Starting phenix.real_space_refine (version: dev)
on Sun Feb 19 10:08:38 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j2p_5499/02_2023/3j2p_5499.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j2p_5499/02_2023/3j2p_5499.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j2p_5499/02_2023/3j2p_5499.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j2p_5499/02_2023/3j2p_5499.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j2p_5499/02_2023/3j2p_5499.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j2p_5499/02_2023/3j2p_5499.pdb"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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=   0.100 sd=   2.332
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
Process input model

  Symmetric amino acids flipped
    Residue "A ARG    2": "NH1" <-> "NH2"
    Residue "A ARG    9": "NH1" <-> "NH2"
    Residue "A GLU   13": "OE1" <-> "OE2"
    Residue "A ASP   22": "OD1" <-> "OD2"
    Residue "A ASP   42": "OD1" <-> "OD2"
    Residue "A ARG   57": "NH1" <-> "NH2"
    Residue "A GLU   62": "OE1" <-> "OE2"
    Residue "A ARG   73": "NH1" <-> "NH2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A GLU   85": "OE1" <-> "OE2"
    Residue "A ASP   87": "OD1" <-> "OD2"
    Residue "A ARG   89": "NH1" <-> "NH2"
    Residue "A PHE   90": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG   99": "NH1" <-> "NH2"
    Residue "A PHE  119": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  147": "OE1" <-> "OE2"
    Residue "A GLU  172": "OE1" <-> "OE2"
    Residue "A TYR  178": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  188": "NH1" <-> "NH2"
    Residue "A PHE  193": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  210": "NH1" <-> "NH2"
    Residue "A ASP  215": "OD1" <-> "OD2"
    Residue "A ASP  225": "OD1" <-> "OD2"
    Residue "A PHE  240": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  279": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  286": "NH1" <-> "NH2"
    Residue "A ARG  288": "NH1" <-> "NH2"
    Residue "A GLU  314": "OE1" <-> "OE2"
    Residue "A ARG  323": "NH1" <-> "NH2"
    Residue "A TYR  326": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  327": "OE1" <-> "OE2"
    Residue "A GLU  343": "OE1" <-> "OE2"
    Residue "A ARG  345": "NH1" <-> "NH2"
    Residue "A ARG  350": "NH1" <-> "NH2"
    Residue "A TYR  377": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  407": "NH1" <-> "NH2"
    Residue "A ARG  411": "NH1" <-> "NH2"
    Residue "A PHE  422": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  429": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  471": "NH1" <-> "NH2"
    Residue "A TYR  488": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU   13": "OE1" <-> "OE2"
    Residue "B GLU   17": "OE1" <-> "OE2"
    Residue "B ARG   31": "NH1" <-> "NH2"
    Residue "B ARG   38": "NH1" <-> "NH2"
    Residue "B ARG   60": "NH1" <-> "NH2"
    Residue "C ARG    2": "NH1" <-> "NH2"
    Residue "C ARG    9": "NH1" <-> "NH2"
    Residue "C GLU   13": "OE1" <-> "OE2"
    Residue "C ASP   22": "OD1" <-> "OD2"
    Residue "C ASP   42": "OD1" <-> "OD2"
    Residue "C ARG   57": "NH1" <-> "NH2"
    Residue "C GLU   62": "OE1" <-> "OE2"
    Residue "C ARG   73": "NH1" <-> "NH2"
    Residue "C GLU   84": "OE1" <-> "OE2"
    Residue "C GLU   85": "OE1" <-> "OE2"
    Residue "C ASP   87": "OD1" <-> "OD2"
    Residue "C ARG   89": "NH1" <-> "NH2"
    Residue "C PHE   90": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG   99": "NH1" <-> "NH2"
    Residue "C PHE  119": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  147": "OE1" <-> "OE2"
    Residue "C GLU  172": "OE1" <-> "OE2"
    Residue "C TYR  178": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG  188": "NH1" <-> "NH2"
    Residue "C PHE  193": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG  210": "NH1" <-> "NH2"
    Residue "C ASP  215": "OD1" <-> "OD2"
    Residue "C ASP  225": "OD1" <-> "OD2"
    Residue "C PHE  240": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  279": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG  286": "NH1" <-> "NH2"
    Residue "C ARG  288": "NH1" <-> "NH2"
    Residue "C GLU  314": "OE1" <-> "OE2"
    Residue "C ARG  323": "NH1" <-> "NH2"
    Residue "C TYR  326": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  327": "OE1" <-> "OE2"
    Residue "C GLU  343": "OE1" <-> "OE2"
    Residue "C ARG  345": "NH1" <-> "NH2"
    Residue "C ARG  350": "NH1" <-> "NH2"
    Residue "C TYR  377": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG  407": "NH1" <-> "NH2"
    Residue "C ARG  411": "NH1" <-> "NH2"
    Residue "C PHE  422": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  429": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG  471": "NH1" <-> "NH2"
    Residue "C TYR  488": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU   13": "OE1" <-> "OE2"
    Residue "D GLU   17": "OE1" <-> "OE2"
    Residue "D ARG   31": "NH1" <-> "NH2"
    Residue "D ARG   38": "NH1" <-> "NH2"
    Residue "D ARG   60": "NH1" <-> "NH2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib"
  Total number of atoms: 9890
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 4276
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 495, 4276
          Classifications: {'peptide': 495}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 475}
    Chain: "B"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 627
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 3, 'TRANS': 68}
    Chain: "C"
      Number of atoms: 4276
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 495, 4276
          Classifications: {'peptide': 495}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 475}
    Chain: "D"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 627
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 3, 'TRANS': 68}
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 5.76, per 1000 atoms: 0.58
  Number of scatterers: 9890
  At special positions: 0
  Unit cell: (98.256, 146.832, 97.152, 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      70     16.00
     O    1642      8.00
     N    1492      7.00
     C    5600      6.00
     H    1086      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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
  Links applied
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG A 501 " - " ASN A  67 "
      " NAG C 501 " - " ASN C  67 "
      " NAG E   1 " - " ASN A 153 "
      " NAG F   1 " - " ASN C 153 "
  Time building additional restraints: 5.50
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2040

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 14 sheets defined
      28.4% alpha, 16.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 82 through 87
    Processing helix  chain 'A' and resid 100 through 105
      removed outlier: 3.597A  pdb=" N   GLY A 104 " --> pdb=" O   GLY A 100 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   CYS A 105 " --> pdb=" O   TRP A 101 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 100 through 105'
    Processing helix  chain 'A' and resid 210 through 214
    Processing helix  chain 'A' and resid 256 through 264
    Processing helix  chain 'A' and resid 396 through 416
      removed outlier: 3.572A  pdb=" N   GLN A 400 " --> pdb=" O   SER A 396 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LEU A 415 " --> pdb=" O   ARG A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 423
    Processing helix  chain 'A' and resid 428 through 443
      removed outlier: 4.240A  pdb=" N   VAL A 439 " --> pdb=" O   ALA A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 447
    Processing helix  chain 'A' and resid 452 through 469
    Processing helix  chain 'A' and resid 473 through 483
      removed outlier: 4.213A  pdb=" N   VAL A 477 " --> pdb=" O   THR A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 493
    Processing helix  chain 'B' and resid 22 through 39
      removed outlier: 4.297A  pdb=" N   ALA B  29 " --> pdb=" O   ALA B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 39 through 53
      removed outlier: 3.667A  pdb=" N   THR B  43 " --> pdb=" O   HIS B  39 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 57 through 71
    Processing helix  chain 'C' and resid 82 through 87
    Processing helix  chain 'C' and resid 100 through 105
      removed outlier: 3.601A  pdb=" N   GLY C 104 " --> pdb=" O   GLY C 100 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   CYS C 105 " --> pdb=" O   TRP C 101 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 100 through 105'
    Processing helix  chain 'C' and resid 210 through 214
    Processing helix  chain 'C' and resid 256 through 264
    Processing helix  chain 'C' and resid 396 through 416
      removed outlier: 3.573A  pdb=" N   GLN C 400 " --> pdb=" O   SER C 396 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU C 415 " --> pdb=" O   ARG C 411 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 417 through 423
    Processing helix  chain 'C' and resid 428 through 443
      removed outlier: 4.243A  pdb=" N   VAL C 439 " --> pdb=" O   ALA C 435 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 444 through 447
    Processing helix  chain 'C' and resid 452 through 469
    Processing helix  chain 'C' and resid 473 through 483
      removed outlier: 4.213A  pdb=" N   VAL C 477 " --> pdb=" O   THR C 473 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 484 through 493
    Processing helix  chain 'D' and resid 22 through 39
      removed outlier: 4.300A  pdb=" N   ALA D  29 " --> pdb=" O   ALA D  25 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 39 through 53
      removed outlier: 3.667A  pdb=" N   THR D  43 " --> pdb=" O   HIS D  39 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 57 through 71
    Processing sheet with id=  A, first strand: chain 'A' and resid 11 through 13
      removed outlier: 5.974A  pdb=" N   VAL A  12 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 4.823A  pdb=" N   THR A 138 " --> pdb=" O   ILE A  46 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 20 through 25
    Processing sheet with id=  C, first strand: chain 'A' and resid 63 through 72
      removed outlier: 4.887A  pdb=" N   LEU A  65 " --> pdb=" O   THR A 120 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   THR A 120 " --> pdb=" O   LEU A  65 " (cutoff:3.500A)
      removed outlier: 5.318A  pdb=" N   ASN A  67 " --> pdb=" O   MET A 118 " (cutoff:3.500A)
      removed outlier: 6.072A  pdb=" N   MET A 118 " --> pdb=" O   ASN A  67 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'A' and resid 196 through 199
    Processing sheet with id=  E, first strand: chain 'A' and resid 239 through 241
    Processing sheet with id=  F, first strand: chain 'A' and resid 305 through 308
      removed outlier: 3.781A  pdb=" N   LYS A 305 " --> pdb=" O   GLU A 327 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'A' and resid 337 through 340
    Processing sheet with id=  H, first strand: chain 'C' and resid 11 through 13
      removed outlier: 5.974A  pdb=" N   VAL C  12 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   THR C 138 " --> pdb=" O   ILE C  46 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'C' and resid 20 through 25
    Processing sheet with id=  J, first strand: chain 'C' and resid 63 through 72
      removed outlier: 4.887A  pdb=" N   LEU C  65 " --> pdb=" O   THR C 120 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   THR C 120 " --> pdb=" O   LEU C  65 " (cutoff:3.500A)
      removed outlier: 5.319A  pdb=" N   ASN C  67 " --> pdb=" O   MET C 118 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   MET C 118 " --> pdb=" O   ASN C  67 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'C' and resid 196 through 200
    Processing sheet with id=  L, first strand: chain 'C' and resid 239 through 241
    Processing sheet with id=  M, first strand: chain 'C' and resid 305 through 308
      removed outlier: 3.776A  pdb=" N   LYS C 305 " --> pdb=" O   GLU C 327 " (cutoff:3.500A)
    Processing sheet with id=  N, first strand: chain 'C' and resid 337 through 340

    320 hydrogen bonds defined for protein.
    843 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.84

  Time building geometry restraints manager: 5.72 seconds

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

  Histogram of bond lengths:
        0.96 -     1.14: 1086
        1.14 -     1.32: 1449
        1.32 -     1.50: 3769
        1.50 -     1.68: 3652
        1.68 -     1.86: 116
  Bond restraints: 10072
  Sorted by residual:
  bond pdb=" N   LEU A 283 "
       pdb=" H   LEU A 283 "
    ideal  model  delta    sigma   weight residual
    0.860  1.030 -0.170 2.00e-02 2.50e+03 7.20e+01
  bond pdb=" N   LEU C 283 "
       pdb=" H   LEU C 283 "
    ideal  model  delta    sigma   weight residual
    0.860  1.029 -0.169 2.00e-02 2.50e+03 7.16e+01
  bond pdb=" N   THR B  34 "
       pdb=" H   THR B  34 "
    ideal  model  delta    sigma   weight residual
    0.860  1.027 -0.167 2.00e-02 2.50e+03 6.99e+01
  bond pdb=" N   THR D  34 "
       pdb=" H   THR D  34 "
    ideal  model  delta    sigma   weight residual
    0.860  1.027 -0.167 2.00e-02 2.50e+03 6.98e+01
  bond pdb=" N   THR A 182 "
       pdb=" H   THR A 182 "
    ideal  model  delta    sigma   weight residual
    0.860  1.026 -0.166 2.00e-02 2.50e+03 6.92e+01
  ... (remaining 10067 not shown)

  Histogram of bond angle deviations from ideal:
       97.68 -   105.91: 368
      105.91 -   114.14: 5144
      114.14 -   122.38: 7006
      122.38 -   130.61: 1755
      130.61 -   138.84: 63
  Bond angle restraints: 14336
  Sorted by residual:
  angle pdb=" C   LEU C 221 "
        pdb=" N   PRO C 222 "
        pdb=" CA  PRO C 222 "
      ideal   model   delta    sigma   weight residual
     119.84  109.97    9.87 1.25e+00 6.40e-01 6.24e+01
  angle pdb=" C   LEU A 221 "
        pdb=" N   PRO A 222 "
        pdb=" CA  PRO A 222 "
      ideal   model   delta    sigma   weight residual
     119.84  109.98    9.86 1.25e+00 6.40e-01 6.22e+01
  angle pdb=" C   GLU C  79 "
        pdb=" N   PRO C  80 "
        pdb=" CA  PRO C  80 "
      ideal   model   delta    sigma   weight residual
     119.84  129.28   -9.44 1.25e+00 6.40e-01 5.71e+01
  angle pdb=" C   THR C 142 "
        pdb=" N   PRO C 143 "
        pdb=" CA  PRO C 143 "
      ideal   model   delta    sigma   weight residual
     119.84  129.24   -9.40 1.25e+00 6.40e-01 5.65e+01
  angle pdb=" C   THR A 142 "
        pdb=" N   PRO A 143 "
        pdb=" CA  PRO A 143 "
      ideal   model   delta    sigma   weight residual
     119.84  129.15   -9.31 1.25e+00 6.40e-01 5.55e+01
  ... (remaining 14331 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.18: 4667
       16.18 -    32.35: 384
       32.35 -    48.53: 149
       48.53 -    64.70: 100
       64.70 -    80.88: 20
  Dihedral angle restraints: 5320
    sinusoidal: 2132
      harmonic: 3188
  Sorted by residual:
  dihedral pdb=" C   GLU A 195 "
           pdb=" N   GLU A 195 "
           pdb=" CA  GLU A 195 "
           pdb=" CB  GLU A 195 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.79   -8.81     0      2.50e+00 1.60e-01 1.24e+01
  dihedral pdb=" C   GLU C 195 "
           pdb=" N   GLU C 195 "
           pdb=" CA  GLU C 195 "
           pdb=" CB  GLU C 195 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.80   -8.80     0      2.50e+00 1.60e-01 1.24e+01
  dihedral pdb=" C   ASN A 124 "
           pdb=" N   ASN A 124 "
           pdb=" CA  ASN A 124 "
           pdb=" CB  ASN A 124 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -114.02   -8.58     0      2.50e+00 1.60e-01 1.18e+01
  ... (remaining 5317 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.083: 830
       0.083 -    0.165: 354
       0.165 -    0.248: 158
       0.248 -    0.330: 52
       0.330 -    0.412: 18
  Chirality restraints: 1412
  Sorted by residual:
  chirality pdb=" CA  LEU A 278 "
            pdb=" N   LEU A 278 "
            pdb=" C   LEU A 278 "
            pdb=" CB  LEU A 278 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.25e+00
  chirality pdb=" CA  LEU C 278 "
            pdb=" N   LEU C 278 "
            pdb=" C   LEU C 278 "
            pdb=" CB  LEU C 278 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.17e+00
  chirality pdb=" CA  TRP A 391 "
            pdb=" N   TRP A 391 "
            pdb=" C   TRP A 391 "
            pdb=" CB  TRP A 391 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.61e+00
  ... (remaining 1409 not shown)

  Planarity restraints: 2610
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG E   1 "    0.366 2.00e-02 2.50e+03   3.12e-01 1.22e+03
        pdb=" C7  NAG E   1 "   -0.092 2.00e-02 2.50e+03
        pdb=" C8  NAG E   1 "    0.118 2.00e-02 2.50e+03
        pdb=" N2  NAG E   1 "   -0.553 2.00e-02 2.50e+03
        pdb=" O7  NAG E   1 "    0.161 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG F   1 "    0.366 2.00e-02 2.50e+03   3.12e-01 1.22e+03
        pdb=" C7  NAG F   1 "   -0.093 2.00e-02 2.50e+03
        pdb=" C8  NAG F   1 "    0.118 2.00e-02 2.50e+03
        pdb=" N2  NAG F   1 "   -0.552 2.00e-02 2.50e+03
        pdb=" O7  NAG F   1 "    0.161 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG E   2 "   -0.367 2.00e-02 2.50e+03   3.10e-01 1.20e+03
        pdb=" C7  NAG E   2 "    0.097 2.00e-02 2.50e+03
        pdb=" C8  NAG E   2 "   -0.163 2.00e-02 2.50e+03
        pdb=" N2  NAG E   2 "    0.545 2.00e-02 2.50e+03
        pdb=" O7  NAG E   2 "   -0.113 2.00e-02 2.50e+03
  ... (remaining 2607 not shown)

  Histogram of nonbonded interaction distances:
        1.20 -     1.88: 74
        1.88 -     2.56: 2739
        2.56 -     3.24: 17314
        3.24 -     3.92: 23022
        3.92 -     4.60: 32760
  Nonbonded interactions: 75909
  Sorted by model distance:
  nonbonded pdb=" H   GLU A 195 "
            pdb=" H   MET A 196 "
     model   vdw
     1.198 2.100
  nonbonded pdb=" H   GLU C 195 "
            pdb=" H   MET C 196 "
     model   vdw
     1.199 2.100
  nonbonded pdb=" H   SER B  22 "
            pdb=" H   GLU B  23 "
     model   vdw
     1.267 2.100
  nonbonded pdb=" H   SER D  22 "
            pdb=" H   GLU D  23 "
     model   vdw
     1.267 2.100
  nonbonded pdb=" H   ALA C 447 "
            pdb=" H   PHE C 448 "
     model   vdw
     1.279 2.100
  ... (remaining 75904 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      70      5.16       5
     C    5600      2.51       5
     N    1492      2.21       5
     O    1642      1.98       5
     H    1086      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.97
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             0.090
  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:             0.230
  Extract box with map and model:          1.470
  Check model and map are aligned:         0.140
  Process input model:                     29.690
  Find NCS groups from input model:        0.480
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Set scattering table:                    0.090
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
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      :  0.009   0.059   8986  Z= 0.610
  Angle     :  1.919  13.972  12164  Z= 1.137
  Chirality :  0.118   0.412   1412
  Planarity :  0.021   0.312   1520
  Dihedral  : 17.487  80.876   3280
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 110.20
  Ramachandran Plot:
    Outliers : 24.07 %
    Allowed  : 29.66 %
    Favored  : 46.27 %
  Rotamer Outliers : 20.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -7.75 (0.15), residues: 1126
  helix: -5.20 (0.09), residues: 294
  sheet: -3.78 (0.32), residues: 216
  loop : -5.90 (0.15), residues: 616

