYR
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  589 MET
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  641 ASP
Chi-restraints excluded: chain A residue  754 ASP
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  313 MET
Chi-restraints excluded: chain B residue  338 GLU
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  561 MET
Chi-restraints excluded: chain B residue  596 SER
Chi-restraints excluded: chain B residue  658 ASN
Chi-restraints excluded: chain B residue  659 ARG
Chi-restraints excluded: chain B residue  683 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 14 optimal weight:    0.1980
   chunk 130 optimal weight:    3.9990
   chunk 70 optimal weight:    9.9990
   chunk 66 optimal weight:    9.9990
   chunk 145 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   chunk 56 optimal weight:    4.9990
   chunk 44 optimal weight:    0.6980
   chunk 62 optimal weight:   10.0000
   chunk 41 optimal weight:    1.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 843 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 652 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 = 0.3774 r_free = 0.3774 target = 0.111079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.065888 restraints weight = 38180.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.2882 rms_B_bonded: 2.57
r_work: 0.2752 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2631 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8778
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  12640  Z= 0.380
  Angle     :  0.543  16.578  17117  Z= 0.280
  Chirality :  0.044   0.181   1875
  Planarity :  0.005   0.170   2265
  Dihedral  :  4.491  34.022   1727
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 23.87
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.90 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 15.52 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.58 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.32 %
    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: -0.33 (0.21), residues: 1594
  helix:  0.06 (0.45), residues: 145
  sheet:  0.37 (0.22), residues: 519
  loop : -0.58 (0.21), residues: 930

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 264 
 HIS   0.009   0.001   HIS B 652 
 PHE   0.015   0.002   PHE A 306 
 TYR   0.016   0.001   TYR B 695 
 ARG   0.010   0.000   ARG B 556 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11737.04 seconds
wall clock time: 207 minutes 40.12 seconds (12460.12 seconds total)