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE    4 is missing expected H atoms. Skipping.
Residue ILE    6 is missing expected H atoms. Skipping.
Residue SER    7 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue VAL   15 is missing expected H atoms. Skipping.
Residue SER   16 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue VAL   21 is missing expected H atoms. Skipping.
Residue ILE   23 is missing expected H atoms. Skipping.
Residue VAL   24 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue SER   29 is missing expected H atoms. Skipping.
Residue VAL   31 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 MET   34 is missing expected H atoms. Skipping.
Residue ALA   35 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue THR   40 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue ILE   46 is missing expected H atoms. Skipping.
Residue THR   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue ALA   54 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue ILE   61 is missing expected H atoms. Skipping.
Residue ALA   63 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue LEU   65 is missing expected H atoms. Skipping.
Residue THR   66 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue THR   70 is missing expected H atoms. Skipping.
Residue SER   72 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue SER   81 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LYS   88 is missing expected H atoms. Skipping.
Residue VAL   91 is missing expected H atoms. Skipping.
Residue LYS   93 is missing expected H atoms. Skipping.
Residue SER   95 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue VAL   97 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue ILE  113 is missing expected H atoms. Skipping.
Residue VAL  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  117 is missing expected H atoms. Skipping.
Residue MET  118 is missing expected H atoms. Skipping.
Residue THR  120 is missing expected H atoms. Skipping.
Residue LYS  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  125 is missing expected H atoms. Skipping.
Residue LYS  126 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue VAL  129 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue TYR  137 is missing expected H atoms. Skipping.
Residue THR  138 is missing expected H atoms. Skipping.
Residue ILE  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue ILE  141 is missing expected H atoms. Skipping.
Residue THR  142 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue ALA  150 is missing expected H atoms. Skipping.
Residue VAL  151 is missing expected H atoms. Skipping.
Residue THR  155 is missing expected H atoms. Skipping.
Residue LYS  157 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Residue ILE  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue ILE  164 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue SER  169 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue ALA  173 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue THR  176 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue THR  182 is missing expected H atoms. Skipping.
Residue MET  183 is missing expected H atoms. Skipping.
Residue SER  186 is missing expected H atoms. Skipping.
Residue THR  189 is missing expected H atoms. Skipping.
Residue LEU  191 is missing expected H atoms. Skipping.
Residue MET  196 is missing expected H atoms. Skipping.
Residue VAL  197 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  201 is missing expected H atoms. Skipping.
Residue LYS  204 is missing expected H atoms. Skipping.
Residue ALA  205 is missing expected H atoms. Skipping.
Residue LEU  207 is missing expected H atoms. Skipping.
Residue VAL  208 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LEU  216 is missing expected H atoms. Skipping.
Residue LEU  218 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue ALA  224 is missing expected H atoms. Skipping.
Residue THR  226 is missing expected H atoms. Skipping.
Residue SER  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue THR  236 is missing expected H atoms. Skipping.
Residue LEU  237 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue THR  239 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue VAL  250 is missing expected H atoms. Skipping.
Residue VAL  251 is missing expected H atoms. Skipping.
Residue VAL  252 is missing expected H atoms. Skipping.
Residue LEU  253 is missing expected H atoms. Skipping.
Residue SER  255 is missing expected H atoms. Skipping.
Residue ALA  259 is missing expected H atoms. Skipping.
Residue MET  260 is missing expected H atoms. Skipping.
Residue THR  262 is missing expected H atoms. Skipping.
Residue ALA  263 is missing expected H atoms. Skipping.
Residue LEU  264 is missing expected H atoms. Skipping.
Residue THR  265 is missing expected H atoms. Skipping.
Residue ALA  267 is missing expected H atoms. Skipping.
Residue THR  268 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue SER  273 is missing expected H atoms. Skipping.
Residue SER  274 is missing expected H atoms. Skipping.
Residue LEU  277 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue LYS  284 is missing expected H atoms. Skipping.
Residue LEU  287 is missing expected H atoms. Skipping.
Residue MET  289 is missing expected H atoms. Skipping.
Residue LYS  291 is missing expected H atoms. Skipping.
Residue LEU  292 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue LYS  295 is missing expected H atoms. Skipping.
Residue MET  297 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue TYR  299 is missing expected H atoms. Skipping.
Residue SER  300 is missing expected H atoms. Skipping.
Residue MET  301 is missing expected H atoms. Skipping.
Residue THR  303 is missing expected H atoms. Skipping.
Residue LYS  305 is missing expected H atoms. Skipping.
Residue LYS  307 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue VAL  309 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue ILE  312 is missing expected H atoms. Skipping.
Residue ALA  313 is missing expected H atoms. Skipping.
Residue THR  315 is missing expected H atoms. Skipping.
Residue THR  319 is missing expected H atoms. Skipping.
Residue ILE  320 is missing expected H atoms. Skipping.
Residue VAL  321 is missing expected H atoms. Skipping.
Residue ILE  322 is missing expected H atoms. Skipping.
Residue VAL  324 is missing expected H atoms. Skipping.
Residue TYR  326 is missing expected H atoms. Skipping.
Residue SER  331 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue ILE  335 is missing expected H atoms. Skipping.
Residue ILE  339 is missing expected H atoms. Skipping.
Residue MET  340 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue LYS  344 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  348 is missing expected H atoms. Skipping.
Residue LEU  351 is missing expected H atoms. Skipping.
Residue ILE  352 is missing expected H atoms. Skipping.
Residue THR  353 is missing expected H atoms. Skipping.
Residue VAL  354 is missing expected H atoms. Skipping.
Residue ILE  357 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LYS  361 is missing expected H atoms. Skipping.
Residue SER  363 is missing expected H atoms. Skipping.
Residue VAL  365 is missing expected H atoms. Skipping.
Residue ILE  367 is missing expected H atoms. Skipping.
Residue ALA  369 is missing expected H atoms. Skipping.
Residue SER  376 is missing expected H atoms. Skipping.
Residue TYR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue ILE  379 is missing expected H atoms. Skipping.
Residue ILE  380 is missing expected H atoms. Skipping.
Residue VAL  382 is missing expected H atoms. Skipping.
Residue LEU  387 is missing expected H atoms. Skipping.
Residue LYS  388 is missing expected H atoms. Skipping.
Residue LEU  389 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue LYS  394 is missing expected H atoms. Skipping.
Residue SER  396 is missing expected H atoms. Skipping.
Residue SER  397 is missing expected H atoms. Skipping.
Residue ILE  398 is missing expected H atoms. Skipping.
Residue MET  401 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue THR  404 is missing expected H atoms. Skipping.
Residue THR  405 is missing expected H atoms. Skipping.
Residue MET  406 is missing expected H atoms. Skipping.
Residue ALA  409 is missing expected H atoms. Skipping.
Residue LYS  410 is missing expected H atoms. Skipping.
Residue MET  412 is missing expected H atoms. Skipping.
Residue ALA  413 is missing expected H atoms. Skipping.
Residue ILE  414 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue ALA  419 is missing expected H atoms. Skipping.
Residue SER  424 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue VAL  428 is missing expected H atoms. Skipping.
Residue THR  430 is missing expected H atoms. Skipping.
Residue SER  431 is missing expected H atoms. Skipping.
Residue ILE  432 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue ALA  435 is missing expected H atoms. Skipping.
Residue LEU  436 is missing expected H atoms. Skipping.
Residue VAL  439 is missing expected H atoms. Skipping.
Residue ALA  442 is missing expected H atoms. Skipping.
Residue ILE  443 is missing expected H atoms. Skipping.
Residue TYR  444 is missing expected H atoms. Skipping.
Residue ALA  446 is missing expected H atoms. Skipping.
Residue ALA  447 is missing expected H atoms. Skipping.
Residue SER  449 is missing expected H atoms. Skipping.
Residue VAL  451 is missing expected H atoms. Skipping.
Residue SER  452 is missing expected H atoms. Skipping.
Residue ILE  454 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue ILE  457 is missing expected H atoms. Skipping.
Residue LEU  458 is missing expected H atoms. Skipping.
Residue ILE  459 is missing expected H atoms. Skipping.
Residue VAL  461 is missing expected H atoms. Skipping.
Residue ILE  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue THR  464 is missing expected H atoms. Skipping.
Residue ILE  466 is missing expected H atoms. Skipping.
Residue MET  468 is missing expected H atoms. Skipping.
Residue SER  470 is missing expected H atoms. Skipping.
Residue SER  472 is missing expected H atoms. Skipping.
Residue THR  473 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue LEU  475 is missing expected H atoms. Skipping.
Residue SER  476 is missing expected H atoms. Skipping.
Residue VAL  477 is missing expected H atoms. Skipping.
Residue SER  478 is missing expected H atoms. Skipping.
Residue LEU  479 is missing expected H atoms. Skipping.
Residue VAL  480 is missing expected H atoms. Skipping.
Residue LEU  481 is missing expected H atoms. Skipping.
Residue VAL  482 is missing expected H atoms. Skipping.
Residue VAL  484 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue LEU  487 is missing expected H atoms. Skipping.
Residue TYR  488 is missing expected H atoms. Skipping.
Residue LEU  489 is missing expected H atoms. Skipping.
Residue VAL  491 is missing expected H atoms. Skipping.
Residue MET  492 is missing expected H atoms. Skipping.
Residue VAL  493 is missing expected H atoms. Skipping.
Residue VAL    2 is missing expected H atoms. Skipping.
Residue ALA    3 is missing expected H atoms. Skipping.
Residue LEU    4 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue MET   10 is missing expected H atoms. Skipping.
Residue LEU   12 is missing expected H atoms. Skipping.
Residue THR   14 is missing expected H atoms. Skipping.
Residue ALA   15 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue THR   18 is missing expected H atoms. Skipping.
Residue MET   20 is missing expected H atoms. Skipping.
Residue SER   21 is missing expected H atoms. Skipping.
Residue SER   22 is missing expected H atoms. Skipping.
Residue ALA   25 is missing expected H atoms. Skipping.
Residue LYS   27 is missing expected H atoms. Skipping.
Residue ALA   29 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue ILE   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue THR   43 is missing expected H atoms. Skipping.
Residue ILE   44 is missing expected H atoms. Skipping.
Residue MET   45 is missing expected H atoms. Skipping.
Residue ALA   46 is missing expected H atoms. Skipping.
Residue ALA   47 is missing expected H atoms. Skipping.
Residue ILE   48 is missing expected H atoms. Skipping.
Residue LEU   49 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue TYR   51 is missing expected H atoms. Skipping.
Residue THR   52 is missing expected H atoms. Skipping.
Residue ILE   53 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue THR   56 is missing expected H atoms. Skipping.
Residue ALA   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue ILE   63 is missing expected H atoms. Skipping.
Residue ILE   65 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 THR   68 is missing expected H atoms. Skipping.
Residue ALA   69 is missing expected H atoms. Skipping.
Residue VAL   70 is missing expected H atoms. Skipping.
Residue ALA   71 is missing expected H atoms. Skipping.
Residue ILE    4 is missing expected H atoms. Skipping.
Residue ILE    6 is missing expected H atoms. Skipping.
Residue SER    7 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue VAL   15 is missing expected H atoms. Skipping.
Residue SER   16 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue VAL   21 is missing expected H atoms. Skipping.
Residue ILE   23 is missing expected H atoms. Skipping.
Residue VAL   24 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue SER   29 is missing expected H atoms. Skipping.
Residue VAL   31 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 MET   34 is missing expected H atoms. Skipping.
Residue ALA   35 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue THR   40 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue ILE   46 is missing expected H atoms. Skipping.
Residue THR   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue ALA   54 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue ILE   61 is missing expected H atoms. Skipping.
Residue ALA   63 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue LEU   65 is missing expected H atoms. Skipping.
Residue THR   66 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue THR   70 is missing expected H atoms. Skipping.
Residue SER   72 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue SER   81 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LYS   88 is missing expected H atoms. Skipping.
Residue VAL   91 is missing expected H atoms. Skipping.
Residue LYS   93 is missing expected H atoms. Skipping.
Residue SER   95 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue VAL   97 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue ILE  113 is missing expected H atoms. Skipping.
Residue VAL  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  117 is missing expected H atoms. Skipping.
Residue MET  118 is missing expected H atoms. Skipping.
Residue THR  120 is missing expected H atoms. Skipping.
Residue LYS  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  125 is missing expected H atoms. Skipping.
Residue LYS  126 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue VAL  129 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue TYR  137 is missing expected H atoms. Skipping.
Residue THR  138 is missing expected H atoms. Skipping.
Residue ILE  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue ILE  141 is missing expected H atoms. Skipping.
Residue THR  142 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue ALA  150 is missing expected H atoms. Skipping.
Residue VAL  151 is missing expected H atoms. Skipping.
Residue THR  155 is missing expected H atoms. Skipping.
Residue LYS  157 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Residue ILE  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue ILE  164 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue SER  169 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue ALA  173 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue THR  176 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue THR  182 is missing expected H atoms. Skipping.
Residue MET  183 is missing expected H atoms. Skipping.
Residue SER  186 is missing expected H atoms. Skipping.
Residue THR  189 is missing expected H atoms. Skipping.
Residue LEU  191 is missing expected H atoms. Skipping.
Residue MET  196 is missing expected H atoms. Skipping.
Residue VAL  197 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  201 is missing expected H atoms. Skipping.
Residue LYS  204 is missing expected H atoms. Skipping.
Residue ALA  205 is missing expected H atoms. Skipping.
Residue LEU  207 is missing expected H atoms. Skipping.
Residue VAL  208 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LEU  216 is missing expected H atoms. Skipping.
Residue LEU  218 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue ALA  224 is missing expected H atoms. Skipping.
Residue THR  226 is missing expected H atoms. Skipping.
Residue SER  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue THR  236 is missing expected H atoms. Skipping.
Residue LEU  237 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue THR  239 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue VAL  250 is missing expected H atoms. Skipping.
Residue VAL  251 is missing expected H atoms. Skipping.
Residue VAL  252 is missing expected H atoms. Skipping.
Residue LEU  253 is missing expected H atoms. Skipping.
Residue SER  255 is missing expected H atoms. Skipping.
Residue ALA  259 is missing expected H atoms. Skipping.
Residue MET  260 is missing expected H atoms. Skipping.
Residue THR  262 is missing expected H atoms. Skipping.
Residue ALA  263 is missing expected H atoms. Skipping.
Residue LEU  264 is missing expected H atoms. Skipping.
Residue THR  265 is missing expected H atoms. Skipping.
Residue ALA  267 is missing expected H atoms. Skipping.
Residue THR  268 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue SER  273 is missing expected H atoms. Skipping.
Residue SER  274 is missing expected H atoms. Skipping.
Residue LEU  277 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue LYS  284 is missing expected H atoms. Skipping.
Residue LEU  287 is missing expected H atoms. Skipping.
Residue MET  289 is missing expected H atoms. Skipping.
Residue LYS  291 is missing expected H atoms. Skipping.
Residue LEU  292 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue LYS  295 is missing expected H atoms. Skipping.
Residue MET  297 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue TYR  299 is missing expected H atoms. Skipping.
Residue SER  300 is missing expected H atoms. Skipping.
Residue MET  301 is missing expected H atoms. Skipping.
Residue THR  303 is missing expected H atoms. Skipping.
Residue LYS  305 is missing expected H atoms. Skipping.
Residue LYS  307 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue VAL  309 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue ILE  312 is missing expected H atoms. Skipping.
Residue ALA  313 is missing expected H atoms. Skipping.
Residue THR  315 is missing expected H atoms. Skipping.
Residue THR  319 is missing expected H atoms. Skipping.
Residue ILE  320 is missing expected H atoms. Skipping.
Residue VAL  321 is missing expected H atoms. Skipping.
Residue ILE  322 is missing expected H atoms. Skipping.
Residue VAL  324 is missing expected H atoms. Skipping.
Residue TYR  326 is missing expected H atoms. Skipping.
Residue SER  331 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue ILE  335 is missing expected H atoms. Skipping.
Residue ILE  339 is missing expected H atoms. Skipping.
Residue MET  340 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue LYS  344 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  348 is missing expected H atoms. Skipping.
Residue LEU  351 is missing expected H atoms. Skipping.
Residue ILE  352 is missing expected H atoms. Skipping.
Residue THR  353 is missing expected H atoms. Skipping.
Residue VAL  354 is missing expected H atoms. Skipping.
Residue ILE  357 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LYS  361 is missing expected H atoms. Skipping.
Residue SER  363 is missing expected H atoms. Skipping.
Residue VAL  365 is missing expected H atoms. Skipping.
Residue ILE  367 is missing expected H atoms. Skipping.
Residue ALA  369 is missing expected H atoms. Skipping.
Residue SER  376 is missing expected H atoms. Skipping.
Residue TYR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue ILE  379 is missing expected H atoms. Skipping.
Residue ILE  380 is missing expected H atoms. Skipping.
Residue VAL  382 is missing expected H atoms. Skipping.
Residue LEU  387 is missing expected H atoms. Skipping.
Residue LYS  388 is missing expected H atoms. Skipping.
Residue LEU  389 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue LYS  394 is missing expected H atoms. Skipping.
Residue SER  396 is missing expected H atoms. Skipping.
Residue SER  397 is missing expected H atoms. Skipping.
Residue ILE  398 is missing expected H atoms. Skipping.
Residue MET  401 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue THR  404 is missing expected H atoms. Skipping.
Residue THR  405 is missing expected H atoms. Skipping.
Residue MET  406 is missing expected H atoms. Skipping.
Residue ALA  409 is missing expected H atoms. Skipping.
Residue LYS  410 is missing expected H atoms. Skipping.
Residue MET  412 is missing expected H atoms. Skipping.
Residue ALA  413 is missing expected H atoms. Skipping.
Residue ILE  414 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue ALA  419 is missing expected H atoms. Skipping.
Residue SER  424 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue VAL  428 is missing expected H atoms. Skipping.
Residue THR  430 is missing expected H atoms. Skipping.
Residue SER  431 is missing expected H atoms. Skipping.
Residue ILE  432 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue ALA  435 is missing expected H atoms. Skipping.
Residue LEU  436 is missing expected H atoms. Skipping.
Residue VAL  439 is missing expected H atoms. Skipping.
Residue ALA  442 is missing expected H atoms. Skipping.
Residue ILE  443 is missing expected H atoms. Skipping.
Residue TYR  444 is missing expected H atoms. Skipping.
Residue ALA  446 is missing expected H atoms. Skipping.
Residue ALA  447 is missing expected H atoms. Skipping.
Residue SER  449 is missing expected H atoms. Skipping.
Residue VAL  451 is missing expected H atoms. Skipping.
Residue SER  452 is missing expected H atoms. Skipping.
Residue ILE  454 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue ILE  457 is missing expected H atoms. Skipping.
Residue LEU  458 is missing expected H atoms. Skipping.
Residue ILE  459 is missing expected H atoms. Skipping.
Residue VAL  461 is missing expected H atoms. Skipping.
Residue ILE  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue THR  464 is missing expected H atoms. Skipping.
Residue ILE  466 is missing expected H atoms. Skipping.
Residue MET  468 is missing expected H atoms. Skipping.
Residue SER  470 is missing expected H atoms. Skipping.
Residue SER  472 is missing expected H atoms. Skipping.
Residue THR  473 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue LEU  475 is missing expected H atoms. Skipping.
Residue SER  476 is missing expected H atoms. Skipping.
Residue VAL  477 is missing expected H atoms. Skipping.
Residue SER  478 is missing expected H atoms. Skipping.
Residue LEU  479 is missing expected H atoms. Skipping.
Residue VAL  480 is missing expected H atoms. Skipping.
Residue LEU  481 is missing expected H atoms. Skipping.
Residue VAL  482 is missing expected H atoms. Skipping.
Residue VAL  484 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue LEU  487 is missing expected H atoms. Skipping.
Residue TYR  488 is missing expected H atoms. Skipping.
Residue LEU  489 is missing expected H atoms. Skipping.
Residue VAL  491 is missing expected H atoms. Skipping.
Residue MET  492 is missing expected H atoms. Skipping.
Residue VAL  493 is missing expected H atoms. Skipping.
Residue VAL    2 is missing expected H atoms. Skipping.
Residue ALA    3 is missing expected H atoms. Skipping.
Residue LEU    4 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue MET   10 is missing expected H atoms. Skipping.
Residue LEU   12 is missing expected H atoms. Skipping.
Residue THR   14 is missing expected H atoms. Skipping.
Residue ALA   15 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue THR   18 is missing expected H atoms. Skipping.
Residue MET   20 is missing expected H atoms. Skipping.
Residue SER   21 is missing expected H atoms. Skipping.
Residue SER   22 is missing expected H atoms. Skipping.
Residue ALA   25 is missing expected H atoms. Skipping.
Residue LYS   27 is missing expected H atoms. Skipping.
Residue ALA   29 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue ILE   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue THR   43 is missing expected H atoms. Skipping.
Residue ILE   44 is missing expected H atoms. Skipping.
Residue MET   45 is missing expected H atoms. Skipping.
Residue ALA   46 is missing expected H atoms. Skipping.
Residue ALA   47 is missing expected H atoms. Skipping.
Residue ILE   48 is missing expected H atoms. Skipping.
Residue LEU   49 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue TYR   51 is missing expected H atoms. Skipping.
Residue THR   52 is missing expected H atoms. Skipping.
Residue ILE   53 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue THR   56 is missing expected H atoms. Skipping.
Residue ALA   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue ILE   63 is missing expected H atoms. Skipping.
Residue ILE   65 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 THR   68 is missing expected H atoms. Skipping.
Residue ALA   69 is missing expected H atoms. Skipping.
Residue VAL   70 is missing expected H atoms. Skipping.
Residue ALA   71 is missing expected H atoms. Skipping.
Evaluate side-chains
  513 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 192
    poor density    : 321
  time to evaluate  : 1.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 192
  outliers final: 124
  residues processed: 461
  average time/residue: 0.2294
  time to fit residues: 145.1437
Evaluate side-chains
  386 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 124
    poor density    : 262
  time to evaluate  : 1.082 
Switching outliers to nearest non-outliers
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 124
  outliers final: 6
  residues processed: 124
  average time/residue: 0.1256
  time to fit residues: 27.0654
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    7.9990
   chunk 84 optimal weight:    6.9990
   chunk 47 optimal weight:    9.9990
   chunk 28 optimal weight:   20.0000
   chunk 57 optimal weight:    6.9990
   chunk 45 optimal weight:    5.9990
   chunk 87 optimal weight:   20.0000
   chunk 33 optimal weight:    6.9990
   chunk 53 optimal weight:    9.9990
   chunk 65 optimal weight:    7.9990
   chunk 101 optimal weight:    6.9990
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  83 ASN
** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 200 GLN
A 203 ASN
** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 233 GLN
A 242 ASN
A 256 GLN
** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   8 ASN
** C  27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  83 ASN
** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 GLN
C 203 ASN
** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 233 GLN
C 242 ASN
C 256 GLN
C 386 GLN
** D   7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.3637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8986  Z= 0.298
  Angle     :  1.017   7.359  12164  Z= 0.533
  Chirality :  0.055   0.363   1412
  Planarity :  0.007   0.056   1520
  Dihedral  :  7.900  82.251   1224
  Min Nonbonded Distance : 1.773

Molprobity Statistics.
  All-atom Clashscore : 82.35
  Ramachandran Plot:
    Outliers :  5.60 %
    Allowed  : 27.98 %
    Favored  : 66.43 %
  Rotamer Outliers :  5.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.92 (0.17), residues: 1126
  helix: -4.29 (0.17), residues: 296
  sheet: -3.14 (0.30), residues: 252
  loop : -5.65 (0.16), residues: 578

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE    4 is missing expected H atoms. Skipping.
Residue ILE    6 is missing expected H atoms. Skipping.
Residue SER    7 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue VAL   15 is missing expected H atoms. Skipping.
Residue SER   16 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue VAL   21 is missing expected H atoms. Skipping.
Residue ILE   23 is missing expected H atoms. Skipping.
Residue VAL   24 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue SER   29 is missing expected H atoms. Skipping.
Residue VAL   31 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 MET   34 is missing expected H atoms. Skipping.
Residue ALA   35 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue THR   40 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue ILE   46 is missing expected H atoms. Skipping.
Residue THR   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue ALA   54 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue ILE   61 is missing expected H atoms. Skipping.
Residue ALA   63 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue LEU   65 is missing expected H atoms. Skipping.
Residue THR   66 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue THR   70 is missing expected H atoms. Skipping.
Residue SER   72 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue SER   81 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LYS   88 is missing expected H atoms. Skipping.
Residue VAL   91 is missing expected H atoms. Skipping.
Residue LYS   93 is missing expected H atoms. Skipping.
Residue SER   95 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue VAL   97 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue ILE  113 is missing expected H atoms. Skipping.
Residue VAL  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  117 is missing expected H atoms. Skipping.
Residue MET  118 is missing expected H atoms. Skipping.
Residue THR  120 is missing expected H atoms. Skipping.
Residue LYS  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  125 is missing expected H atoms. Skipping.
Residue LYS  126 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue VAL  129 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue TYR  137 is missing expected H atoms. Skipping.
Residue THR  138 is missing expected H atoms. Skipping.
Residue ILE  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue ILE  141 is missing expected H atoms. Skipping.
Residue THR  142 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue ALA  150 is missing expected H atoms. Skipping.
Residue VAL  151 is missing expected H atoms. Skipping.
Residue THR  155 is missing expected H atoms. Skipping.
Residue LYS  157 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Residue ILE  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue ILE  164 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue SER  169 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue ALA  173 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue THR  176 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue THR  182 is missing expected H atoms. Skipping.
Residue MET  183 is missing expected H atoms. Skipping.
Residue SER  186 is missing expected H atoms. Skipping.
Residue THR  189 is missing expected H atoms. Skipping.
Residue LEU  191 is missing expected H atoms. Skipping.
Residue MET  196 is missing expected H atoms. Skipping.
Residue VAL  197 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  201 is missing expected H atoms. Skipping.
Residue LYS  204 is missing expected H atoms. Skipping.
Residue ALA  205 is missing expected H atoms. Skipping.
Residue LEU  207 is missing expected H atoms. Skipping.
Residue VAL  208 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LEU  216 is missing expected H atoms. Skipping.
Residue LEU  218 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue ALA  224 is missing expected H atoms. Skipping.
Residue THR  226 is missing expected H atoms. Skipping.
Residue SER  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue THR  236 is missing expected H atoms. Skipping.
Residue LEU  237 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue THR  239 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue VAL  250 is missing expected H atoms. Skipping.
Residue VAL  251 is missing expected H atoms. Skipping.
Residue VAL  252 is missing expected H atoms. Skipping.
Residue LEU  253 is missing expected H atoms. Skipping.
Residue SER  255 is missing expected H atoms. Skipping.
Residue ALA  259 is missing expected H atoms. Skipping.
Residue MET  260 is missing expected H atoms. Skipping.
Residue THR  262 is missing expected H atoms. Skipping.
Residue ALA  263 is missing expected H atoms. Skipping.
Residue LEU  264 is missing expected H atoms. Skipping.
Residue THR  265 is missing expected H atoms. Skipping.
Residue ALA  267 is missing expected H atoms. Skipping.
Residue THR  268 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue SER  273 is missing expected H atoms. Skipping.
Residue SER  274 is missing expected H atoms. Skipping.
Residue LEU  277 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue LYS  284 is missing expected H atoms. Skipping.
Residue LEU  287 is missing expected H atoms. Skipping.
Residue MET  289 is missing expected H atoms. Skipping.
Residue LYS  291 is missing expected H atoms. Skipping.
Residue LEU  292 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue LYS  295 is missing expected H atoms. Skipping.
Residue MET  297 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue TYR  299 is missing expected H atoms. Skipping.
Residue SER  300 is missing expected H atoms. Skipping.
Residue MET  301 is missing expected H atoms. Skipping.
Residue THR  303 is missing expected H atoms. Skipping.
Residue LYS  305 is missing expected H atoms. Skipping.
Residue LYS  307 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue VAL  309 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue ILE  312 is missing expected H atoms. Skipping.
Residue ALA  313 is missing expected H atoms. Skipping.
Residue THR  315 is missing expected H atoms. Skipping.
Residue THR  319 is missing expected H atoms. Skipping.
Residue ILE  320 is missing expected H atoms. Skipping.
Residue VAL  321 is missing expected H atoms. Skipping.
Residue ILE  322 is missing expected H atoms. Skipping.
Residue VAL  324 is missing expected H atoms. Skipping.
Residue TYR  326 is missing expected H atoms. Skipping.
Residue SER  331 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue ILE  335 is missing expected H atoms. Skipping.
Residue ILE  339 is missing expected H atoms. Skipping.
Residue MET  340 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue LYS  344 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  348 is missing expected H atoms. Skipping.
Residue LEU  351 is missing expected H atoms. Skipping.
Residue ILE  352 is missing expected H atoms. Skipping.
Residue THR  353 is missing expected H atoms. Skipping.
Residue VAL  354 is missing expected H atoms. Skipping.
Residue ILE  357 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LYS  361 is missing expected H atoms. Skipping.
Residue SER  363 is missing expected H atoms. Skipping.
Residue VAL  365 is missing expected H atoms. Skipping.
Residue ILE  367 is missing expected H atoms. Skipping.
Residue ALA  369 is missing expected H atoms. Skipping.
Residue SER  376 is missing expected H atoms. Skipping.
Residue TYR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue ILE  379 is missing expected H atoms. Skipping.
Residue ILE  380 is missing expected H atoms. Skipping.
Residue VAL  382 is missing expected H atoms. Skipping.
Residue LEU  387 is missing expected H atoms. Skipping.
Residue LYS  388 is missing expected H atoms. Skipping.
Residue LEU  389 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue LYS  394 is missing expected H atoms. Skipping.
Residue SER  396 is missing expected H atoms. Skipping.
Residue SER  397 is missing expected H atoms. Skipping.
Residue ILE  398 is missing expected H atoms. Skipping.
Residue MET  401 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue THR  404 is missing expected H atoms. Skipping.
Residue THR  405 is missing expected H atoms. Skipping.
Residue MET  406 is missing expected H atoms. Skipping.
Residue ALA  409 is missing expected H atoms. Skipping.
Residue LYS  410 is missing expected H atoms. Skipping.
Residue MET  412 is missing expected H atoms. Skipping.
Residue ALA  413 is missing expected H atoms. Skipping.
Residue ILE  414 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue ALA  419 is missing expected H atoms. Skipping.
Residue SER  424 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue VAL  428 is missing expected H atoms. Skipping.
Residue THR  430 is missing expected H atoms. Skipping.
Residue SER  431 is missing expected H atoms. Skipping.
Residue ILE  432 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue ALA  435 is missing expected H atoms. Skipping.
Residue LEU  436 is missing expected H atoms. Skipping.
Residue VAL  439 is missing expected H atoms. Skipping.
Residue ALA  442 is missing expected H atoms. Skipping.
Residue ILE  443 is missing expected H atoms. Skipping.
Residue TYR  444 is missing expected H atoms. Skipping.
Residue ALA  446 is missing expected H atoms. Skipping.
Residue ALA  447 is missing expected H atoms. Skipping.
Residue SER  449 is missing expected H atoms. Skipping.
Residue VAL  451 is missing expected H atoms. Skipping.
Residue SER  452 is missing expected H atoms. Skipping.
Residue ILE  454 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue ILE  457 is missing expected H atoms. Skipping.
Residue LEU  458 is missing expected H atoms. Skipping.
Residue ILE  459 is missing expected H atoms. Skipping.
Residue VAL  461 is missing expected H atoms. Skipping.
Residue ILE  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue THR  464 is missing expected H atoms. Skipping.
Residue ILE  466 is missing expected H atoms. Skipping.
Residue MET  468 is missing expected H atoms. Skipping.
Residue SER  470 is missing expected H atoms. Skipping.
Residue SER  472 is missing expected H atoms. Skipping.
Residue THR  473 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue LEU  475 is missing expected H atoms. Skipping.
Residue SER  476 is missing expected H atoms. Skipping.
Residue VAL  477 is missing expected H atoms. Skipping.
Residue SER  478 is missing expected H atoms. Skipping.
Residue LEU  479 is missing expected H atoms. Skipping.
Residue VAL  480 is missing expected H atoms. Skipping.
Residue LEU  481 is missing expected H atoms. Skipping.
Residue VAL  482 is missing expected H atoms. Skipping.
Residue VAL  484 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue LEU  487 is missing expected H atoms. Skipping.
Residue TYR  488 is missing expected H atoms. Skipping.
Residue LEU  489 is missing expected H atoms. Skipping.
Residue VAL  491 is missing expected H atoms. Skipping.
Residue MET  492 is missing expected H atoms. Skipping.
Residue VAL  493 is missing expected H atoms. Skipping.
Residue VAL    2 is missing expected H atoms. Skipping.
Residue ALA    3 is missing expected H atoms. Skipping.
Residue LEU    4 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue MET   10 is missing expected H atoms. Skipping.
Residue LEU   12 is missing expected H atoms. Skipping.
Residue THR   14 is missing expected H atoms. Skipping.
Residue ALA   15 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue THR   18 is missing expected H atoms. Skipping.
Residue MET   20 is missing expected H atoms. Skipping.
Residue SER   21 is missing expected H atoms. Skipping.
Residue SER   22 is missing expected H atoms. Skipping.
Residue ALA   25 is missing expected H atoms. Skipping.
Residue LYS   27 is missing expected H atoms. Skipping.
Residue ALA   29 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue ILE   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue THR   43 is missing expected H atoms. Skipping.
Residue ILE   44 is missing expected H atoms. Skipping.
Residue MET   45 is missing expected H atoms. Skipping.
Residue ALA   46 is missing expected H atoms. Skipping.
Residue ALA   47 is missing expected H atoms. Skipping.
Residue ILE   48 is missing expected H atoms. Skipping.
Residue LEU   49 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue TYR   51 is missing expected H atoms. Skipping.
Residue THR   52 is missing expected H atoms. Skipping.
Residue ILE   53 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue THR   56 is missing expected H atoms. Skipping.
Residue ALA   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue ILE   63 is missing expected H atoms. Skipping.
Residue ILE   65 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 THR   68 is missing expected H atoms. Skipping.
Residue ALA   69 is missing expected H atoms. Skipping.
Residue VAL   70 is missing expected H atoms. Skipping.
Residue ALA   71 is missing expected H atoms. Skipping.
Residue ILE    4 is missing expected H atoms. Skipping.
Residue ILE    6 is missing expected H atoms. Skipping.
Residue SER    7 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue VAL   15 is missing expected H atoms. Skipping.
Residue SER   16 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue VAL   21 is missing expected H atoms. Skipping.
Residue ILE   23 is missing expected H atoms. Skipping.
Residue VAL   24 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue SER   29 is missing expected H atoms. Skipping.
Residue VAL   31 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 MET   34 is missing expected H atoms. Skipping.
Residue ALA   35 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue THR   40 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue ILE   46 is missing expected H atoms. Skipping.
Residue THR   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue ALA   54 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue ILE   61 is missing expected H atoms. Skipping.
Residue ALA   63 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue LEU   65 is missing expected H atoms. Skipping.
Residue THR   66 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue THR   70 is missing expected H atoms. Skipping.
Residue SER   72 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue SER   81 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LYS   88 is missing expected H atoms. Skipping.
Residue VAL   91 is missing expected H atoms. Skipping.
Residue LYS   93 is missing expected H atoms. Skipping.
Residue SER   95 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue VAL   97 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue ILE  113 is missing expected H atoms. Skipping.
Residue VAL  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  117 is missing expected H atoms. Skipping.
Residue MET  118 is missing expected H atoms. Skipping.
Residue THR  120 is missing expected H atoms. Skipping.
Residue LYS  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  125 is missing expected H atoms. Skipping.
Residue LYS  126 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue VAL  129 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue TYR  137 is missing expected H atoms. Skipping.
Residue THR  138 is missing expected H atoms. Skipping.
Residue ILE  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue ILE  141 is missing expected H atoms. Skipping.
Residue THR  142 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue ALA  150 is missing expected H atoms. Skipping.
Residue VAL  151 is missing expected H atoms. Skipping.
Residue THR  155 is missing expected H atoms. Skipping.
Residue LYS  157 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Residue ILE  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue ILE  164 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue SER  169 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue ALA  173 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue THR  176 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue THR  182 is missing expected H atoms. Skipping.
Residue MET  183 is missing expected H atoms. Skipping.
Residue SER  186 is missing expected H atoms. Skipping.
Residue THR  189 is missing expected H atoms. Skipping.
Residue LEU  191 is missing expected H atoms. Skipping.
Residue MET  196 is missing expected H atoms. Skipping.
Residue VAL  197 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  201 is missing expected H atoms. Skipping.
Residue LYS  204 is missing expected H atoms. Skipping.
Residue ALA  205 is missing expected H atoms. Skipping.
Residue LEU  207 is missing expected H atoms. Skipping.
Residue VAL  208 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LEU  216 is missing expected H atoms. Skipping.
Residue LEU  218 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue ALA  224 is missing expected H atoms. Skipping.
Residue THR  226 is missing expected H atoms. Skipping.
Residue SER  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue THR  236 is missing expected H atoms. Skipping.
Residue LEU  237 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue THR  239 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue VAL  250 is missing expected H atoms. Skipping.
Residue VAL  251 is missing expected H atoms. Skipping.
Residue VAL  252 is missing expected H atoms. Skipping.
Residue LEU  253 is missing expected H atoms. Skipping.
Residue SER  255 is missing expected H atoms. Skipping.
Residue ALA  259 is missing expected H atoms. Skipping.
Residue MET  260 is missing expected H atoms. Skipping.
Residue THR  262 is missing expected H atoms. Skipping.
Residue ALA  263 is missing expected H atoms. Skipping.
Residue LEU  264 is missing expected H atoms. Skipping.
Residue THR  265 is missing expected H atoms. Skipping.
Residue ALA  267 is missing expected H atoms. Skipping.
Residue THR  268 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue SER  273 is missing expected H atoms. Skipping.
Residue SER  274 is missing expected H atoms. Skipping.
Residue LEU  277 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue LYS  284 is missing expected H atoms. Skipping.
Residue LEU  287 is missing expected H atoms. Skipping.
Residue MET  289 is missing expected H atoms. Skipping.
Residue LYS  291 is missing expected H atoms. Skipping.
Residue LEU  292 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue LYS  295 is missing expected H atoms. Skipping.
Residue MET  297 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue TYR  299 is missing expected H atoms. Skipping.
Residue SER  300 is missing expected H atoms. Skipping.
Residue MET  301 is missing expected H atoms. Skipping.
Residue THR  303 is missing expected H atoms. Skipping.
Residue LYS  305 is missing expected H atoms. Skipping.
Residue LYS  307 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue VAL  309 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue ILE  312 is missing expected H atoms. Skipping.
Residue ALA  313 is missing expected H atoms. Skipping.
Residue THR  315 is missing expected H atoms. Skipping.
Residue THR  319 is missing expected H atoms. Skipping.
Residue ILE  320 is missing expected H atoms. Skipping.
Residue VAL  321 is missing expected H atoms. Skipping.
Residue ILE  322 is missing expected H atoms. Skipping.
Residue VAL  324 is missing expected H atoms. Skipping.
Residue TYR  326 is missing expected H atoms. Skipping.
Residue SER  331 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue ILE  335 is missing expected H atoms. Skipping.
Residue ILE  339 is missing expected H atoms. Skipping.
Residue MET  340 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue LYS  344 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  348 is missing expected H atoms. Skipping.
Residue LEU  351 is missing expected H atoms. Skipping.
Residue ILE  352 is missing expected H atoms. Skipping.
Residue THR  353 is missing expected H atoms. Skipping.
Residue VAL  354 is missing expected H atoms. Skipping.
Residue ILE  357 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LYS  361 is missing expected H atoms. Skipping.
Residue SER  363 is missing expected H atoms. Skipping.
Residue VAL  365 is missing expected H atoms. Skipping.
Residue ILE  367 is missing expected H atoms. Skipping.
Residue ALA  369 is missing expected H atoms. Skipping.
Residue SER  376 is missing expected H atoms. Skipping.
Residue TYR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue ILE  379 is missing expected H atoms. Skipping.
Residue ILE  380 is missing expected H atoms. Skipping.
Residue VAL  382 is missing expected H atoms. Skipping.
Residue LEU  387 is missing expected H atoms. Skipping.
Residue LYS  388 is missing expected H atoms. Skipping.
Residue LEU  389 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue LYS  394 is missing expected H atoms. Skipping.
Residue SER  396 is missing expected H atoms. Skipping.
Residue SER  397 is missing expected H atoms. Skipping.
Residue ILE  398 is missing expected H atoms. Skipping.
Residue MET  401 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue THR  404 is missing expected H atoms. Skipping.
Residue THR  405 is missing expected H atoms. Skipping.
Residue MET  406 is missing expected H atoms. Skipping.
Residue ALA  409 is missing expected H atoms. Skipping.
Residue LYS  410 is missing expected H atoms. Skipping.
Residue MET  412 is missing expected H atoms. Skipping.
Residue ALA  413 is missing expected H atoms. Skipping.
Residue ILE  414 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue ALA  419 is missing expected H atoms. Skipping.
Residue SER  424 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue VAL  428 is missing expected H atoms. Skipping.
Residue THR  430 is missing expected H atoms. Skipping.
Residue SER  431 is missing expected H atoms. Skipping.
Residue ILE  432 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue ALA  435 is missing expected H atoms. Skipping.
Residue LEU  436 is missing expected H atoms. Skipping.
Residue VAL  439 is missing expected H atoms. Skipping.
Residue ALA  442 is missing expected H atoms. Skipping.
Residue ILE  443 is missing expected H atoms. Skipping.
Residue TYR  444 is missing expected H atoms. Skipping.
Residue ALA  446 is missing expected H atoms. Skipping.
Residue ALA  447 is missing expected H atoms. Skipping.
Residue SER  449 is missing expected H atoms. Skipping.
Residue VAL  451 is missing expected H atoms. Skipping.
Residue SER  452 is missing expected H atoms. Skipping.
Residue ILE  454 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue ILE  457 is missing expected H atoms. Skipping.
Residue LEU  458 is missing expected H atoms. Skipping.
Residue ILE  459 is missing expected H atoms. Skipping.
Residue VAL  461 is missing expected H atoms. Skipping.
Residue ILE  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue THR  464 is missing expected H atoms. Skipping.
Residue ILE  466 is missing expected H atoms. Skipping.
Residue MET  468 is missing expected H atoms. Skipping.
Residue SER  470 is missing expected H atoms. Skipping.
Residue SER  472 is missing expected H atoms. Skipping.
Residue THR  473 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue LEU  475 is missing expected H atoms. Skipping.
Residue SER  476 is missing expected H atoms. Skipping.
Residue VAL  477 is missing expected H atoms. Skipping.
Residue SER  478 is missing expected H atoms. Skipping.
Residue LEU  479 is missing expected H atoms. Skipping.
Residue VAL  480 is missing expected H atoms. Skipping.
Residue LEU  481 is missing expected H atoms. Skipping.
Residue VAL  482 is missing expected H atoms. Skipping.
Residue VAL  484 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue LEU  487 is missing expected H atoms. Skipping.
Residue TYR  488 is missing expected H atoms. Skipping.
Residue LEU  489 is missing expected H atoms. Skipping.
Residue VAL  491 is missing expected H atoms. Skipping.
Residue MET  492 is missing expected H atoms. Skipping.
Residue VAL  493 is missing expected H atoms. Skipping.
Residue VAL    2 is missing expected H atoms. Skipping.
Residue ALA    3 is missing expected H atoms. Skipping.
Residue LEU    4 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue MET   10 is missing expected H atoms. Skipping.
Residue LEU   12 is missing expected H atoms. Skipping.
Residue THR   14 is missing expected H atoms. Skipping.
Residue ALA   15 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue THR   18 is missing expected H atoms. Skipping.
Residue MET   20 is missing expected H atoms. Skipping.
Residue SER   21 is missing expected H atoms. Skipping.
Residue SER   22 is missing expected H atoms. Skipping.
Residue ALA   25 is missing expected H atoms. Skipping.
Residue LYS   27 is missing expected H atoms. Skipping.
Residue ALA   29 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue ILE   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue THR   43 is missing expected H atoms. Skipping.
Residue ILE   44 is missing expected H atoms. Skipping.
Residue MET   45 is missing expected H atoms. Skipping.
Residue ALA   46 is missing expected H atoms. Skipping.
Residue ALA   47 is missing expected H atoms. Skipping.
Residue ILE   48 is missing expected H atoms. Skipping.
Residue LEU   49 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue TYR   51 is missing expected H atoms. Skipping.
Residue THR   52 is missing expected H atoms. Skipping.
Residue ILE   53 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue THR   56 is missing expected H atoms. Skipping.
Residue ALA   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue ILE   63 is missing expected H atoms. Skipping.
Residue ILE   65 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 THR   68 is missing expected H atoms. Skipping.
Residue ALA   69 is missing expected H atoms. Skipping.
Residue VAL   70 is missing expected H atoms. Skipping.
Residue ALA   71 is missing expected H atoms. Skipping.
Evaluate side-chains
  349 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 56
    poor density    : 293
  time to evaluate  : 1.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 56
  outliers final: 31
  residues processed: 319
  average time/residue: 0.2218
  time to fit residues: 100.4226
Evaluate side-chains
  282 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 251
  time to evaluate  : 1.133 
Switching outliers to nearest non-outliers
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 31
  outliers final: 2
  residues processed: 31
  average time/residue: 0.1192
  time to fit residues: 8.1498
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 84 optimal weight:    7.9990
   chunk 69 optimal weight:    9.9990
   chunk 28 optimal weight:    7.9990
   chunk 101 optimal weight:    9.9990
   chunk 110 optimal weight:   20.0000
   chunk 90 optimal weight:   30.0000
   chunk 34 optimal weight:   20.0000
   chunk 81 optimal weight:   20.0000
   chunk 100 optimal weight:    0.4980
   overall best weight:    3.6784

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

Flipped N/Q/H residues before XYZ refinement:
** A  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  94 HIS
** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 230 ASN
A 276 ASN
** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 386 GLN
** B   7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   8 ASN
** C  27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  94 HIS
** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 248 GLN
C 276 ASN
** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.4516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8986  Z= 0.193
  Angle     :  0.813   7.011  12164  Z= 0.419
  Chirality :  0.046   0.268   1412
  Planarity :  0.005   0.044   1520
  Dihedral  :  7.230  70.119   1224
  Min Nonbonded Distance : 1.907

Molprobity Statistics.
  All-atom Clashscore : 74.09
  Ramachandran Plot:
    Outliers :  5.06 %
    Allowed  : 25.58 %
    Favored  : 69.36 %
  Rotamer Outliers :  4.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -6.15 (0.19), residues: 1126
  helix: -3.20 (0.21), residues: 296
  sheet: -2.87 (0.29), residues: 272
  loop : -5.40 (0.18), residues: 558

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE    4 is missing expected H atoms. Skipping.
Residue ILE    6 is missing expected H atoms. Skipping.
Residue SER    7 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue VAL   15 is missing expected H atoms. Skipping.
Residue SER   16 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue VAL   21 is missing expected H atoms. Skipping.
Residue ILE   23 is missing expected H atoms. Skipping.
Residue VAL   24 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue SER   29 is missing expected H atoms. Skipping.
Residue VAL   31 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 MET   34 is missing expected H atoms. Skipping.
Residue ALA   35 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue THR   40 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue ILE   46 is missing expected H atoms. Skipping.
Residue THR   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue ALA   54 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue ILE   61 is missing expected H atoms. Skipping.
Residue ALA   63 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue LEU   65 is missing expected H atoms. Skipping.
Residue THR   66 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue THR   70 is missing expected H atoms. Skipping.
Residue SER   72 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue SER   81 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LYS   88 is missing expected H atoms. Skipping.
Residue VAL   91 is missing expected H atoms. Skipping.
Residue LYS   93 is missing expected H atoms. Skipping.
Residue SER   95 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue VAL   97 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue ILE  113 is missing expected H atoms. Skipping.
Residue VAL  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  117 is missing expected H atoms. Skipping.
Residue MET  118 is missing expected H atoms. Skipping.
Residue THR  120 is missing expected H atoms. Skipping.
Residue LYS  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  125 is missing expected H atoms. Skipping.
Residue LYS  126 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue VAL  129 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue TYR  137 is missing expected H atoms. Skipping.
Residue THR  138 is missing expected H atoms. Skipping.
Residue ILE  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue ILE  141 is missing expected H atoms. Skipping.
Residue THR  142 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue ALA  150 is missing expected H atoms. Skipping.
Residue VAL  151 is missing expected H atoms. Skipping.
Residue THR  155 is missing expected H atoms. Skipping.
Residue LYS  157 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Residue ILE  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue ILE  164 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue SER  169 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue ALA  173 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue THR  176 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue THR  182 is missing expected H atoms. Skipping.
Residue MET  183 is missing expected H atoms. Skipping.
Residue SER  186 is missing expected H atoms. Skipping.
Residue THR  189 is missing expected H atoms. Skipping.
Residue LEU  191 is missing expected H atoms. Skipping.
Residue MET  196 is missing expected H atoms. Skipping.
Residue VAL  197 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  201 is missing expected H atoms. Skipping.
Residue LYS  204 is missing expected H atoms. Skipping.
Residue ALA  205 is missing expected H atoms. Skipping.
Residue LEU  207 is missing expected H atoms. Skipping.
Residue VAL  208 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LEU  216 is missing expected H atoms. Skipping.
Residue LEU  218 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue ALA  224 is missing expected H atoms. Skipping.
Residue THR  226 is missing expected H atoms. Skipping.
Residue SER  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue THR  236 is missing expected H atoms. Skipping.
Residue LEU  237 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue THR  239 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue VAL  250 is missing expected H atoms. Skipping.
Residue VAL  251 is missing expected H atoms. Skipping.
Residue VAL  252 is missing expected H atoms. Skipping.
Residue LEU  253 is missing expected H atoms. Skipping.
Residue SER  255 is missing expected H atoms. Skipping.
Residue ALA  259 is missing expected H atoms. Skipping.
Residue MET  260 is missing expected H atoms. Skipping.
Residue THR  262 is missing expected H atoms. Skipping.
Residue ALA  263 is missing expected H atoms. Skipping.
Residue LEU  264 is missing expected H atoms. Skipping.
Residue THR  265 is missing expected H atoms. Skipping.
Residue ALA  267 is missing expected H atoms. Skipping.
Residue THR  268 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue SER  273 is missing expected H atoms. Skipping.
Residue SER  274 is missing expected H atoms. Skipping.
Residue LEU  277 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue LYS  284 is missing expected H atoms. Skipping.
Residue LEU  287 is missing expected H atoms. Skipping.
Residue MET  289 is missing expected H atoms. Skipping.
Residue LYS  291 is missing expected H atoms. Skipping.
Residue LEU  292 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue LYS  295 is missing expected H atoms. Skipping.
Residue MET  297 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue TYR  299 is missing expected H atoms. Skipping.
Residue SER  300 is missing expected H atoms. Skipping.
Residue MET  301 is missing expected H atoms. Skipping.
Residue THR  303 is missing expected H atoms. Skipping.
Residue LYS  305 is missing expected H atoms. Skipping.
Residue LYS  307 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue VAL  309 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue ILE  312 is missing expected H atoms. Skipping.
Residue ALA  313 is missing expected H atoms. Skipping.
Residue THR  315 is missing expected H atoms. Skipping.
Residue THR  319 is missing expected H atoms. Skipping.
Residue ILE  320 is missing expected H atoms. Skipping.
Residue VAL  321 is missing expected H atoms. Skipping.
Residue ILE  322 is missing expected H atoms. Skipping.
Residue VAL  324 is missing expected H atoms. Skipping.
Residue TYR  326 is missing expected H atoms. Skipping.
Residue SER  331 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue ILE  335 is missing expected H atoms. Skipping.
Residue ILE  339 is missing expected H atoms. Skipping.
Residue MET  340 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue LYS  344 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  348 is missing expected H atoms. Skipping.
Residue LEU  351 is missing expected H atoms. Skipping.
Residue ILE  352 is missing expected H atoms. Skipping.
Residue THR  353 is missing expected H atoms. Skipping.
Residue VAL  354 is missing expected H atoms. Skipping.
Residue ILE  357 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LYS  361 is missing expected H atoms. Skipping.
Residue SER  363 is missing expected H atoms. Skipping.
Residue VAL  365 is missing expected H atoms. Skipping.
Residue ILE  367 is missing expected H atoms. Skipping.
Residue ALA  369 is missing expected H atoms. Skipping.
Residue SER  376 is missing expected H atoms. Skipping.
Residue TYR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue ILE  379 is missing expected H atoms. Skipping.
Residue ILE  380 is missing expected H atoms. Skipping.
Residue VAL  382 is missing expected H atoms. Skipping.
Residue LEU  387 is missing expected H atoms. Skipping.
Residue LYS  388 is missing expected H atoms. Skipping.
Residue LEU  389 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue LYS  394 is missing expected H atoms. Skipping.
Residue SER  396 is missing expected H atoms. Skipping.
Residue SER  397 is missing expected H atoms. Skipping.
Residue ILE  398 is missing expected H atoms. Skipping.
Residue MET  401 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue THR  404 is missing expected H atoms. Skipping.
Residue THR  405 is missing expected H atoms. Skipping.
Residue MET  406 is missing expected H atoms. Skipping.
Residue ALA  409 is missing expected H atoms. Skipping.
Residue LYS  410 is missing expected H atoms. Skipping.
Residue MET  412 is missing expected H atoms. Skipping.
Residue ALA  413 is missing expected H atoms. Skipping.
Residue ILE  414 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue ALA  419 is missing expected H atoms. Skipping.
Residue SER  424 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue VAL  428 is missing expected H atoms. Skipping.
Residue THR  430 is missing expected H atoms. Skipping.
Residue SER  431 is missing expected H atoms. Skipping.
Residue ILE  432 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue ALA  435 is missing expected H atoms. Skipping.
Residue LEU  436 is missing expected H atoms. Skipping.
Residue VAL  439 is missing expected H atoms. Skipping.
Residue ALA  442 is missing expected H atoms. Skipping.
Residue ILE  443 is missing expected H atoms. Skipping.
Residue TYR  444 is missing expected H atoms. Skipping.
Residue ALA  446 is missing expected H atoms. Skipping.
Residue ALA  447 is missing expected H atoms. Skipping.
Residue SER  449 is missing expected H atoms. Skipping.
Residue VAL  451 is missing expected H atoms. Skipping.
Residue SER  452 is missing expected H atoms. Skipping.
Residue ILE  454 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue ILE  457 is missing expected H atoms. Skipping.
Residue LEU  458 is missing expected H atoms. Skipping.
Residue ILE  459 is missing expected H atoms. Skipping.
Residue VAL  461 is missing expected H atoms. Skipping.
Residue ILE  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue THR  464 is missing expected H atoms. Skipping.
Residue ILE  466 is missing expected H atoms. Skipping.
Residue MET  468 is missing expected H atoms. Skipping.
Residue SER  470 is missing expected H atoms. Skipping.
Residue SER  472 is missing expected H atoms. Skipping.
Residue THR  473 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue LEU  475 is missing expected H atoms. Skipping.
Residue SER  476 is missing expected H atoms. Skipping.
Residue VAL  477 is missing expected H atoms. Skipping.
Residue SER  478 is missing expected H atoms. Skipping.
Residue LEU  479 is missing expected H atoms. Skipping.
Residue VAL  480 is missing expected H atoms. Skipping.
Residue LEU  481 is missing expected H atoms. Skipping.
Residue VAL  482 is missing expected H atoms. Skipping.
Residue VAL  484 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue LEU  487 is missing expected H atoms. Skipping.
Residue TYR  488 is missing expected H atoms. Skipping.
Residue LEU  489 is missing expected H atoms. Skipping.
Residue VAL  491 is missing expected H atoms. Skipping.
Residue MET  492 is missing expected H atoms. Skipping.
Residue VAL  493 is missing expected H atoms. Skipping.
Residue VAL    2 is missing expected H atoms. Skipping.
Residue ALA    3 is missing expected H atoms. Skipping.
Residue LEU    4 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue MET   10 is missing expected H atoms. Skipping.
Residue LEU   12 is missing expected H atoms. Skipping.
Residue THR   14 is missing expected H atoms. Skipping.
Residue ALA   15 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue THR   18 is missing expected H atoms. Skipping.
Residue MET   20 is missing expected H atoms. Skipping.
Residue SER   21 is missing expected H atoms. Skipping.
Residue SER   22 is missing expected H atoms. Skipping.
Residue ALA   25 is missing expected H atoms. Skipping.
Residue LYS   27 is missing expected H atoms. Skipping.
Residue ALA   29 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue ILE   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue THR   43 is missing expected H atoms. Skipping.
Residue ILE   44 is missing expected H atoms. Skipping.
Residue MET   45 is missing expected H atoms. Skipping.
Residue ALA   46 is missing expected H atoms. Skipping.
Residue ALA   47 is missing expected H atoms. Skipping.
Residue ILE   48 is missing expected H atoms. Skipping.
Residue LEU   49 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue TYR   51 is missing expected H atoms. Skipping.
Residue THR   52 is missing expected H atoms. Skipping.
Residue ILE   53 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue THR   56 is missing expected H atoms. Skipping.
Residue ALA   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue ILE   63 is missing expected H atoms. Skipping.
Residue ILE   65 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 THR   68 is missing expected H atoms. Skipping.
Residue ALA   69 is missing expected H atoms. Skipping.
Residue VAL   70 is missing expected H atoms. Skipping.
Residue ALA   71 is missing expected H atoms. Skipping.
Residue ILE    4 is missing expected H atoms. Skipping.
Residue ILE    6 is missing expected H atoms. Skipping.
Residue SER    7 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue VAL   15 is missing expected H atoms. Skipping.
Residue SER   16 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue VAL   21 is missing expected H atoms. Skipping.
Residue ILE   23 is missing expected H atoms. Skipping.
Residue VAL   24 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue SER   29 is missing expected H atoms. Skipping.
Residue VAL   31 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 MET   34 is missing expected H atoms. Skipping.
Residue ALA   35 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue THR   40 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue ILE   46 is missing expected H atoms. Skipping.
Residue THR   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue ALA   54 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue ILE   61 is missing expected H atoms. Skipping.
Residue ALA   63 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue LEU   65 is missing expected H atoms. Skipping.
Residue THR   66 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue THR   70 is missing expected H atoms. Skipping.
Residue SER   72 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue SER   81 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LYS   88 is missing expected H atoms. Skipping.
Residue VAL   91 is missing expected H atoms. Skipping.
Residue LYS   93 is missing expected H atoms. Skipping.
Residue SER   95 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue VAL   97 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue ILE  113 is missing expected H atoms. Skipping.
Residue VAL  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  117 is missing expected H atoms. Skipping.
Residue MET  118 is missing expected H atoms. Skipping.
Residue THR  120 is missing expected H atoms. Skipping.
Residue LYS  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  125 is missing expected H atoms. Skipping.
Residue LYS  126 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue VAL  129 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue TYR  137 is missing expected H atoms. Skipping.
Residue THR  138 is missing expected H atoms. Skipping.
Residue ILE  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue ILE  141 is missing expected H atoms. Skipping.
Residue THR  142 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue ALA  150 is missing expected H atoms. Skipping.
Residue VAL  151 is missing expected H atoms. Skipping.
Residue THR  155 is missing expected H atoms. Skipping.
Residue LYS  157 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Residue ILE  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue ILE  164 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue SER  169 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue ALA  173 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue THR  176 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue THR  182 is missing expected H atoms. Skipping.
Residue MET  183 is missing expected H atoms. Skipping.
Residue SER  186 is missing expected H atoms. Skipping.
Residue THR  189 is missing expected H atoms. Skipping.
Residue LEU  191 is missing expected H atoms. Skipping.
Residue MET  196 is missing expected H atoms. Skipping.
Residue VAL  197 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  201 is missing expected H atoms. Skipping.
Residue LYS  204 is missing expected H atoms. Skipping.
Residue ALA  205 is missing expected H atoms. Skipping.
Residue LEU  207 is missing expected H atoms. Skipping.
Residue VAL  208 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LEU  216 is missing expected H atoms. Skipping.
Residue LEU  218 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue ALA  224 is missing expected H atoms. Skipping.
Residue THR  226 is missing expected H atoms. Skipping.
Residue SER  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue THR  236 is missing expected H atoms. Skipping.
Residue LEU  237 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue THR  239 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue VAL  250 is missing expected H atoms. Skipping.
Residue VAL  251 is missing expected H atoms. Skipping.
Residue VAL  252 is missing expected H atoms. Skipping.
Residue LEU  253 is missing expected H atoms. Skipping.
Residue SER  255 is missing expected H atoms. Skipping.
Residue ALA  259 is missing expected H atoms. Skipping.
Residue MET  260 is missing expected H atoms. Skipping.
Residue THR  262 is missing expected H atoms. Skipping.
Residue ALA  263 is missing expected H atoms. Skipping.
Residue LEU  264 is missing expected H atoms. Skipping.
Residue THR  265 is missing expected H atoms. Skipping.
Residue ALA  267 is missing expected H atoms. Skipping.
Residue THR  268 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue SER  273 is missing expected H atoms. Skipping.
Residue SER  274 is missing expected H atoms. Skipping.
Residue LEU  277 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue LYS  284 is missing expected H atoms. Skipping.
Residue LEU  287 is missing expected H atoms. Skipping.
Residue MET  289 is missing expected H atoms. Skipping.
Residue LYS  291 is missing expected H atoms. Skipping.
Residue LEU  292 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue LYS  295 is missing expected H atoms. Skipping.
Residue MET  297 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue TYR  299 is missing expected H atoms. Skipping.
Residue SER  300 is missing expected H atoms. Skipping.
Residue MET  301 is missing expected H atoms. Skipping.
Residue THR  303 is missing expected H atoms. Skipping.
Residue LYS  305 is missing expected H atoms. Skipping.
Residue LYS  307 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue VAL  309 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue ILE  312 is missing expected H atoms. Skipping.
Residue ALA  313 is missing expected H atoms. Skipping.
Residue THR  315 is missing expected H atoms. Skipping.
Residue THR  319 is missing expected H atoms. Skipping.
Residue ILE  320 is missing expected H atoms. Skipping.
Residue VAL  321 is missing expected H atoms. Skipping.
Residue ILE  322 is missing expected H atoms. Skipping.
Residue VAL  324 is missing expected H atoms. Skipping.
Residue TYR  326 is missing expected H atoms. Skipping.
Residue SER  331 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue ILE  335 is missing expected H atoms. Skipping.
Residue ILE  339 is missing expected H atoms. Skipping.
Residue MET  340 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue LYS  344 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  348 is missing expected H atoms. Skipping.
Residue LEU  351 is missing expected H atoms. Skipping.
Residue ILE  352 is missing expected H atoms. Skipping.
Residue THR  353 is missing expected H atoms. Skipping.
Residue VAL  354 is missing expected H atoms. Skipping.
Residue ILE  357 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LYS  361 is missing expected H atoms. Skipping.
Residue SER  363 is missing expected H atoms. Skipping.
Residue VAL  365 is missing expected H atoms. Skipping.
Residue ILE  367 is missing expected H atoms. Skipping.
Residue ALA  369 is missing expected H atoms. Skipping.
Residue SER  376 is missing expected H atoms. Skipping.
Residue TYR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue ILE  379 is missing expected H atoms. Skipping.
Residue ILE  380 is missing expected H atoms. Skipping.
Residue VAL  382 is missing expected H atoms. Skipping.
Residue LEU  387 is missing expected H atoms. Skipping.
Residue LYS  388 is missing expected H atoms. Skipping.
Residue LEU  389 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue LYS  394 is missing expected H atoms. Skipping.
Residue SER  396 is missing expected H atoms. Skipping.
Residue SER  397 is missing expected H atoms. Skipping.
Residue ILE  398 is missing expected H atoms. Skipping.
Residue MET  401 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue THR  404 is missing expected H atoms. Skipping.
Residue THR  405 is missing expected H atoms. Skipping.
Residue MET  406 is missing expected H atoms. Skipping.
Residue ALA  409 is missing expected H atoms. Skipping.
Residue LYS  410 is missing expected H atoms. Skipping.
Residue MET  412 is missing expected H atoms. Skipping.
Residue ALA  413 is missing expected H atoms. Skipping.
Residue ILE  414 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue ALA  419 is missing expected H atoms. Skipping.
Residue SER  424 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue VAL  428 is missing expected H atoms. Skipping.
Residue THR  430 is missing expected H atoms. Skipping.
Residue SER  431 is missing expected H atoms. Skipping.
Residue ILE  432 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue ALA  435 is missing expected H atoms. Skipping.
Residue LEU  436 is missing expected H atoms. Skipping.
Residue VAL  439 is missing expected H atoms. Skipping.
Residue ALA  442 is missing expected H atoms. Skipping.
Residue ILE  443 is missing expected H atoms. Skipping.
Residue TYR  444 is missing expected H atoms. Skipping.
Residue ALA  446 is missing expected H atoms. Skipping.
Residue ALA  447 is missing expected H atoms. Skipping.
Residue SER  449 is missing expected H atoms. Skipping.
Residue VAL  451 is missing expected H atoms. Skipping.
Residue SER  452 is missing expected H atoms. Skipping.
Residue ILE  454 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue ILE  457 is missing expected H atoms. Skipping.
Residue LEU  458 is missing expected H atoms. Skipping.
Residue ILE  459 is missing expected H atoms. Skipping.
Residue VAL  461 is missing expected H atoms. Skipping.
Residue ILE  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue THR  464 is missing expected H atoms. Skipping.
Residue ILE  466 is missing expected H atoms. Skipping.
Residue MET  468 is missing expected H atoms. Skipping.
Residue SER  470 is missing expected H atoms. Skipping.
Residue SER  472 is missing expected H atoms. Skipping.
Residue THR  473 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue LEU  475 is missing expected H atoms. Skipping.
Residue SER  476 is missing expected H atoms. Skipping.
Residue VAL  477 is missing expected H atoms. Skipping.
Residue SER  478 is missing expected H atoms. Skipping.
Residue LEU  479 is missing expected H atoms. Skipping.
Residue VAL  480 is missing expected H atoms. Skipping.
Residue LEU  481 is missing expected H atoms. Skipping.
Residue VAL  482 is missing expected H atoms. Skipping.
Residue VAL  484 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue LEU  487 is missing expected H atoms. Skipping.
Residue TYR  488 is missing expected H atoms. Skipping.
Residue LEU  489 is missing expected H atoms. Skipping.
Residue VAL  491 is missing expected H atoms. Skipping.
Residue MET  492 is missing expected H atoms. Skipping.
Residue VAL  493 is missing expected H atoms. Skipping.
Residue VAL    2 is missing expected H atoms. Skipping.
Residue ALA    3 is missing expected H atoms. Skipping.
Residue LEU    4 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue MET   10 is missing expected H atoms. Skipping.
Residue LEU   12 is missing expected H atoms. Skipping.
Residue THR   14 is missing expected H atoms. Skipping.
Residue ALA   15 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue THR   18 is missing expected H atoms. Skipping.
Residue MET   20 is missing expected H atoms. Skipping.
Residue SER   21 is missing expected H atoms. Skipping.
Residue SER   22 is missing expected H atoms. Skipping.
Residue ALA   25 is missing expected H atoms. Skipping.
Residue LYS   27 is missing expected H atoms. Skipping.
Residue ALA   29 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue ILE   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue THR   43 is missing expected H atoms. Skipping.
Residue ILE   44 is missing expected H atoms. Skipping.
Residue MET   45 is missing expected H atoms. Skipping.
Residue ALA   46 is missing expected H atoms. Skipping.
Residue ALA   47 is missing expected H atoms. Skipping.
Residue ILE   48 is missing expected H atoms. Skipping.
Residue LEU   49 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue TYR   51 is missing expected H atoms. Skipping.
Residue THR   52 is missing expected H atoms. Skipping.
Residue ILE   53 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue THR   56 is missing expected H atoms. Skipping.
Residue ALA   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue ILE   63 is missing expected H atoms. Skipping.
Residue ILE   65 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 THR   68 is missing expected H atoms. Skipping.
Residue ALA   69 is missing expected H atoms. Skipping.
Residue VAL   70 is missing expected H atoms. Skipping.
Residue ALA   71 is missing expected H atoms. Skipping.
Evaluate side-chains
  332 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 47
    poor density    : 285
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 47
  outliers final: 22
  residues processed: 301
  average time/residue: 0.2020
  time to fit residues: 86.8482
Evaluate side-chains
  279 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 257
  time to evaluate  : 1.021 
Switching outliers to nearest non-outliers
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 22
  outliers final: 2
  residues processed: 22
  average time/residue: 0.1236
  time to fit residues: 5.9959
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 76 optimal weight:   20.0000
   chunk 52 optimal weight:   20.0000
   chunk 11 optimal weight:   30.0000
   chunk 48 optimal weight:   20.0000
   chunk 68 optimal weight:    8.9990
   chunk 102 optimal weight:    7.9990
   chunk 108 optimal weight:   20.0000
   chunk 53 optimal weight:   10.0000
   chunk 96 optimal weight:    5.9990
   chunk 29 optimal weight:   40.0000
   chunk 90 optimal weight:   30.0000
   overall best weight:   10.5994

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

Flipped N/Q/H residues before XYZ refinement:
** A  27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 158 HIS
** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   7 HIS
** B  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 244 HIS
** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   7 HIS
** D  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.4793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.044   8986  Z= 0.347
  Angle     :  0.882   7.404  12164  Z= 0.451
  Chirality :  0.049   0.243   1412
  Planarity :  0.006   0.044   1520
  Dihedral  :  7.388  67.086   1224
  Min Nonbonded Distance : 1.857

Molprobity Statistics.
  All-atom Clashscore : 79.81
  Ramachandran Plot:
    Outliers :  4.62 %
    Allowed  : 26.55 %
    Favored  : 68.83 %
  Rotamer Outliers :  8.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -5.92 (0.19), residues: 1126
  helix: -2.90 (0.22), residues: 302
  sheet: -2.62 (0.30), residues: 280
  loop : -5.45 (0.17), residues: 544

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE    4 is missing expected H atoms. Skipping.
Residue ILE    6 is missing expected H atoms. Skipping.
Residue SER    7 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue VAL   15 is missing expected H atoms. Skipping.
Residue SER   16 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue VAL   21 is missing expected H atoms. Skipping.
Residue ILE   23 is missing expected H atoms. Skipping.
Residue VAL   24 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue SER   29 is missing expected H atoms. Skipping.
Residue VAL   31 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 MET   34 is missing expected H atoms. Skipping.
Residue ALA   35 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue THR   40 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue ILE   46 is missing expected H atoms. Skipping.
Residue THR   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue ALA   54 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue ILE   61 is missing expected H atoms. Skipping.
Residue ALA   63 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue LEU   65 is missing expected H atoms. Skipping.
Residue THR   66 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue THR   70 is missing expected H atoms. Skipping.
Residue SER   72 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue SER   81 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LYS   88 is missing expected H atoms. Skipping.
Residue VAL   91 is missing expected H atoms. Skipping.
Residue LYS   93 is missing expected H atoms. Skipping.
Residue SER   95 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue VAL   97 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue ILE  113 is missing expected H atoms. Skipping.
Residue VAL  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  117 is missing expected H atoms. Skipping.
Residue MET  118 is missing expected H atoms. Skipping.
Residue THR  120 is missing expected H atoms. Skipping.
Residue LYS  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  125 is missing expected H atoms. Skipping.
Residue LYS  126 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue VAL  129 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue TYR  137 is missing expected H atoms. Skipping.
Residue THR  138 is missing expected H atoms. Skipping.
Residue ILE  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue ILE  141 is missing expected H atoms. Skipping.
Residue THR  142 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue ALA  150 is missing expected H atoms. Skipping.
Residue VAL  151 is missing expected H atoms. Skipping.
Residue THR  155 is missing expected H atoms. Skipping.
Residue LYS  157 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Residue ILE  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue ILE  164 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue SER  169 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue ALA  173 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue THR  176 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue THR  182 is missing expected H atoms. Skipping.
Residue MET  183 is missing expected H atoms. Skipping.
Residue SER  186 is missing expected H atoms. Skipping.
Residue THR  189 is missing expected H atoms. Skipping.
Residue LEU  191 is missing expected H atoms. Skipping.
Residue MET  196 is missing expected H atoms. Skipping.
Residue VAL  197 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  201 is missing expected H atoms. Skipping.
Residue LYS  204 is missing expected H atoms. Skipping.
Residue ALA  205 is missing expected H atoms. Skipping.
Residue LEU  207 is missing expected H atoms. Skipping.
Residue VAL  208 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LEU  216 is missing expected H atoms. Skipping.
Residue LEU  218 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue ALA  224 is missing expected H atoms. Skipping.
Residue THR  226 is missing expected H atoms. Skipping.
Residue SER  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue THR  236 is missing expected H atoms. Skipping.
Residue LEU  237 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue THR  239 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue VAL  250 is missing expected H atoms. Skipping.
Residue VAL  251 is missing expected H atoms. Skipping.
Residue VAL  252 is missing expected H atoms. Skipping.
Residue LEU  253 is missing expected H atoms. Skipping.
Residue SER  255 is missing expected H atoms. Skipping.
Residue ALA  259 is missing expected H atoms. Skipping.
Residue MET  260 is missing expected H atoms. Skipping.
Residue THR  262 is missing expected H atoms. Skipping.
Residue ALA  263 is missing expected H atoms. Skipping.
Residue LEU  264 is missing expected H atoms. Skipping.
Residue THR  265 is missing expected H atoms. Skipping.
Residue ALA  267 is missing expected H atoms. Skipping.
Residue THR  268 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue SER  273 is missing expected H atoms. Skipping.
Residue SER  274 is missing expected H atoms. Skipping.
Residue LEU  277 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue LYS  284 is missing expected H atoms. Skipping.
Residue LEU  287 is missing expected H atoms. Skipping.
Residue MET  289 is missing expected H atoms. Skipping.
Residue LYS  291 is missing expected H atoms. Skipping.
Residue LEU  292 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue LYS  295 is missing expected H atoms. Skipping.
Residue MET  297 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue TYR  299 is missing expected H atoms. Skipping.
Residue SER  300 is missing expected H atoms. Skipping.
Residue MET  301 is missing expected H atoms. Skipping.
Residue THR  303 is missing expected H atoms. Skipping.
Residue LYS  305 is missing expected H atoms. Skipping.
Residue LYS  307 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue VAL  309 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue ILE  312 is missing expected H atoms. Skipping.
Residue ALA  313 is missing expected H atoms. Skipping.
Residue THR  315 is missing expected H atoms. Skipping.
Residue THR  319 is missing expected H atoms. Skipping.
Residue ILE  320 is missing expected H atoms. Skipping.
Residue VAL  321 is missing expected H atoms. Skipping.
Residue ILE  322 is missing expected H atoms. Skipping.
Residue VAL  324 is missing expected H atoms. Skipping.
Residue TYR  326 is missing expected H atoms. Skipping.
Residue SER  331 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue ILE  335 is missing expected H atoms. Skipping.
Residue ILE  339 is missing expected H atoms. Skipping.
Residue MET  340 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue LYS  344 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  348 is missing expected H atoms. Skipping.
Residue LEU  351 is missing expected H atoms. Skipping.
Residue ILE  352 is missing expected H atoms. Skipping.
Residue THR  353 is missing expected H atoms. Skipping.
Residue VAL  354 is missing expected H atoms. Skipping.
Residue ILE  357 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LYS  361 is missing expected H atoms. Skipping.
Residue SER  363 is missing expected H atoms. Skipping.
Residue VAL  365 is missing expected H atoms. Skipping.
Residue ILE  367 is missing expected H atoms. Skipping.
Residue ALA  369 is missing expected H atoms. Skipping.
Residue SER  376 is missing expected H atoms. Skipping.
Residue TYR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue ILE  379 is missing expected H atoms. Skipping.
Residue ILE  380 is missing expected H atoms. Skipping.
Residue VAL  382 is missing expected H atoms. Skipping.
Residue LEU  387 is missing expected H atoms. Skipping.
Residue LYS  388 is missing expected H atoms. Skipping.
Residue LEU  389 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue LYS  394 is missing expected H atoms. Skipping.
Residue SER  396 is missing expected H atoms. Skipping.
Residue SER  397 is missing expected H atoms. Skipping.
Residue ILE  398 is missing expected H atoms. Skipping.
Residue MET  401 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue THR  404 is missing expected H atoms. Skipping.
Residue THR  405 is missing expected H atoms. Skipping.
Residue MET  406 is missing expected H atoms. Skipping.
Residue ALA  409 is missing expected H atoms. Skipping.
Residue LYS  410 is missing expected H atoms. Skipping.
Residue MET  412 is missing expected H atoms. Skipping.
Residue ALA  413 is missing expected H atoms. Skipping.
Residue ILE  414 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue ALA  419 is missing expected H atoms. Skipping.
Residue SER  424 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue VAL  428 is missing expected H atoms. Skipping.
Residue THR  430 is missing expected H atoms. Skipping.
Residue SER  431 is missing expected H atoms. Skipping.
Residue ILE  432 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue ALA  435 is missing expected H atoms. Skipping.
Residue LEU  436 is missing expected H atoms. Skipping.
Residue VAL  439 is missing expected H atoms. Skipping.
Residue ALA  442 is missing expected H atoms. Skipping.
Residue ILE  443 is missing expected H atoms. Skipping.
Residue TYR  444 is missing expected H atoms. Skipping.
Residue ALA  446 is missing expected H atoms. Skipping.
Residue ALA  447 is missing expected H atoms. Skipping.
Residue SER  449 is missing expected H atoms. Skipping.
Residue VAL  451 is missing expected H atoms. Skipping.
Residue SER  452 is missing expected H atoms. Skipping.
Residue ILE  454 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue ILE  457 is missing expected H atoms. Skipping.
Residue LEU  458 is missing expected H atoms. Skipping.
Residue ILE  459 is missing expected H atoms. Skipping.
Residue VAL  461 is missing expected H atoms. Skipping.
Residue ILE  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue THR  464 is missing expected H atoms. Skipping.
Residue ILE  466 is missing expected H atoms. Skipping.
Residue MET  468 is missing expected H atoms. Skipping.
Residue SER  470 is missing expected H atoms. Skipping.
Residue SER  472 is missing expected H atoms. Skipping.
Residue THR  473 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue LEU  475 is missing expected H atoms. Skipping.
Residue SER  476 is missing expected H atoms. Skipping.
Residue VAL  477 is missing expected H atoms. Skipping.
Residue SER  478 is missing expected H atoms. Skipping.
Residue LEU  479 is missing expected H atoms. Skipping.
Residue VAL  480 is missing expected H atoms. Skipping.
Residue LEU  481 is missing expected H atoms. Skipping.
Residue VAL  482 is missing expected H atoms. Skipping.
Residue VAL  484 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue LEU  487 is missing expected H atoms. Skipping.
Residue TYR  488 is missing expected H atoms. Skipping.
Residue LEU  489 is missing expected H atoms. Skipping.
Residue VAL  491 is missing expected H atoms. Skipping.
Residue MET  492 is missing expected H atoms. Skipping.
Residue VAL  493 is missing expected H atoms. Skipping.
Residue VAL    2 is missing expected H atoms. Skipping.
Residue ALA    3 is missing expected H atoms. Skipping.
Residue LEU    4 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue MET   10 is missing expected H atoms. Skipping.
Residue LEU   12 is missing expected H atoms. Skipping.
Residue THR   14 is missing expected H atoms. Skipping.
Residue ALA   15 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue THR   18 is missing expected H atoms. Skipping.
Residue MET   20 is missing expected H atoms. Skipping.
Residue SER   21 is missing expected H atoms. Skipping.
Residue SER   22 is missing expected H atoms. Skipping.
Residue ALA   25 is missing expected H atoms. Skipping.
Residue LYS   27 is missing expected H atoms. Skipping.
Residue ALA   29 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue ILE   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue THR   43 is missing expected H atoms. Skipping.
Residue ILE   44 is missing expected H atoms. Skipping.
Residue MET   45 is missing expected H atoms. Skipping.
Residue ALA   46 is missing expected H atoms. Skipping.
Residue ALA   47 is missing expected H atoms. Skipping.
Residue ILE   48 is missing expected H atoms. Skipping.
Residue LEU   49 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue TYR   51 is missing expected H atoms. Skipping.
Residue THR   52 is missing expected H atoms. Skipping.
Residue ILE   53 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue THR   56 is missing expected H atoms. Skipping.
Residue ALA   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue ILE   63 is missing expected H atoms. Skipping.
Residue ILE   65 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 THR   68 is missing expected H atoms. Skipping.
Residue ALA   69 is missing expected H atoms. Skipping.
Residue VAL   70 is missing expected H atoms. Skipping.
Residue ALA   71 is missing expected H atoms. Skipping.
Residue ILE    4 is missing expected H atoms. Skipping.
Residue ILE    6 is missing expected H atoms. Skipping.
Residue SER    7 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue VAL   15 is missing expected H atoms. Skipping.
Residue SER   16 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue VAL   21 is missing expected H atoms. Skipping.
Residue ILE   23 is missing expected H atoms. Skipping.
Residue VAL   24 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue SER   29 is missing expected H atoms. Skipping.
Residue VAL   31 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 MET   34 is missing expected H atoms. Skipping.
Residue ALA   35 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue THR   40 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue ILE   46 is missing expected H atoms. Skipping.
Residue THR   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue ALA   54 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue ILE   61 is missing expected H atoms. Skipping.
Residue ALA   63 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue LEU   65 is missing expected H atoms. Skipping.
Residue THR   66 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue THR   70 is missing expected H atoms. Skipping.
Residue SER   72 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue SER   81 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LYS   88 is missing expected H atoms. Skipping.
Residue VAL   91 is missing expected H atoms. Skipping.
Residue LYS   93 is missing expected H atoms. Skipping.
Residue SER   95 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue VAL   97 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue ILE  113 is missing expected H atoms. Skipping.
Residue VAL  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  117 is missing expected H atoms. Skipping.
Residue MET  118 is missing expected H atoms. Skipping.
Residue THR  120 is missing expected H atoms. Skipping.
Residue LYS  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  125 is missing expected H atoms. Skipping.
Residue LYS  126 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue VAL  129 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue TYR  137 is missing expected H atoms. Skipping.
Residue THR  138 is missing expected H atoms. Skipping.
Residue ILE  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue ILE  141 is missing expected H atoms. Skipping.
Residue THR  142 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue ALA  150 is missing expected H atoms. Skipping.
Residue VAL  151 is missing expected H atoms. Skipping.
Residue THR  155 is missing expected H atoms. Skipping.
Residue LYS  157 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Residue ILE  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue ILE  164 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue SER  169 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue ALA  173 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue THR  176 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue THR  182 is missing expected H atoms. Skipping.
Residue MET  183 is missing expected H atoms. Skipping.
Residue SER  186 is missing expected H atoms. Skipping.
Residue THR  189 is missing expected H atoms. Skipping.
Residue LEU  191 is missing expected H atoms. Skipping.
Residue MET  196 is missing expected H atoms. Skipping.
Residue VAL  197 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  201 is missing expected H atoms. Skipping.
Residue LYS  204 is missing expected H atoms. Skipping.
Residue ALA  205 is missing expected H atoms. Skipping.
Residue LEU  207 is missing expected H atoms. Skipping.
Residue VAL  208 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LEU  216 is missing expected H atoms. Skipping.
Residue LEU  218 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue ALA  224 is missing expected H atoms. Skipping.
Residue THR  226 is missing expected H atoms. Skipping.
Residue SER  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue THR  236 is missing expected H atoms. Skipping.
Residue LEU  237 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue THR  239 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue VAL  250 is missing expected H atoms. Skipping.
Residue VAL  251 is missing expected H atoms. Skipping.
Residue VAL  252 is missing expected H atoms. Skipping.
Residue LEU  253 is missing expected H atoms. Skipping.
Residue SER  255 is missing expected H atoms. Skipping.
Residue ALA  259 is missing expected H atoms. Skipping.
Residue MET  260 is missing expected H atoms. Skipping.
Residue THR  262 is missing expected H atoms. Skipping.
Residue ALA  263 is missing expected H atoms. Skipping.
Residue LEU  264 is missing expected H atoms. Skipping.
Residue THR  265 is missing expected H atoms. Skipping.
Residue ALA  267 is missing expected H atoms. Skipping.
Residue THR  268 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue SER  273 is missing expected H atoms. Skipping.
Residue SER  274 is missing expected H atoms. Skipping.
Residue LEU  277 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue LYS  284 is missing expected H atoms. Skipping.
Residue LEU  287 is missing expected H atoms. Skipping.
Residue MET  289 is missing expected H atoms. Skipping.
Residue LYS  291 is missing expected H atoms. Skipping.
Residue LEU  292 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue LYS  295 is missing expected H atoms. Skipping.
Residue MET  297 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue TYR  299 is missing expected H atoms. Skipping.
Residue SER  300 is missing expected H atoms. Skipping.
Residue MET  301 is missing expected H atoms. Skipping.
Residue THR  303 is missing expected H atoms. Skipping.
Residue LYS  305 is missing expected H atoms. Skipping.
Residue LYS  307 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue VAL  309 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue ILE  312 is missing expected H atoms. Skipping.
Residue ALA  313 is missing expected H atoms. Skipping.
Residue THR  315 is missing expected H atoms. Skipping.
Residue THR  319 is missing expected H atoms. Skipping.
Residue ILE  320 is missing expected H atoms. Skipping.
Residue VAL  321 is missing expected H atoms. Skipping.
Residue ILE  322 is missing expected H atoms. Skipping.
Residue VAL  324 is missing expected H atoms. Skipping.
Residue TYR  326 is missing expected H atoms. Skipping.
Residue SER  331 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue ILE  335 is missing expected H atoms. Skipping.
Residue ILE  339 is missing expected H atoms. Skipping.
Residue MET  340 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue LYS  344 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  348 is missing expected H atoms. Skipping.
Residue LEU  351 is missing expected H atoms. Skipping.
Residue ILE  352 is missing expected H atoms. Skipping.
Residue THR  353 is missing expected H atoms. Skipping.
Residue VAL  354 is missing expected H atoms. Skipping.
Residue ILE  357 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LYS  361 is missing expected H atoms. Skipping.
Residue SER  363 is missing expected H atoms. Skipping.
Residue VAL  365 is missing expected H atoms. Skipping.
Residue ILE  367 is missing expected H atoms. Skipping.
Residue ALA  369 is missing expected H atoms. Skipping.
Residue SER  376 is missing expected H atoms. Skipping.
Residue TYR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue ILE  379 is missing expected H atoms. Skipping.
Residue ILE  380 is missing expected H atoms. Skipping.
Residue VAL  382 is missing expected H atoms. Skipping.
Residue LEU  387 is missing expected H atoms. Skipping.
Residue LYS  388 is missing expected H atoms. Skipping.
Residue LEU  389 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue LYS  394 is missing expected H atoms. Skipping.
Residue SER  396 is missing expected H atoms. Skipping.
Residue SER  397 is missing expected H atoms. Skipping.
Residue ILE  398 is missing expected H atoms. Skipping.
Residue MET  401 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue THR  404 is missing expected H atoms. Skipping.
Residue THR  405 is missing expected H atoms. Skipping.
Residue MET  406 is missing expected H atoms. Skipping.
Residue ALA  409 is missing expected H atoms. Skipping.
Residue LYS  410 is missing expected H atoms. Skipping.
Residue MET  412 is missing expected H atoms. Skipping.
Residue ALA  413 is missing expected H atoms. Skipping.
Residue ILE  414 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue ALA  419 is missing expected H atoms. Skipping.
Residue SER  424 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue VAL  428 is missing expected H atoms. Skipping.
Residue THR  430 is missing expected H atoms. Skipping.
Residue SER  431 is missing expected H atoms. Skipping.
Residue ILE  432 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue ALA  435 is missing expected H atoms. Skipping.
Residue LEU  436 is missing expected H atoms. Skipping.
Residue VAL  439 is missing expected H atoms. Skipping.
Residue ALA  442 is missing expected H atoms. Skipping.
Residue ILE  443 is missing expected H atoms. Skipping.
Residue TYR  444 is missing expected H atoms. Skipping.
Residue ALA  446 is missing expected H atoms. Skipping.
Residue ALA  447 is missing expected H atoms. Skipping.
Residue SER  449 is missing expected H atoms. Skipping.
Residue VAL  451 is missing expected H atoms. Skipping.
Residue SER  452 is missing expected H atoms. Skipping.
Residue ILE  454 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue ILE  457 is missing expected H atoms. Skipping.
Residue LEU  458 is missing expected H atoms. Skipping.
Residue ILE  459 is missing expected H atoms. Skipping.
Residue VAL  461 is missing expected H atoms. Skipping.
Residue ILE  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue THR  464 is missing expected H atoms. Skipping.
Residue ILE  466 is missing expected H atoms. Skipping.
Residue MET  468 is missing expected H atoms. Skipping.
Residue SER  470 is missing expected H atoms. Skipping.
Residue SER  472 is missing expected H atoms. Skipping.
Residue THR  473 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue LEU  475 is missing expected H atoms. Skipping.
Residue SER  476 is missing expected H atoms. Skipping.
Residue VAL  477 is missing expected H atoms. Skipping.
Residue SER  478 is missing expected H atoms. Skipping.
Residue LEU  479 is missing expected H atoms. Skipping.
Residue VAL  480 is missing expected H atoms. Skipping.
Residue LEU  481 is missing expected H atoms. Skipping.
Residue VAL  482 is missing expected H atoms. Skipping.
Residue VAL  484 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue LEU  487 is missing expected H atoms. Skipping.
Residue TYR  488 is missing expected H atoms. Skipping.
Residue LEU  489 is missing expected H atoms. Skipping.
Residue VAL  491 is missing expected H atoms. Skipping.
Residue MET  492 is missing expected H atoms. Skipping.
Residue VAL  493 is missing expected H atoms. Skipping.
Residue VAL    2 is missing expected H atoms. Skipping.
Residue ALA    3 is missing expected H atoms. Skipping.
Residue LEU    4 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue MET   10 is missing expected H atoms. Skipping.
Residue LEU   12 is missing expected H atoms. Skipping.
Residue THR   14 is missing expected H atoms. Skipping.
Residue ALA   15 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue THR   18 is missing expected H atoms. Skipping.
Residue MET   20 is missing expected H atoms. Skipping.
Residue SER   21 is missing expected H atoms. Skipping.
Residue SER   22 is missing expected H atoms. Skipping.
Residue ALA   25 is missing expected H atoms. Skipping.
Residue LYS   27 is missing expected H atoms. Skipping.
Residue ALA   29 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue ILE   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue THR   43 is missing expected H atoms. Skipping.
Residue ILE   44 is missing expected H atoms. Skipping.
Residue MET   45 is missing expected H atoms. Skipping.
Residue ALA   46 is missing expected H atoms. Skipping.
Residue ALA   47 is missing expected H atoms. Skipping.
Residue ILE   48 is missing expected H atoms. Skipping.
Residue LEU   49 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue TYR   51 is missing expected H atoms. Skipping.
Residue THR   52 is missing expected H atoms. Skipping.
Residue ILE   53 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue THR   56 is missing expected H atoms. Skipping.
Residue ALA   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue ILE   63 is missing expected H atoms. Skipping.
Residue ILE   65 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 THR   68 is missing expected H atoms. Skipping.
Residue ALA   69 is missing expected H atoms. Skipping.
Residue VAL   70 is missing expected H atoms. Skipping.
Residue ALA   71 is missing expected H atoms. Skipping.
Evaluate side-chains
  339 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 79
    poor density    : 260
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 79
  outliers final: 53
  residues processed: 300
  average time/residue: 0.2117
  time to fit residues: 90.7370
Evaluate side-chains
  298 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 53
    poor density    : 245
  time to evaluate  : 0.987 
Switching outliers to nearest non-outliers
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 53
  outliers final: 2
  residues processed: 53
  average time/residue: 0.0982
  time to fit residues: 10.9104
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 61 optimal weight:    7.9990
   chunk 1 optimal weight:   30.0000
   chunk 80 optimal weight:   20.0000
   chunk 44 optimal weight:   20.0000
   chunk 92 optimal weight:    9.9990
   chunk 74 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 55 optimal weight:    9.9990
   chunk 97 optimal weight:    9.9990
   chunk 27 optimal weight:    0.0670
   chunk 36 optimal weight:    8.9990
   overall best weight:    7.4126

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

Flipped N/Q/H residues before XYZ refinement:
** A  27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 244 HIS
** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   7 HIS
** B  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   7 HIS
** D  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.5152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8986  Z= 0.255
  Angle     :  0.787   7.353  12164  Z= 0.403
  Chirality :  0.046   0.259   1412
  Planarity :  0.005   0.038   1520
  Dihedral  :  7.179  67.148   1224
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 76.29
  Ramachandran Plot:
    Outliers :  4.35 %
    Allowed  : 23.80 %
    Favored  : 71.85 %
  Rotamer Outliers :  4.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -5.43 (0.20), residues: 1126
  helix: -2.56 (0.23), residues: 306
  sheet: -2.17 (0.33), residues: 242
  loop : -5.07 (0.18), residues: 578

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE    4 is missing expected H atoms. Skipping.
Residue ILE    6 is missing expected H atoms. Skipping.
Residue SER    7 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue VAL   15 is missing expected H atoms. Skipping.
Residue SER   16 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue VAL   21 is missing expected H atoms. Skipping.
Residue ILE   23 is missing expected H atoms. Skipping.
Residue VAL   24 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue SER   29 is missing expected H atoms. Skipping.
Residue VAL   31 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 MET   34 is missing expected H atoms. Skipping.
Residue ALA   35 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue THR   40 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue ILE   46 is missing expected H atoms. Skipping.
Residue THR   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue ALA   54 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue ILE   61 is missing expected H atoms. Skipping.
Residue ALA   63 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue LEU   65 is missing expected H atoms. Skipping.
Residue THR   66 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue THR   70 is missing expected H atoms. Skipping.
Residue SER   72 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue SER   81 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LYS   88 is missing expected H atoms. Skipping.
Residue VAL   91 is missing expected H atoms. Skipping.
Residue LYS   93 is missing expected H atoms. Skipping.
Residue SER   95 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue VAL   97 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue ILE  113 is missing expected H atoms. Skipping.
Residue VAL  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  117 is missing expected H atoms. Skipping.
Residue MET  118 is missing expected H atoms. Skipping.
Residue THR  120 is missing expected H atoms. Skipping.
Residue LYS  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  125 is missing expected H atoms. Skipping.
Residue LYS  126 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue VAL  129 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue TYR  137 is missing expected H atoms. Skipping.
Residue THR  138 is missing expected H atoms. Skipping.
Residue ILE  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue ILE  141 is missing expected H atoms. Skipping.
Residue THR  142 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue ALA  150 is missing expected H atoms. Skipping.
Residue VAL  151 is missing expected H atoms. Skipping.
Residue THR  155 is missing expected H atoms. Skipping.
Residue LYS  157 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Residue ILE  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue ILE  164 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue SER  169 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue ALA  173 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue THR  176 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue THR  182 is missing expected H atoms. Skipping.
Residue MET  183 is missing expected H atoms. Skipping.
Residue SER  186 is missing expected H atoms. Skipping.
Residue THR  189 is missing expected H atoms. Skipping.
Residue LEU  191 is missing expected H atoms. Skipping.
Residue MET  196 is missing expected H atoms. Skipping.
Residue VAL  197 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  201 is missing expected H atoms. Skipping.
Residue LYS  204 is missing expected H atoms. Skipping.
Residue ALA  205 is missing expected H atoms. Skipping.
Residue LEU  207 is missing expected H atoms. Skipping.
Residue VAL  208 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LEU  216 is missing expected H atoms. Skipping.
Residue LEU  218 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue ALA  224 is missing expected H atoms. Skipping.
Residue THR  226 is missing expected H atoms. Skipping.
Residue SER  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue THR  236 is missing expected H atoms. Skipping.
Residue LEU  237 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue THR  239 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue VAL  250 is missing expected H atoms. Skipping.
Residue VAL  251 is missing expected H atoms. Skipping.
Residue VAL  252 is missing expected H atoms. Skipping.
Residue LEU  253 is missing expected H atoms. Skipping.
Residue SER  255 is missing expected H atoms. Skipping.
Residue ALA  259 is missing expected H atoms. Skipping.
Residue MET  260 is missing expected H atoms. Skipping.
Residue THR  262 is missing expected H atoms. Skipping.
Residue ALA  263 is missing expected H atoms. Skipping.
Residue LEU  264 is missing expected H atoms. Skipping.
Residue THR  265 is missing expected H atoms. Skipping.
Residue ALA  267 is missing expected H atoms. Skipping.
Residue THR  268 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue SER  273 is missing expected H atoms. Skipping.
Residue SER  274 is missing expected H atoms. Skipping.
Residue LEU  277 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue LYS  284 is missing expected H atoms. Skipping.
Residue LEU  287 is missing expected H atoms. Skipping.
Residue MET  289 is missing expected H atoms. Skipping.
Residue LYS  291 is missing expected H atoms. Skipping.
Residue LEU  292 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue LYS  295 is missing expected H atoms. Skipping.
Residue MET  297 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue TYR  299 is missing expected H atoms. Skipping.
Residue SER  300 is missing expected H atoms. Skipping.
Residue MET  301 is missing expected H atoms. Skipping.
Residue THR  303 is missing expected H atoms. Skipping.
Residue LYS  305 is missing expected H atoms. Skipping.
Residue LYS  307 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue VAL  309 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue ILE  312 is missing expected H atoms. Skipping.
Residue ALA  313 is missing expected H atoms. Skipping.
Residue THR  315 is missing expected H atoms. Skipping.
Residue THR  319 is missing expected H atoms. Skipping.
Residue ILE  320 is missing expected H atoms. Skipping.
Residue VAL  321 is missing expected H atoms. Skipping.
Residue ILE  322 is missing expected H atoms. Skipping.
Residue VAL  324 is missing expected H atoms. Skipping.
Residue TYR  326 is missing expected H atoms. Skipping.
Residue SER  331 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue ILE  335 is missing expected H atoms. Skipping.
Residue ILE  339 is missing expected H atoms. Skipping.
Residue MET  340 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue LYS  344 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  348 is missing expected H atoms. Skipping.
Residue LEU  351 is missing expected H atoms. Skipping.
Residue ILE  352 is missing expected H atoms. Skipping.
Residue THR  353 is missing expected H atoms. Skipping.
Residue VAL  354 is missing expected H atoms. Skipping.
Residue ILE  357 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LYS  361 is missing expected H atoms. Skipping.
Residue SER  363 is missing expected H atoms. Skipping.
Residue VAL  365 is missing expected H atoms. Skipping.
Residue ILE  367 is missing expected H atoms. Skipping.
Residue ALA  369 is missing expected H atoms. Skipping.
Residue SER  376 is missing expected H atoms. Skipping.
Residue TYR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue ILE  379 is missing expected H atoms. Skipping.
Residue ILE  380 is missing expected H atoms. Skipping.
Residue VAL  382 is missing expected H atoms. Skipping.
Residue LEU  387 is missing expected H atoms. Skipping.
Residue LYS  388 is missing expected H atoms. Skipping.
Residue LEU  389 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue LYS  394 is missing expected H atoms. Skipping.
Residue SER  396 is missing expected H atoms. Skipping.
Residue SER  397 is missing expected H atoms. Skipping.
Residue ILE  398 is missing expected H atoms. Skipping.
Residue MET  401 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue THR  404 is missing expected H atoms. Skipping.
Residue THR  405 is missing expected H atoms. Skipping.
Residue MET  406 is missing expected H atoms. Skipping.
Residue ALA  409 is missing expected H atoms. Skipping.
Residue LYS  410 is missing expected H atoms. Skipping.
Residue MET  412 is missing expected H atoms. Skipping.
Residue ALA  413 is missing expected H atoms. Skipping.
Residue ILE  414 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue ALA  419 is missing expected H atoms. Skipping.
Residue SER  424 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue VAL  428 is missing expected H atoms. Skipping.
Residue THR  430 is missing expected H atoms. Skipping.
Residue SER  431 is missing expected H atoms. Skipping.
Residue ILE  432 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue ALA  435 is missing expected H atoms. Skipping.
Residue LEU  436 is missing expected H atoms. Skipping.
Residue VAL  439 is missing expected H atoms. Skipping.
Residue ALA  442 is missing expected H atoms. Skipping.
Residue ILE  443 is missing expected H atoms. Skipping.
Residue TYR  444 is missing expected H atoms. Skipping.
Residue ALA  446 is missing expected H atoms. Skipping.
Residue ALA  447 is missing expected H atoms. Skipping.
Residue SER  449 is missing expected H atoms. Skipping.
Residue VAL  451 is missing expected H atoms. Skipping.
Residue SER  452 is missing expected H atoms. Skipping.
Residue ILE  454 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue ILE  457 is missing expected H atoms. Skipping.
Residue LEU  458 is missing expected H atoms. Skipping.
Residue ILE  459 is missing expected H atoms. Skipping.
Residue VAL  461 is missing expected H atoms. Skipping.
Residue ILE  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue THR  464 is missing expected H atoms. Skipping.
Residue ILE  466 is missing expected H atoms. Skipping.
Residue MET  468 is missing expected H atoms. Skipping.
Residue SER  470 is missing expected H atoms. Skipping.
Residue SER  472 is missing expected H atoms. Skipping.
Residue THR  473 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue LEU  475 is missing expected H atoms. Skipping.
Residue SER  476 is missing expected H atoms. Skipping.
Residue VAL  477 is missing expected H atoms. Skipping.
Residue SER  478 is missing expected H atoms. Skipping.
Residue LEU  479 is missing expected H atoms. Skipping.
Residue VAL  480 is missing expected H atoms. Skipping.
Residue LEU  481 is missing expected H atoms. Skipping.
Residue VAL  482 is missing expected H atoms. Skipping.
Residue VAL  484 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue LEU  487 is missing expected H atoms. Skipping.
Residue TYR  488 is missing expected H atoms. Skipping.
Residue LEU  489 is missing expected H atoms. Skipping.
Residue VAL  491 is missing expected H atoms. Skipping.
Residue MET  492 is missing expected H atoms. Skipping.
Residue VAL  493 is missing expected H atoms. Skipping.
Residue VAL    2 is missing expected H atoms. Skipping.
Residue ALA    3 is missing expected H atoms. Skipping.
Residue LEU    4 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue MET   10 is missing expected H atoms. Skipping.
Residue LEU   12 is missing expected H atoms. Skipping.
Residue THR   14 is missing expected H atoms. Skipping.
Residue ALA   15 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue THR   18 is missing expected H atoms. Skipping.
Residue MET   20 is missing expected H atoms. Skipping.
Residue SER   21 is missing expected H atoms. Skipping.
Residue SER   22 is missing expected H atoms. Skipping.
Residue ALA   25 is missing expected H atoms. Skipping.
Residue LYS   27 is missing expected H atoms. Skipping.
Residue ALA   29 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue ILE   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue THR   43 is missing expected H atoms. Skipping.
Residue ILE   44 is missing expected H atoms. Skipping.
Residue MET   45 is missing expected H atoms. Skipping.
Residue ALA   46 is missing expected H atoms. Skipping.
Residue ALA   47 is missing expected H atoms. Skipping.
Residue ILE   48 is missing expected H atoms. Skipping.
Residue LEU   49 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue TYR   51 is missing expected H atoms. Skipping.
Residue THR   52 is missing expected H atoms. Skipping.
Residue ILE   53 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue THR   56 is missing expected H atoms. Skipping.
Residue ALA   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue ILE   63 is missing expected H atoms. Skipping.
Residue ILE   65 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 THR   68 is missing expected H atoms. Skipping.
Residue ALA   69 is missing expected H atoms. Skipping.
Residue VAL   70 is missing expected H atoms. Skipping.
Residue ALA   71 is missing expected H atoms. Skipping.
Residue ILE    4 is missing expected H atoms. Skipping.
Residue ILE    6 is missing expected H atoms. Skipping.
Residue SER    7 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue VAL   15 is missing expected H atoms. Skipping.
Residue SER   16 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue VAL   21 is missing expected H atoms. Skipping.
Residue ILE   23 is missing expected H atoms. Skipping.
Residue VAL   24 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue SER   29 is missing expected H atoms. Skipping.
Residue VAL   31 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 MET   34 is missing expected H atoms. Skipping.
Residue ALA   35 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue THR   40 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue ILE   46 is missing expected H atoms. Skipping.
Residue THR   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue ALA   54 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue ILE   61 is missing expected H atoms. Skipping.
Residue ALA   63 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue LEU   65 is missing expected H atoms. Skipping.
Residue THR   66 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue THR   70 is missing expected H atoms. Skipping.
Residue SER   72 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue SER   81 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LYS   88 is missing expected H atoms. Skipping.
Residue VAL   91 is missing expected H atoms. Skipping.
Residue LYS   93 is missing expected H atoms. Skipping.
Residue SER   95 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue VAL   97 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue ILE  113 is missing expected H atoms. Skipping.
Residue VAL  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  117 is missing expected H atoms. Skipping.
Residue MET  118 is missing expected H atoms. Skipping.
Residue THR  120 is missing expected H atoms. Skipping.
Residue LYS  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  125 is missing expected H atoms. Skipping.
Residue LYS  126 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue VAL  129 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue TYR  137 is missing expected H atoms. Skipping.
Residue THR  138 is missing expected H atoms. Skipping.
Residue ILE  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue ILE  141 is missing expected H atoms. Skipping.
Residue THR  142 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue ALA  150 is missing expected H atoms. Skipping.
Residue VAL  151 is missing expected H atoms. Skipping.
Residue THR  155 is missing expected H atoms. Skipping.
Residue LYS  157 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Residue ILE  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue ILE  164 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue SER  169 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue ALA  173 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue THR  176 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue THR  182 is missing expected H atoms. Skipping.
Residue MET  183 is missing expected H atoms. Skipping.
Residue SER  186 is missing expected H atoms. Skipping.
Residue THR  189 is missing expected H atoms. Skipping.
Residue LEU  191 is missing expected H atoms. Skipping.
Residue MET  196 is missing expected H atoms. Skipping.
Residue VAL  197 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  201 is missing expected H atoms. Skipping.
Residue LYS  204 is missing expected H atoms. Skipping.
Residue ALA  205 is missing expected H atoms. Skipping.
Residue LEU  207 is missing expected H atoms. Skipping.
Residue VAL  208 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LEU  216 is missing expected H atoms. Skipping.
Residue LEU  218 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue ALA  224 is missing expected H atoms. Skipping.
Residue THR  226 is missing expected H atoms. Skipping.
Residue SER  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue THR  236 is missing expected H atoms. Skipping.
Residue LEU  237 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue THR  239 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue VAL  250 is missing expected H atoms. Skipping.
Residue VAL  251 is missing expected H atoms. Skipping.
Residue VAL  252 is missing expected H atoms. Skipping.
Residue LEU  253 is missing expected H atoms. Skipping.
Residue SER  255 is missing expected H atoms. Skipping.
Residue ALA  259 is missing expected H atoms. Skipping.
Residue MET  260 is missing expected H atoms. Skipping.
Residue THR  262 is missing expected H atoms. Skipping.
Residue ALA  263 is missing expected H atoms. Skipping.
Residue LEU  264 is missing expected H atoms. Skipping.
Residue THR  265 is missing expected H atoms. Skipping.
Residue ALA  267 is missing expected H atoms. Skipping.
Residue THR  268 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue SER  273 is missing expected H atoms. Skipping.
Residue SER  274 is missing expected H atoms. Skipping.
Residue LEU  277 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue LYS  284 is missing expected H atoms. Skipping.
Residue LEU  287 is missing expected H atoms. Skipping.
Residue MET  289 is missing expected H atoms. Skipping.
Residue LYS  291 is missing expected H atoms. Skipping.
Residue LEU  292 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue LYS  295 is missing expected H atoms. Skipping.
Residue MET  297 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue TYR  299 is missing expected H atoms. Skipping.
Residue SER  300 is missing expected H atoms. Skipping.
Residue MET  301 is missing expected H atoms. Skipping.
Residue THR  303 is missing expected H atoms. Skipping.
Residue LYS  305 is missing expected H atoms. Skipping.
Residue LYS  307 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue VAL  309 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue ILE  312 is missing expected H atoms. Skipping.
Residue ALA  313 is missing expected H atoms. Skipping.
Residue THR  315 is missing expected H atoms. Skipping.
Residue THR  319 is missing expected H atoms. Skipping.
Residue ILE  320 is missing expected H atoms. Skipping.
Residue VAL  321 is missing expected H atoms. Skipping.
Residue ILE  322 is missing expected H atoms. Skipping.
Residue VAL  324 is missing expected H atoms. Skipping.
Residue TYR  326 is missing expected H atoms. Skipping.
Residue SER  331 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue ILE  335 is missing expected H atoms. Skipping.
Residue ILE  339 is missing expected H atoms. Skipping.
Residue MET  340 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue LYS  344 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  348 is missing expected H atoms. Skipping.
Residue LEU  351 is missing expected H atoms. Skipping.
Residue ILE  352 is missing expected H atoms. Skipping.
Residue THR  353 is missing expected H atoms. Skipping.
Residue VAL  354 is missing expected H atoms. Skipping.
Residue ILE  357 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LYS  361 is missing expected H atoms. Skipping.
Residue SER  363 is missing expected H atoms. Skipping.
Residue VAL  365 is missing expected H atoms. Skipping.
Residue ILE  367 is missing expected H atoms. Skipping.
Residue ALA  369 is missing expected H atoms. Skipping.
Residue SER  376 is missing expected H atoms. Skipping.
Residue TYR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue ILE  379 is missing expected H atoms. Skipping.
Residue ILE  380 is missing expected H atoms. Skipping.
Residue VAL  382 is missing expected H atoms. Skipping.
Residue LEU  387 is missing expected H atoms. Skipping.
Residue LYS  388 is missing expected H atoms. Skipping.
Residue LEU  389 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue LYS  394 is missing expected H atoms. Skipping.
Residue SER  396 is missing expected H atoms. Skipping.
Residue SER  397 is missing expected H atoms. Skipping.
Residue ILE  398 is missing expected H atoms. Skipping.
Residue MET  401 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue THR  404 is missing expected H atoms. Skipping.
Residue THR  405 is missing expected H atoms. Skipping.
Residue MET  406 is missing expected H atoms. Skipping.
Residue ALA  409 is missing expected H atoms. Skipping.
Residue LYS  410 is missing expected H atoms. Skipping.
Residue MET  412 is missing expected H atoms. Skipping.
Residue ALA  413 is missing expected H atoms. Skipping.
Residue ILE  414 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue ALA  419 is missing expected H atoms. Skipping.
Residue SER  424 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue VAL  428 is missing expected H atoms. Skipping.
Residue THR  430 is missing expected H atoms. Skipping.
Residue SER  431 is missing expected H atoms. Skipping.
Residue ILE  432 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue ALA  435 is missing expected H atoms. Skipping.
Residue LEU  436 is missing expected H atoms. Skipping.
Residue VAL  439 is missing expected H atoms. Skipping.
Residue ALA  442 is missing expected H atoms. Skipping.
Residue ILE  443 is missing expected H atoms. Skipping.
Residue TYR  444 is missing expected H atoms. Skipping.
Residue ALA  446 is missing expected H atoms. Skipping.
Residue ALA  447 is missing expected H atoms. Skipping.
Residue SER  449 is missing expected H atoms. Skipping.
Residue VAL  451 is missing expected H atoms. Skipping.
Residue SER  452 is missing expected H atoms. Skipping.
Residue ILE  454 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue ILE  457 is missing expected H atoms. Skipping.
Residue LEU  458 is missing expected H atoms. Skipping.
Residue ILE  459 is missing expected H atoms. Skipping.
Residue VAL  461 is missing expected H atoms. Skipping.
Residue ILE  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue THR  464 is missing expected H atoms. Skipping.
Residue ILE  466 is missing expected H atoms. Skipping.
Residue MET  468 is missing expected H atoms. Skipping.
Residue SER  470 is missing expected H atoms. Skipping.
Residue SER  472 is missing expected H atoms. Skipping.
Residue THR  473 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue LEU  475 is missing expected H atoms. Skipping.
Residue SER  476 is missing expected H atoms. Skipping.
Residue VAL  477 is missing expected H atoms. Skipping.
Residue SER  478 is missing expected H atoms. Skipping.
Residue LEU  479 is missing expected H atoms. Skipping.
Residue VAL  480 is missing expected H atoms. Skipping.
Residue LEU  481 is missing expected H atoms. Skipping.
Residue VAL  482 is missing expected H atoms. Skipping.
Residue VAL  484 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue LEU  487 is missing expected H atoms. Skipping.
Residue TYR  488 is missing expected H atoms. Skipping.
Residue LEU  489 is missing expected H atoms. Skipping.
Residue VAL  491 is missing expected H atoms. Skipping.
Residue MET  492 is missing expected H atoms. Skipping.
Residue VAL  493 is missing expected H atoms. Skipping.
Residue VAL    2 is missing expected H atoms. Skipping.
Residue ALA    3 is missing expected H atoms. Skipping.
Residue LEU    4 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue MET   10 is missing expected H atoms. Skipping.
Residue LEU   12 is missing expected H atoms. Skipping.
Residue THR   14 is missing expected H atoms. Skipping.
Residue ALA   15 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue THR   18 is missing expected H atoms. Skipping.
Residue MET   20 is missing expected H atoms. Skipping.
Residue SER   21 is missing expected H atoms. Skipping.
Residue SER   22 is missing expected H atoms. Skipping.
Residue ALA   25 is missing expected H atoms. Skipping.
Residue LYS   27 is missing expected H atoms. Skipping.
Residue ALA   29 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue ILE   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue THR   43 is missing expected H atoms. Skipping.
Residue ILE   44 is missing expected H atoms. Skipping.
Residue MET   45 is missing expected H atoms. Skipping.
Residue ALA   46 is missing expected H atoms. Skipping.
Residue ALA   47 is missing expected H atoms. Skipping.
Residue ILE   48 is missing expected H atoms. Skipping.
Residue LEU   49 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue TYR   51 is missing expected H atoms. Skipping.
Residue THR   52 is missing expected H atoms. Skipping.
Residue ILE   53 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue THR   56 is missing expected H atoms. Skipping.
Residue ALA   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue ILE   63 is missing expected H atoms. Skipping.
Residue ILE   65 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 THR   68 is missing expected H atoms. Skipping.
Residue ALA   69 is missing expected H atoms. Skipping.
Residue VAL   70 is missing expected H atoms. Skipping.
Residue ALA   71 is missing expected H atoms. Skipping.
Evaluate side-chains
  306 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 260
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 46
  outliers final: 28
  residues processed: 289
  average time/residue: 0.2167
  time to fit residues: 89.2765
Evaluate side-chains
  272 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 244
  time to evaluate  : 1.094 
Switching outliers to nearest non-outliers
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 28
  outliers final: 2
  residues processed: 28
  average time/residue: 0.1158
  time to fit residues: 6.9923
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 97 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 63 optimal weight:   10.0000
   chunk 26 optimal weight:   20.0000
   chunk 108 optimal weight:   10.0000
   chunk 89 optimal weight:    9.9990
   chunk 50 optimal weight:    7.9990
   chunk 9 optimal weight:   20.0000
   chunk 35 optimal weight:    0.9990
   chunk 56 optimal weight:   20.0000
   chunk 104 optimal weight:    0.1980
   overall best weight:    4.8388

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

Flipped N/Q/H residues before XYZ refinement:
** A  27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 158 HIS
** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 203 ASN
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   7 HIS
** D  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.5461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8986  Z= 0.199
  Angle     :  0.735   7.288  12164  Z= 0.375
  Chirality :  0.045   0.257   1412
  Planarity :  0.005   0.081   1520
  Dihedral  :  6.838  64.959   1224
  Min Nonbonded Distance : 1.867

Molprobity Statistics.
  All-atom Clashscore : 71.15
  Ramachandran Plot:
    Outliers :  4.00 %
    Allowed  : 22.02 %
    Favored  : 73.98 %
  Rotamer Outliers :  4.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -5.11 (0.21), residues: 1126
  helix: -1.96 (0.25), residues: 294
  sheet: -1.97 (0.33), residues: 264
  loop : -5.13 (0.18), residues: 568

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE    4 is missing expected H atoms. Skipping.
Residue ILE    6 is missing expected H atoms. Skipping.
Residue SER    7 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue VAL   15 is missing expected H atoms. Skipping.
Residue SER   16 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue VAL   21 is missing expected H atoms. Skipping.
Residue ILE   23 is missing expected H atoms. Skipping.
Residue VAL   24 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue SER   29 is missing expected H atoms. Skipping.
Residue VAL   31 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 MET   34 is missing expected H atoms. Skipping.
Residue ALA   35 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue THR   40 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue ILE   46 is missing expected H atoms. Skipping.
Residue THR   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue ALA   54 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue ILE   61 is missing expected H atoms. Skipping.
Residue ALA   63 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue LEU   65 is missing expected H atoms. Skipping.
Residue THR   66 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue THR   70 is missing expected H atoms. Skipping.
Residue SER   72 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue SER   81 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LYS   88 is missing expected H atoms. Skipping.
Residue VAL   91 is missing expected H atoms. Skipping.
Residue LYS   93 is missing expected H atoms. Skipping.
Residue SER   95 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue VAL   97 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue ILE  113 is missing expected H atoms. Skipping.
Residue VAL  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  117 is missing expected H atoms. Skipping.
Residue MET  118 is missing expected H atoms. Skipping.
Residue THR  120 is missing expected H atoms. Skipping.
Residue LYS  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  125 is missing expected H atoms. Skipping.
Residue LYS  126 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue VAL  129 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue TYR  137 is missing expected H atoms. Skipping.
Residue THR  138 is missing expected H atoms. Skipping.
Residue ILE  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue ILE  141 is missing expected H atoms. Skipping.
Residue THR  142 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue ALA  150 is missing expected H atoms. Skipping.
Residue VAL  151 is missing expected H atoms. Skipping.
Residue THR  155 is missing expected H atoms. Skipping.
Residue LYS  157 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Residue ILE  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue ILE  164 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue SER  169 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue ALA  173 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue THR  176 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue THR  182 is missing expected H atoms. Skipping.
Residue MET  183 is missing expected H atoms. Skipping.
Residue SER  186 is missing expected H atoms. Skipping.
Residue THR  189 is missing expected H atoms. Skipping.
Residue LEU  191 is missing expected H atoms. Skipping.
Residue MET  196 is missing expected H atoms. Skipping.
Residue VAL  197 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  201 is missing expected H atoms. Skipping.
Residue LYS  204 is missing expected H atoms. Skipping.
Residue ALA  205 is missing expected H atoms. Skipping.
Residue LEU  207 is missing expected H atoms. Skipping.
Residue VAL  208 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LEU  216 is missing expected H atoms. Skipping.
Residue LEU  218 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue ALA  224 is missing expected H atoms. Skipping.
Residue THR  226 is missing expected H atoms. Skipping.
Residue SER  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue THR  236 is missing expected H atoms. Skipping.
Residue LEU  237 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue THR  239 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue VAL  250 is missing expected H atoms. Skipping.
Residue VAL  251 is missing expected H atoms. Skipping.
Residue VAL  252 is missing expected H atoms. Skipping.
Residue LEU  253 is missing expected H atoms. Skipping.
Residue SER  255 is missing expected H atoms. Skipping.
Residue ALA  259 is missing expected H atoms. Skipping.
Residue MET  260 is missing expected H atoms. Skipping.
Residue THR  262 is missing expected H atoms. Skipping.
Residue ALA  263 is missing expected H atoms. Skipping.
Residue LEU  264 is missing expected H atoms. Skipping.
Residue THR  265 is missing expected H atoms. Skipping.
Residue ALA  267 is missing expected H atoms. Skipping.
Residue THR  268 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue SER  273 is missing expected H atoms. Skipping.
Residue SER  274 is missing expected H atoms. Skipping.
Residue LEU  277 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue LYS  284 is missing expected H atoms. Skipping.
Residue LEU  287 is missing expected H atoms. Skipping.
Residue MET  289 is missing expected H atoms. Skipping.
Residue LYS  291 is missing expected H atoms. Skipping.
Residue LEU  292 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue LYS  295 is missing expected H atoms. Skipping.
Residue MET  297 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue TYR  299 is missing expected H atoms. Skipping.
Residue SER  300 is missing expected H atoms. Skipping.
Residue MET  301 is missing expected H atoms. Skipping.
Residue THR  303 is missing expected H atoms. Skipping.
Residue LYS  305 is missing expected H atoms. Skipping.
Residue LYS  307 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue VAL  309 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue ILE  312 is missing expected H atoms. Skipping.
Residue ALA  313 is missing expected H atoms. Skipping.
Residue THR  315 is missing expected H atoms. Skipping.
Residue THR  319 is missing expected H atoms. Skipping.
Residue ILE  320 is missing expected H atoms. Skipping.
Residue VAL  321 is missing expected H atoms. Skipping.
Residue ILE  322 is missing expected H atoms. Skipping.
Residue VAL  324 is missing expected H atoms. Skipping.
Residue TYR  326 is missing expected H atoms. Skipping.
Residue SER  331 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue ILE  335 is missing expected H atoms. Skipping.
Residue ILE  339 is missing expected H atoms. Skipping.
Residue MET  340 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue LYS  344 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  348 is missing expected H atoms. Skipping.
Residue LEU  351 is missing expected H atoms. Skipping.
Residue ILE  352 is missing expected H atoms. Skipping.
Residue THR  353 is missing expected H atoms. Skipping.
Residue VAL  354 is missing expected H atoms. Skipping.
Residue ILE  357 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LYS  361 is missing expected H atoms. Skipping.
Residue SER  363 is missing expected H atoms. Skipping.
Residue VAL  365 is missing expected H atoms. Skipping.
Residue ILE  367 is missing expected H atoms. Skipping.
Residue ALA  369 is missing expected H atoms. Skipping.
Residue SER  376 is missing expected H atoms. Skipping.
Residue TYR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue ILE  379 is missing expected H atoms. Skipping.
Residue ILE  380 is missing expected H atoms. Skipping.
Residue VAL  382 is missing expected H atoms. Skipping.
Residue LEU  387 is missing expected H atoms. Skipping.
Residue LYS  388 is missing expected H atoms. Skipping.
Residue LEU  389 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue LYS  394 is missing expected H atoms. Skipping.
Residue SER  396 is missing expected H atoms. Skipping.
Residue SER  397 is missing expected H atoms. Skipping.
Residue ILE  398 is missing expected H atoms. Skipping.
Residue MET  401 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue THR  404 is missing expected H atoms. Skipping.
Residue THR  405 is missing expected H atoms. Skipping.
Residue MET  406 is missing expected H atoms. Skipping.
Residue ALA  409 is missing expected H atoms. Skipping.
Residue LYS  410 is missing expected H atoms. Skipping.
Residue MET  412 is missing expected H atoms. Skipping.
Residue ALA  413 is missing expected H atoms. Skipping.
Residue ILE  414 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue ALA  419 is missing expected H atoms. Skipping.
Residue SER  424 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue VAL  428 is missing expected H atoms. Skipping.
Residue THR  430 is missing expected H atoms. Skipping.
Residue SER  431 is missing expected H atoms. Skipping.
Residue ILE  432 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue ALA  435 is missing expected H atoms. Skipping.
Residue LEU  436 is missing expected H atoms. Skipping.
Residue VAL  439 is missing expected H atoms. Skipping.
Residue ALA  442 is missing expected H atoms. Skipping.
Residue ILE  443 is missing expected H atoms. Skipping.
Residue TYR  444 is missing expected H atoms. Skipping.
Residue ALA  446 is missing expected H atoms. Skipping.
Residue ALA  447 is missing expected H atoms. Skipping.
Residue SER  449 is missing expected H atoms. Skipping.
Residue VAL  451 is missing expected H atoms. Skipping.
Residue SER  452 is missing expected H atoms. Skipping.
Residue ILE  454 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue ILE  457 is missing expected H atoms. Skipping.
Residue LEU  458 is missing expected H atoms. Skipping.
Residue ILE  459 is missing expected H atoms. Skipping.
Residue VAL  461 is missing expected H atoms. Skipping.
Residue ILE  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue THR  464 is missing expected H atoms. Skipping.
Residue ILE  466 is missing expected H atoms. Skipping.
Residue MET  468 is missing expected H atoms. Skipping.
Residue SER  470 is missing expected H atoms. Skipping.
Residue SER  472 is missing expected H atoms. Skipping.
Residue THR  473 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue LEU  475 is missing expected H atoms. Skipping.
Residue SER  476 is missing expected H atoms. Skipping.
Residue VAL  477 is missing expected H atoms. Skipping.
Residue SER  478 is missing expected H atoms. Skipping.
Residue LEU  479 is missing expected H atoms. Skipping.
Residue VAL  480 is missing expected H atoms. Skipping.
Residue LEU  481 is missing expected H atoms. Skipping.
Residue VAL  482 is missing expected H atoms. Skipping.
Residue VAL  484 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue LEU  487 is missing expected H atoms. Skipping.
Residue TYR  488 is missing expected H atoms. Skipping.
Residue LEU  489 is missing expected H atoms. Skipping.
Residue VAL  491 is missing expected H atoms. Skipping.
Residue MET  492 is missing expected H atoms. Skipping.
Residue VAL  493 is missing expected H atoms. Skipping.
Residue VAL    2 is missing expected H atoms. Skipping.
Residue ALA    3 is missing expected H atoms. Skipping.
Residue LEU    4 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue MET   10 is missing expected H atoms. Skipping.
Residue LEU   12 is missing expected H atoms. Skipping.
Residue THR   14 is missing expected H atoms. Skipping.
Residue ALA   15 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue THR   18 is missing expected H atoms. Skipping.
Residue MET   20 is missing expected H atoms. Skipping.
Residue SER   21 is missing expected H atoms. Skipping.
Residue SER   22 is missing expected H atoms. Skipping.
Residue ALA   25 is missing expected H atoms. Skipping.
Residue LYS   27 is missing expected H atoms. Skipping.
Residue ALA   29 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue ILE   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue THR   43 is missing expected H atoms. Skipping.
Residue ILE   44 is missing expected H atoms. Skipping.
Residue MET   45 is missing expected H atoms. Skipping.
Residue ALA   46 is missing expected H atoms. Skipping.
Residue ALA   47 is missing expected H atoms. Skipping.
Residue ILE   48 is missing expected H atoms. Skipping.
Residue LEU   49 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue TYR   51 is missing expected H atoms. Skipping.
Residue THR   52 is missing expected H atoms. Skipping.
Residue ILE   53 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue THR   56 is missing expected H atoms. Skipping.
Residue ALA   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue ILE   63 is missing expected H atoms. Skipping.
Residue ILE   65 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 THR   68 is missing expected H atoms. Skipping.
Residue ALA   69 is missing expected H atoms. Skipping.
Residue VAL   70 is missing expected H atoms. Skipping.
Residue ALA   71 is missing expected H atoms. Skipping.
Residue ILE    4 is missing expected H atoms. Skipping.
Residue ILE    6 is missing expected H atoms. Skipping.
Residue SER    7 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue VAL   15 is missing expected H atoms. Skipping.
Residue SER   16 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue VAL   21 is missing expected H atoms. Skipping.
Residue ILE   23 is missing expected H atoms. Skipping.
Residue VAL   24 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue SER   29 is missing expected H atoms. Skipping.
Residue VAL   31 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 MET   34 is missing expected H atoms. Skipping.
Residue ALA   35 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue THR   40 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue ILE   46 is missing expected H atoms. Skipping.
Residue THR   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue ALA   54 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue ILE   61 is missing expected H atoms. Skipping.
Residue ALA   63 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue LEU   65 is missing expected H atoms. Skipping.
Residue THR   66 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue THR   70 is missing expected H atoms. Skipping.
Residue SER   72 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue SER   81 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LYS   88 is missing expected H atoms. Skipping.
Residue VAL   91 is missing expected H atoms. Skipping.
Residue LYS   93 is missing expected H atoms. Skipping.
Residue SER   95 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue VAL   97 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue ILE  113 is missing expected H atoms. Skipping.
Residue VAL  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  117 is missing expected H atoms. Skipping.
Residue MET  118 is missing expected H atoms. Skipping.
Residue THR  120 is missing expected H atoms. Skipping.
Residue LYS  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  125 is missing expected H atoms. Skipping.
Residue LYS  126 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue VAL  129 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue TYR  137 is missing expected H atoms. Skipping.
Residue THR  138 is missing expected H atoms. Skipping.
Residue ILE  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue ILE  141 is missing expected H atoms. Skipping.
Residue THR  142 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue ALA  150 is missing expected H atoms. Skipping.
Residue VAL  151 is missing expected H atoms. Skipping.
Residue THR  155 is missing expected H atoms. Skipping.
Residue LYS  157 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Residue ILE  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue ILE  164 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue SER  169 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue ALA  173 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue THR  176 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue THR  182 is missing expected H atoms. Skipping.
Residue MET  183 is missing expected H atoms. Skipping.
Residue SER  186 is missing expected H atoms. Skipping.
Residue THR  189 is missing expected H atoms. Skipping.
Residue LEU  191 is missing expected H atoms. Skipping.
Residue MET  196 is missing expected H atoms. Skipping.
Residue VAL  197 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  201 is missing expected H atoms. Skipping.
Residue LYS  204 is missing expected H atoms. Skipping.
Residue ALA  205 is missing expected H atoms. Skipping.
Residue LEU  207 is missing expected H atoms. Skipping.
Residue VAL  208 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LEU  216 is missing expected H atoms. Skipping.
Residue LEU  218 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue ALA  224 is missing expected H atoms. Skipping.
Residue THR  226 is missing expected H atoms. Skipping.
Residue SER  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue THR  236 is missing expected H atoms. Skipping.
Residue LEU  237 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue THR  239 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue VAL  250 is missing expected H atoms. Skipping.
Residue VAL  251 is missing expected H atoms. Skipping.
Residue VAL  252 is missing expected H atoms. Skipping.
Residue LEU  253 is missing expected H atoms. Skipping.
Residue SER  255 is missing expected H atoms. Skipping.
Residue ALA  259 is missing expected H atoms. Skipping.
Residue MET  260 is missing expected H atoms. Skipping.
Residue THR  262 is missing expected H atoms. Skipping.
Residue ALA  263 is missing expected H atoms. Skipping.
Residue LEU  264 is missing expected H atoms. Skipping.
Residue THR  265 is missing expected H atoms. Skipping.
Residue ALA  267 is missing expected H atoms. Skipping.
Residue THR  268 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue SER  273 is missing expected H atoms. Skipping.
Residue SER  274 is missing expected H atoms. Skipping.
Residue LEU  277 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue LYS  284 is missing expected H atoms. Skipping.
Residue LEU  287 is missing expected H atoms. Skipping.
Residue MET  289 is missing expected H atoms. Skipping.
Residue LYS  291 is missing expected H atoms. Skipping.
Residue LEU  292 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue LYS  295 is missing expected H atoms. Skipping.
Residue MET  297 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue TYR  299 is missing expected H atoms. Skipping.
Residue SER  300 is missing expected H atoms. Skipping.
Residue MET  301 is missing expected H atoms. Skipping.
Residue THR  303 is missing expected H atoms. Skipping.
Residue LYS  305 is missing expected H atoms. Skipping.
Residue LYS  307 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue VAL  309 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue ILE  312 is missing expected H atoms. Skipping.
Residue ALA  313 is missing expected H atoms. Skipping.
Residue THR  315 is missing expected H atoms. Skipping.
Residue THR  319 is missing expected H atoms. Skipping.
Residue ILE  320 is missing expected H atoms. Skipping.
Residue VAL  321 is missing expected H atoms. Skipping.
Residue ILE  322 is missing expected H atoms. Skipping.
Residue VAL  324 is missing expected H atoms. Skipping.
Residue TYR  326 is missing expected H atoms. Skipping.
Residue SER  331 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue ILE  335 is missing expected H atoms. Skipping.
Residue ILE  339 is missing expected H atoms. Skipping.
Residue MET  340 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue LYS  344 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  348 is missing expected H atoms. Skipping.
Residue LEU  351 is missing expected H atoms. Skipping.
Residue ILE  352 is missing expected H atoms. Skipping.
Residue THR  353 is missing expected H atoms. Skipping.
Residue VAL  354 is missing expected H atoms. Skipping.
Residue ILE  357 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LYS  361 is missing expected H atoms. Skipping.
Residue SER  363 is missing expected H atoms. Skipping.
Residue VAL  365 is missing expected H atoms. Skipping.
Residue ILE  367 is missing expected H atoms. Skipping.
Residue ALA  369 is missing expected H atoms. Skipping.
Residue SER  376 is missing expected H atoms. Skipping.
Residue TYR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue ILE  379 is missing expected H atoms. Skipping.
Residue ILE  380 is missing expected H atoms. Skipping.
Residue VAL  382 is missing expected H atoms. Skipping.
Residue LEU  387 is missing expected H atoms. Skipping.
Residue LYS  388 is missing expected H atoms. Skipping.
Residue LEU  389 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue LYS  394 is missing expected H atoms. Skipping.
Residue SER  396 is missing expected H atoms. Skipping.
Residue SER  397 is missing expected H atoms. Skipping.
Residue ILE  398 is missing expected H atoms. Skipping.
Residue MET  401 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue THR  404 is missing expected H atoms. Skipping.
Residue THR  405 is missing expected H atoms. Skipping.
Residue MET  406 is missing expected H atoms. Skipping.
Residue ALA  409 is missing expected H atoms. Skipping.
Residue LYS  410 is missing expected H atoms. Skipping.
Residue MET  412 is missing expected H atoms. Skipping.
Residue ALA  413 is missing expected H atoms. Skipping.
Residue ILE  414 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue ALA  419 is missing expected H atoms. Skipping.
Residue SER  424 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue VAL  428 is missing expected H atoms. Skipping.
Residue THR  430 is missing expected H atoms. Skipping.
Residue SER  431 is missing expected H atoms. Skipping.
Residue ILE  432 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue ALA  435 is missing expected H atoms. Skipping.
Residue LEU  436 is missing expected H atoms. Skipping.
Residue VAL  439 is missing expected H atoms. Skipping.
Residue ALA  442 is missing expected H atoms. Skipping.
Residue ILE  443 is missing expected H atoms. Skipping.
Residue TYR  444 is missing expected H atoms. Skipping.
Residue ALA  446 is missing expected H atoms. Skipping.
Residue ALA  447 is missing expected H atoms. Skipping.
Residue SER  449 is missing expected H atoms. Skipping.
Residue VAL  451 is missing expected H atoms. Skipping.
Residue SER  452 is missing expected H atoms. Skipping.
Residue ILE  454 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue ILE  457 is missing expected H atoms. Skipping.
Residue LEU  458 is missing expected H atoms. Skipping.
Residue ILE  459 is missing expected H atoms. Skipping.
Residue VAL  461 is missing expected H atoms. Skipping.
Residue ILE  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue THR  464 is missing expected H atoms. Skipping.
Residue ILE  466 is missing expected H atoms. Skipping.
Residue MET  468 is missing expected H atoms. Skipping.
Residue SER  470 is missing expected H atoms. Skipping.
Residue SER  472 is missing expected H atoms. Skipping.
Residue THR  473 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue LEU  475 is missing expected H atoms. Skipping.
Residue SER  476 is missing expected H atoms. Skipping.
Residue VAL  477 is missing expected H atoms. Skipping.
Residue SER  478 is missing expected H atoms. Skipping.
Residue LEU  479 is missing expected H atoms. Skipping.
Residue VAL  480 is missing expected H atoms. Skipping.
Residue LEU  481 is missing expected H atoms. Skipping.
Residue VAL  482 is missing expected H atoms. Skipping.
Residue VAL  484 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue LEU  487 is missing expected H atoms. Skipping.
Residue TYR  488 is missing expected H atoms. Skipping.
Residue LEU  489 is missing expected H atoms. Skipping.
Residue VAL  491 is missing expected H atoms. Skipping.
Residue MET  492 is missing expected H atoms. Skipping.
Residue VAL  493 is missing expected H atoms. Skipping.
Residue VAL    2 is missing expected H atoms. Skipping.
Residue ALA    3 is missing expected H atoms. Skipping.
Residue LEU    4 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue MET   10 is missing expected H atoms. Skipping.
Residue LEU   12 is missing expected H atoms. Skipping.
Residue THR   14 is missing expected H atoms. Skipping.
Residue ALA   15 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue THR   18 is missing expected H atoms. Skipping.
Residue MET   20 is missing expected H atoms. Skipping.
Residue SER   21 is missing expected H atoms. Skipping.
Residue SER   22 is missing expected H atoms. Skipping.
Residue ALA   25 is missing expected H atoms. Skipping.
Residue LYS   27 is missing expected H atoms. Skipping.
Residue ALA   29 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue ILE   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue THR   43 is missing expected H atoms. Skipping.
Residue ILE   44 is missing expected H atoms. Skipping.
Residue MET   45 is missing expected H atoms. Skipping.
Residue ALA   46 is missing expected H atoms. Skipping.
Residue ALA   47 is missing expected H atoms. Skipping.
Residue ILE   48 is missing expected H atoms. Skipping.
Residue LEU   49 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue TYR   51 is missing expected H atoms. Skipping.
Residue THR   52 is missing expected H atoms. Skipping.
Residue ILE   53 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue THR   56 is missing expected H atoms. Skipping.
Residue ALA   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue ILE   63 is missing expected H atoms. Skipping.
Residue ILE   65 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 THR   68 is missing expected H atoms. Skipping.
Residue ALA   69 is missing expected H atoms. Skipping.
Residue VAL   70 is missing expected H atoms. Skipping.
Residue ALA   71 is missing expected H atoms. Skipping.
Evaluate side-chains
  313 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 41
    poor density    : 272
  time to evaluate  : 1.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 41
  outliers final: 23
  residues processed: 289
  average time/residue: 0.2201
  time to fit residues: 89.8262
Evaluate side-chains
  269 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 246
  time to evaluate  : 1.087 
Switching outliers to nearest non-outliers
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 23
  outliers final: 2
  residues processed: 23
  average time/residue: 0.1122
  time to fit residues: 5.9890
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:   30.0000
   chunk 61 optimal weight:    5.9990
   chunk 79 optimal weight:   20.0000
   chunk 91 optimal weight:    0.0770
   chunk 60 optimal weight:    3.9990
   chunk 107 optimal weight:   30.0000
   chunk 67 optimal weight:   20.0000
   chunk 65 optimal weight:    5.9990
   chunk 49 optimal weight:    0.6980
   chunk 66 optimal weight:    6.9990
   chunk 43 optimal weight:   30.0000
   overall best weight:    3.3544

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

Flipped N/Q/H residues before XYZ refinement:
** A  27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 203 ASN
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  27 HIS
** C  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 103 ASN
** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   7 HIS
** D  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.5782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8986  Z= 0.175
  Angle     :  0.700   7.280  12164  Z= 0.356
  Chirality :  0.044   0.281   1412
  Planarity :  0.004   0.039   1520
  Dihedral  :  6.540  63.035   1224
  Min Nonbonded Distance : 1.829

Molprobity Statistics.
  All-atom Clashscore : 71.32
  Ramachandran Plot:
    Outliers :  3.73 %
    Allowed  : 19.89 %
    Favored  : 76.38 %
  Rotamer Outliers :  2.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -4.73 (0.22), residues: 1126
  helix: -1.44 (0.26), residues: 298
  sheet: -1.82 (0.33), residues: 264
  loop : -4.99 (0.19), residues: 564

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE    4 is missing expected H atoms. Skipping.
Residue ILE    6 is missing expected H atoms. Skipping.
Residue SER    7 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue VAL   15 is missing expected H atoms. Skipping.
Residue SER   16 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue VAL   21 is missing expected H atoms. Skipping.
Residue ILE   23 is missing expected H atoms. Skipping.
Residue VAL   24 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue SER   29 is missing expected H atoms. Skipping.
Residue VAL   31 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 MET   34 is missing expected H atoms. Skipping.
Residue ALA   35 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue THR   40 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue ILE   46 is missing expected H atoms. Skipping.
Residue THR   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue ALA   54 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue ILE   61 is missing expected H atoms. Skipping.
Residue ALA   63 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue LEU   65 is missing expected H atoms. Skipping.
Residue THR   66 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue THR   70 is missing expected H atoms. Skipping.
Residue SER   72 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue SER   81 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LYS   88 is missing expected H atoms. Skipping.
Residue VAL   91 is missing expected H atoms. Skipping.
Residue LYS   93 is missing expected H atoms. Skipping.
Residue SER   95 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue VAL   97 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue ILE  113 is missing expected H atoms. Skipping.
Residue VAL  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  117 is missing expected H atoms. Skipping.
Residue MET  118 is missing expected H atoms. Skipping.
Residue THR  120 is missing expected H atoms. Skipping.
Residue LYS  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  125 is missing expected H atoms. Skipping.
Residue LYS  126 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue VAL  129 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue TYR  137 is missing expected H atoms. Skipping.
Residue THR  138 is missing expected H atoms. Skipping.
Residue ILE  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue ILE  141 is missing expected H atoms. Skipping.
Residue THR  142 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue ALA  150 is missing expected H atoms. Skipping.
Residue VAL  151 is missing expected H atoms. Skipping.
Residue THR  155 is missing expected H atoms. Skipping.
Residue LYS  157 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Residue ILE  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue ILE  164 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue SER  169 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue ALA  173 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue THR  176 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue THR  182 is missing expected H atoms. Skipping.
Residue MET  183 is missing expected H atoms. Skipping.
Residue SER  186 is missing expected H atoms. Skipping.
Residue THR  189 is missing expected H atoms. Skipping.
Residue LEU  191 is missing expected H atoms. Skipping.
Residue MET  196 is missing expected H atoms. Skipping.
Residue VAL  197 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  201 is missing expected H atoms. Skipping.
Residue LYS  204 is missing expected H atoms. Skipping.
Residue ALA  205 is missing expected H atoms. Skipping.
Residue LEU  207 is missing expected H atoms. Skipping.
Residue VAL  208 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LEU  216 is missing expected H atoms. Skipping.
Residue LEU  218 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue ALA  224 is missing expected H atoms. Skipping.
Residue THR  226 is missing expected H atoms. Skipping.
Residue SER  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue THR  236 is missing expected H atoms. Skipping.
Residue LEU  237 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue THR  239 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue VAL  250 is missing expected H atoms. Skipping.
Residue VAL  251 is missing expected H atoms. Skipping.
Residue VAL  252 is missing expected H atoms. Skipping.
Residue LEU  253 is missing expected H atoms. Skipping.
Residue SER  255 is missing expected H atoms. Skipping.
Residue ALA  259 is missing expected H atoms. Skipping.
Residue MET  260 is missing expected H atoms. Skipping.
Residue THR  262 is missing expected H atoms. Skipping.
Residue ALA  263 is missing expected H atoms. Skipping.
Residue LEU  264 is missing expected H atoms. Skipping.
Residue THR  265 is missing expected H atoms. Skipping.
Residue ALA  267 is missing expected H atoms. Skipping.
Residue THR  268 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue SER  273 is missing expected H atoms. Skipping.
Residue SER  274 is missing expected H atoms. Skipping.
Residue LEU  277 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue LYS  284 is missing expected H atoms. Skipping.
Residue LEU  287 is missing expected H atoms. Skipping.
Residue MET  289 is missing expected H atoms. Skipping.
Residue LYS  291 is missing expected H atoms. Skipping.
Residue LEU  292 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue LYS  295 is missing expected H atoms. Skipping.
Residue MET  297 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue TYR  299 is missing expected H atoms. Skipping.
Residue SER  300 is missing expected H atoms. Skipping.
Residue MET  301 is missing expected H atoms. Skipping.
Residue THR  303 is missing expected H atoms. Skipping.
Residue LYS  305 is missing expected H atoms. Skipping.
Residue LYS  307 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue VAL  309 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue ILE  312 is missing expected H atoms. Skipping.
Residue ALA  313 is missing expected H atoms. Skipping.
Residue THR  315 is missing expected H atoms. Skipping.
Residue THR  319 is missing expected H atoms. Skipping.
Residue ILE  320 is missing expected H atoms. Skipping.
Residue VAL  321 is missing expected H atoms. Skipping.
Residue ILE  322 is missing expected H atoms. Skipping.
Residue VAL  324 is missing expected H atoms. Skipping.
Residue TYR  326 is missing expected H atoms. Skipping.
Residue SER  331 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue ILE  335 is missing expected H atoms. Skipping.
Residue ILE  339 is missing expected H atoms. Skipping.
Residue MET  340 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue LYS  344 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  348 is missing expected H atoms. Skipping.
Residue LEU  351 is missing expected H atoms. Skipping.
Residue ILE  352 is missing expected H atoms. Skipping.
Residue THR  353 is missing expected H atoms. Skipping.
Residue VAL  354 is missing expected H atoms. Skipping.
Residue ILE  357 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LYS  361 is missing expected H atoms. Skipping.
Residue SER  363 is missing expected H atoms. Skipping.
Residue VAL  365 is missing expected H atoms. Skipping.
Residue ILE  367 is missing expected H atoms. Skipping.
Residue ALA  369 is missing expected H atoms. Skipping.
Residue SER  376 is missing expected H atoms. Skipping.
Residue TYR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue ILE  379 is missing expected H atoms. Skipping.
Residue ILE  380 is missing expected H atoms. Skipping.
Residue VAL  382 is missing expected H atoms. Skipping.
Residue LEU  387 is missing expected H atoms. Skipping.
Residue LYS  388 is missing expected H atoms. Skipping.
Residue LEU  389 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue LYS  394 is missing expected H atoms. Skipping.
Residue SER  396 is missing expected H atoms. Skipping.
Residue SER  397 is missing expected H atoms. Skipping.
Residue ILE  398 is missing expected H atoms. Skipping.
Residue MET  401 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue THR  404 is missing expected H atoms. Skipping.
Residue THR  405 is missing expected H atoms. Skipping.
Residue MET  406 is missing expected H atoms. Skipping.
Residue ALA  409 is missing expected H atoms. Skipping.
Residue LYS  410 is missing expected H atoms. Skipping.
Residue MET  412 is missing expected H atoms. Skipping.
Residue ALA  413 is missing expected H atoms. Skipping.
Residue ILE  414 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue ALA  419 is missing expected H atoms. Skipping.
Residue SER  424 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue VAL  428 is missing expected H atoms. Skipping.
Residue THR  430 is missing expected H atoms. Skipping.
Residue SER  431 is missing expected H atoms. Skipping.
Residue ILE  432 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue ALA  435 is missing expected H atoms. Skipping.
Residue LEU  436 is missing expected H atoms. Skipping.
Residue VAL  439 is missing expected H atoms. Skipping.
Residue ALA  442 is missing expected H atoms. Skipping.
Residue ILE  443 is missing expected H atoms. Skipping.
Residue TYR  444 is missing expected H atoms. Skipping.
Residue ALA  446 is missing expected H atoms. Skipping.
Residue ALA  447 is missing expected H atoms. Skipping.
Residue SER  449 is missing expected H atoms. Skipping.
Residue VAL  451 is missing expected H atoms. Skipping.
Residue SER  452 is missing expected H atoms. Skipping.
Residue ILE  454 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue ILE  457 is missing expected H atoms. Skipping.
Residue LEU  458 is missing expected H atoms. Skipping.
Residue ILE  459 is missing expected H atoms. Skipping.
Residue VAL  461 is missing expected H atoms. Skipping.
Residue ILE  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue THR  464 is missing expected H atoms. Skipping.
Residue ILE  466 is missing expected H atoms. Skipping.
Residue MET  468 is missing expected H atoms. Skipping.
Residue SER  470 is missing expected H atoms. Skipping.
Residue SER  472 is missing expected H atoms. Skipping.
Residue THR  473 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue LEU  475 is missing expected H atoms. Skipping.
Residue SER  476 is missing expected H atoms. Skipping.
Residue VAL  477 is missing expected H atoms. Skipping.
Residue SER  478 is missing expected H atoms. Skipping.
Residue LEU  479 is missing expected H atoms. Skipping.
Residue VAL  480 is missing expected H atoms. Skipping.
Residue LEU  481 is missing expected H atoms. Skipping.
Residue VAL  482 is missing expected H atoms. Skipping.
Residue VAL  484 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue LEU  487 is missing expected H atoms. Skipping.
Residue TYR  488 is missing expected H atoms. Skipping.
Residue LEU  489 is missing expected H atoms. Skipping.
Residue VAL  491 is missing expected H atoms. Skipping.
Residue MET  492 is missing expected H atoms. Skipping.
Residue VAL  493 is missing expected H atoms. Skipping.
Residue VAL    2 is missing expected H atoms. Skipping.
Residue ALA    3 is missing expected H atoms. Skipping.
Residue LEU    4 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue MET   10 is missing expected H atoms. Skipping.
Residue LEU   12 is missing expected H atoms. Skipping.
Residue THR   14 is missing expected H atoms. Skipping.
Residue ALA   15 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue THR   18 is missing expected H atoms. Skipping.
Residue MET   20 is missing expected H atoms. Skipping.
Residue SER   21 is missing expected H atoms. Skipping.
Residue SER   22 is missing expected H atoms. Skipping.
Residue ALA   25 is missing expected H atoms. Skipping.
Residue LYS   27 is missing expected H atoms. Skipping.
Residue ALA   29 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue ILE   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue THR   43 is missing expected H atoms. Skipping.
Residue ILE   44 is missing expected H atoms. Skipping.
Residue MET   45 is missing expected H atoms. Skipping.
Residue ALA   46 is missing expected H atoms. Skipping.
Residue ALA   47 is missing expected H atoms. Skipping.
Residue ILE   48 is missing expected H atoms. Skipping.
Residue LEU   49 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue TYR   51 is missing expected H atoms. Skipping.
Residue THR   52 is missing expected H atoms. Skipping.
Residue ILE   53 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue THR   56 is missing expected H atoms. Skipping.
Residue ALA   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue ILE   63 is missing expected H atoms. Skipping.
Residue ILE   65 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 THR   68 is missing expected H atoms. Skipping.
Residue ALA   69 is missing expected H atoms. Skipping.
Residue VAL   70 is missing expected H atoms. Skipping.
Residue ALA   71 is missing expected H atoms. Skipping.
Residue ILE    4 is missing expected H atoms. Skipping.
Residue ILE    6 is missing expected H atoms. Skipping.
Residue SER    7 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue VAL   15 is missing expected H atoms. Skipping.
Residue SER   16 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue VAL   21 is missing expected H atoms. Skipping.
Residue ILE   23 is missing expected H atoms. Skipping.
Residue VAL   24 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue SER   29 is missing expected H atoms. Skipping.
Residue VAL   31 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 MET   34 is missing expected H atoms. Skipping.
Residue ALA   35 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue THR   40 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue ILE   46 is missing expected H atoms. Skipping.
Residue THR   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue ALA   54 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue ILE   61 is missing expected H atoms. Skipping.
Residue ALA   63 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue LEU   65 is missing expected H atoms. Skipping.
Residue THR   66 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue THR   70 is missing expected H atoms. Skipping.
Residue SER   72 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue SER   81 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LYS   88 is missing expected H atoms. Skipping.
Residue VAL   91 is missing expected H atoms. Skipping.
Residue LYS   93 is missing expected H atoms. Skipping.
Residue SER   95 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue VAL   97 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue ILE  113 is missing expected H atoms. Skipping.
Residue VAL  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  117 is missing expected H atoms. Skipping.
Residue MET  118 is missing expected H atoms. Skipping.
Residue THR  120 is missing expected H atoms. Skipping.
Residue LYS  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  125 is missing expected H atoms. Skipping.
Residue LYS  126 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue VAL  129 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue TYR  137 is missing expected H atoms. Skipping.
Residue THR  138 is missing expected H atoms. Skipping.
Residue ILE  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue ILE  141 is missing expected H atoms. Skipping.
Residue THR  142 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue ALA  150 is missing expected H atoms. Skipping.
Residue VAL  151 is missing expected H atoms. Skipping.
Residue THR  155 is missing expected H atoms. Skipping.
Residue LYS  157 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Residue ILE  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue ILE  164 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue SER  169 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue ALA  173 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue THR  176 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue THR  182 is missing expected H atoms. Skipping.
Residue MET  183 is missing expected H atoms. Skipping.
Residue SER  186 is missing expected H atoms. Skipping.
Residue THR  189 is missing expected H atoms. Skipping.
Residue LEU  191 is missing expected H atoms. Skipping.
Residue MET  196 is missing expected H atoms. Skipping.
Residue VAL  197 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  201 is missing expected H atoms. Skipping.
Residue LYS  204 is missing expected H atoms. Skipping.
Residue ALA  205 is missing expected H atoms. Skipping.
Residue LEU  207 is missing expected H atoms. Skipping.
Residue VAL  208 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LEU  216 is missing expected H atoms. Skipping.
Residue LEU  218 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue ALA  224 is missing expected H atoms. Skipping.
Residue THR  226 is missing expected H atoms. Skipping.
Residue SER  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue THR  236 is missing expected H atoms. Skipping.
Residue LEU  237 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue THR  239 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue VAL  250 is missing expected H atoms. Skipping.
Residue VAL  251 is missing expected H atoms. Skipping.
Residue VAL  252 is missing expected H atoms. Skipping.
Residue LEU  253 is missing expected H atoms. Skipping.
Residue SER  255 is missing expected H atoms. Skipping.
Residue ALA  259 is missing expected H atoms. Skipping.
Residue MET  260 is missing expected H atoms. Skipping.
Residue THR  262 is missing expected H atoms. Skipping.
Residue ALA  263 is missing expected H atoms. Skipping.
Residue LEU  264 is missing expected H atoms. Skipping.
Residue THR  265 is missing expected H atoms. Skipping.
Residue ALA  267 is missing expected H atoms. Skipping.
Residue THR  268 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue SER  273 is missing expected H atoms. Skipping.
Residue SER  274 is missing expected H atoms. Skipping.
Residue LEU  277 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue LYS  284 is missing expected H atoms. Skipping.
Residue LEU  287 is missing expected H atoms. Skipping.
Residue MET  289 is missing expected H atoms. Skipping.
Residue LYS  291 is missing expected H atoms. Skipping.
Residue LEU  292 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue LYS  295 is missing expected H atoms. Skipping.
Residue MET  297 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue TYR  299 is missing expected H atoms. Skipping.
Residue SER  300 is missing expected H atoms. Skipping.
Residue MET  301 is missing expected H atoms. Skipping.
Residue THR  303 is missing expected H atoms. Skipping.
Residue LYS  305 is missing expected H atoms. Skipping.
Residue LYS  307 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue VAL  309 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue ILE  312 is missing expected H atoms. Skipping.
Residue ALA  313 is missing expected H atoms. Skipping.
Residue THR  315 is missing expected H atoms. Skipping.
Residue THR  319 is missing expected H atoms. Skipping.
Residue ILE  320 is missing expected H atoms. Skipping.
Residue VAL  321 is missing expected H atoms. Skipping.
Residue ILE  322 is missing expected H atoms. Skipping.
Residue VAL  324 is missing expected H atoms. Skipping.
Residue TYR  326 is missing expected H atoms. Skipping.
Residue SER  331 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue ILE  335 is missing expected H atoms. Skipping.
Residue ILE  339 is missing expected H atoms. Skipping.
Residue MET  340 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue LYS  344 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  348 is missing expected H atoms. Skipping.
Residue LEU  351 is missing expected H atoms. Skipping.
Residue ILE  352 is missing expected H atoms. Skipping.
Residue THR  353 is missing expected H atoms. Skipping.
Residue VAL  354 is missing expected H atoms. Skipping.
Residue ILE  357 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LYS  361 is missing expected H atoms. Skipping.
Residue SER  363 is missing expected H atoms. Skipping.
Residue VAL  365 is missing expected H atoms. Skipping.
Residue ILE  367 is missing expected H atoms. Skipping.
Residue ALA  369 is missing expected H atoms. Skipping.
Residue SER  376 is missing expected H atoms. Skipping.
Residue TYR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue ILE  379 is missing expected H atoms. Skipping.
Residue ILE  380 is missing expected H atoms. Skipping.
Residue VAL  382 is missing expected H atoms. Skipping.
Residue LEU  387 is missing expected H atoms. Skipping.
Residue LYS  388 is missing expected H atoms. Skipping.
Residue LEU  389 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue LYS  394 is missing expected H atoms. Skipping.
Residue SER  396 is missing expected H atoms. Skipping.
Residue SER  397 is missing expected H atoms. Skipping.
Residue ILE  398 is missing expected H atoms. Skipping.
Residue MET  401 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue THR  404 is missing expected H atoms. Skipping.
Residue THR  405 is missing expected H atoms. Skipping.
Residue MET  406 is missing expected H atoms. Skipping.
Residue ALA  409 is missing expected H atoms. Skipping.
Residue LYS  410 is missing expected H atoms. Skipping.
Residue MET  412 is missing expected H atoms. Skipping.
Residue ALA  413 is missing expected H atoms. Skipping.
Residue ILE  414 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue ALA  419 is missing expected H atoms. Skipping.
Residue SER  424 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue VAL  428 is missing expected H atoms. Skipping.
Residue THR  430 is missing expected H atoms. Skipping.
Residue SER  431 is missing expected H atoms. Skipping.
Residue ILE  432 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue ALA  435 is missing expected H atoms. Skipping.
Residue LEU  436 is missing expected H atoms. Skipping.
Residue VAL  439 is missing expected H atoms. Skipping.
Residue ALA  442 is missing expected H atoms. Skipping.
Residue ILE  443 is missing expected H atoms. Skipping.
Residue TYR  444 is missing expected H atoms. Skipping.
Residue ALA  446 is missing expected H atoms. Skipping.
Residue ALA  447 is missing expected H atoms. Skipping.
Residue SER  449 is missing expected H atoms. Skipping.
Residue VAL  451 is missing expected H atoms. Skipping.
Residue SER  452 is missing expected H atoms. Skipping.
Residue ILE  454 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue ILE  457 is missing expected H atoms. Skipping.
Residue LEU  458 is missing expected H atoms. Skipping.
Residue ILE  459 is missing expected H atoms. Skipping.
Residue VAL  461 is missing expected H atoms. Skipping.
Residue ILE  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue THR  464 is missing expected H atoms. Skipping.
Residue ILE  466 is missing expected H atoms. Skipping.
Residue MET  468 is missing expected H atoms. Skipping.
Residue SER  470 is missing expected H atoms. Skipping.
Residue SER  472 is missing expected H atoms. Skipping.
Residue THR  473 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue LEU  475 is missing expected H atoms. Skipping.
Residue SER  476 is missing expected H atoms. Skipping.
Residue VAL  477 is missing expected H atoms. Skipping.
Residue SER  478 is missing expected H atoms. Skipping.
Residue LEU  479 is missing expected H atoms. Skipping.
Residue VAL  480 is missing expected H atoms. Skipping.
Residue LEU  481 is missing expected H atoms. Skipping.
Residue VAL  482 is missing expected H atoms. Skipping.
Residue VAL  484 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue LEU  487 is missing expected H atoms. Skipping.
Residue TYR  488 is missing expected H atoms. Skipping.
Residue LEU  489 is missing expected H atoms. Skipping.
Residue VAL  491 is missing expected H atoms. Skipping.
Residue MET  492 is missing expected H atoms. Skipping.
Residue VAL  493 is missing expected H atoms. Skipping.
Residue VAL    2 is missing expected H atoms. Skipping.
Residue ALA    3 is missing expected H atoms. Skipping.
Residue LEU    4 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue MET   10 is missing expected H atoms. Skipping.
Residue LEU   12 is missing expected H atoms. Skipping.
Residue THR   14 is missing expected H atoms. Skipping.
Residue ALA   15 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue THR   18 is missing expected H atoms. Skipping.
Residue MET   20 is missing expected H atoms. Skipping.
Residue SER   21 is missing expected H atoms. Skipping.
Residue SER   22 is missing expected H atoms. Skipping.
Residue ALA   25 is missing expected H atoms. Skipping.
Residue LYS   27 is missing expected H atoms. Skipping.
Residue ALA   29 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue ILE   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue THR   43 is missing expected H atoms. Skipping.
Residue ILE   44 is missing expected H atoms. Skipping.
Residue MET   45 is missing expected H atoms. Skipping.
Residue ALA   46 is missing expected H atoms. Skipping.
Residue ALA   47 is missing expected H atoms. Skipping.
Residue ILE   48 is missing expected H atoms. Skipping.
Residue LEU   49 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue TYR   51 is missing expected H atoms. Skipping.
Residue THR   52 is missing expected H atoms. Skipping.
Residue ILE   53 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue THR   56 is missing expected H atoms. Skipping.
Residue ALA   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue ILE   63 is missing expected H atoms. Skipping.
Residue ILE   65 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 THR   68 is missing expected H atoms. Skipping.
Residue ALA   69 is missing expected H atoms. Skipping.
Residue VAL   70 is missing expected H atoms. Skipping.
Residue ALA   71 is missing expected H atoms. Skipping.
Evaluate side-chains
  283 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 258
  time to evaluate  : 1.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 25
  outliers final: 15
  residues processed: 277
  average time/residue: 0.2330
  time to fit residues: 90.0899
Evaluate side-chains
  256 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 241
  time to evaluate  : 1.073 
Switching outliers to nearest non-outliers
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 15
  outliers final: 2
  residues processed: 15
  average time/residue: 0.1066
  time to fit residues: 4.2810
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    7.9990
   chunk 32 optimal weight:   20.0000
   chunk 21 optimal weight:    8.9990
   chunk 20 optimal weight:   10.0000
   chunk 68 optimal weight:   30.0000
   chunk 73 optimal weight:    0.5980
   chunk 53 optimal weight:    6.9990
   chunk 10 optimal weight:   20.0000
   chunk 84 optimal weight:   30.0000
   chunk 98 optimal weight:    3.9990
   chunk 103 optimal weight:   30.0000
   overall best weight:    5.7188

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

Flipped N/Q/H residues before XYZ refinement:
** A  27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 158 HIS
A 167 GLN
A 203 ASN
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   7 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.5890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8986  Z= 0.217
  Angle     :  0.723   7.696  12164  Z= 0.368
  Chirality :  0.044   0.223   1412
  Planarity :  0.004   0.033   1520
  Dihedral  :  6.589  64.607   1224
  Min Nonbonded Distance : 1.855

Molprobity Statistics.
  All-atom Clashscore : 70.05
  Ramachandran Plot:
    Outliers :  3.64 %
    Allowed  : 21.49 %
    Favored  : 74.87 %
  Rotamer Outliers :  2.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -4.63 (0.22), residues: 1126
  helix: -1.41 (0.27), residues: 302
  sheet: -1.73 (0.34), residues: 264
  loop : -4.93 (0.19), residues: 560

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE    4 is missing expected H atoms. Skipping.
Residue ILE    6 is missing expected H atoms. Skipping.
Residue SER    7 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue VAL   15 is missing expected H atoms. Skipping.
Residue SER   16 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue VAL   21 is missing expected H atoms. Skipping.
Residue ILE   23 is missing expected H atoms. Skipping.
Residue VAL   24 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue SER   29 is missing expected H atoms. Skipping.
Residue VAL   31 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 MET   34 is missing expected H atoms. Skipping.
Residue ALA   35 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue THR   40 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue ILE   46 is missing expected H atoms. Skipping.
Residue THR   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue ALA   54 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue ILE   61 is missing expected H atoms. Skipping.
Residue ALA   63 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue LEU   65 is missing expected H atoms. Skipping.
Residue THR   66 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue THR   70 is missing expected H atoms. Skipping.
Residue SER   72 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue SER   81 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LYS   88 is missing expected H atoms. Skipping.
Residue VAL   91 is missing expected H atoms. Skipping.
Residue LYS   93 is missing expected H atoms. Skipping.
Residue SER   95 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue VAL   97 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue ILE  113 is missing expected H atoms. Skipping.
Residue VAL  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  117 is missing expected H atoms. Skipping.
Residue MET  118 is missing expected H atoms. Skipping.
Residue THR  120 is missing expected H atoms. Skipping.
Residue LYS  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  125 is missing expected H atoms. Skipping.
Residue LYS  126 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue VAL  129 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue TYR  137 is missing expected H atoms. Skipping.
Residue THR  138 is missing expected H atoms. Skipping.
Residue ILE  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue ILE  141 is missing expected H atoms. Skipping.
Residue THR  142 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue ALA  150 is missing expected H atoms. Skipping.
Residue VAL  151 is missing expected H atoms. Skipping.
Residue THR  155 is missing expected H atoms. Skipping.
Residue LYS  157 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Residue ILE  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue ILE  164 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue SER  169 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue ALA  173 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue THR  176 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue THR  182 is missing expected H atoms. Skipping.
Residue MET  183 is missing expected H atoms. Skipping.
Residue SER  186 is missing expected H atoms. Skipping.
Residue THR  189 is missing expected H atoms. Skipping.
Residue LEU  191 is missing expected H atoms. Skipping.
Residue MET  196 is missing expected H atoms. Skipping.
Residue VAL  197 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  201 is missing expected H atoms. Skipping.
Residue LYS  204 is missing expected H atoms. Skipping.
Residue ALA  205 is missing expected H atoms. Skipping.
Residue LEU  207 is missing expected H atoms. Skipping.
Residue VAL  208 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LEU  216 is missing expected H atoms. Skipping.
Residue LEU  218 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue ALA  224 is missing expected H atoms. Skipping.
Residue THR  226 is missing expected H atoms. Skipping.
Residue SER  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue THR  236 is missing expected H atoms. Skipping.
Residue LEU  237 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue THR  239 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue VAL  250 is missing expected H atoms. Skipping.
Residue VAL  251 is missing expected H atoms. Skipping.
Residue VAL  252 is missing expected H atoms. Skipping.
Residue LEU  253 is missing expected H atoms. Skipping.
Residue SER  255 is missing expected H atoms. Skipping.
Residue ALA  259 is missing expected H atoms. Skipping.
Residue MET  260 is missing expected H atoms. Skipping.
Residue THR  262 is missing expected H atoms. Skipping.
Residue ALA  263 is missing expected H atoms. Skipping.
Residue LEU  264 is missing expected H atoms. Skipping.
Residue THR  265 is missing expected H atoms. Skipping.
Residue ALA  267 is missing expected H atoms. Skipping.
Residue THR  268 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue SER  273 is missing expected H atoms. Skipping.
Residue SER  274 is missing expected H atoms. Skipping.
Residue LEU  277 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue LYS  284 is missing expected H atoms. Skipping.
Residue LEU  287 is missing expected H atoms. Skipping.
Residue MET  289 is missing expected H atoms. Skipping.
Residue LYS  291 is missing expected H atoms. Skipping.
Residue LEU  292 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue LYS  295 is missing expected H atoms. Skipping.
Residue MET  297 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue TYR  299 is missing expected H atoms. Skipping.
Residue SER  300 is missing expected H atoms. Skipping.
Residue MET  301 is missing expected H atoms. Skipping.
Residue THR  303 is missing expected H atoms. Skipping.
Residue LYS  305 is missing expected H atoms. Skipping.
Residue LYS  307 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue VAL  309 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue ILE  312 is missing expected H atoms. Skipping.
Residue ALA  313 is missing expected H atoms. Skipping.
Residue THR  315 is missing expected H atoms. Skipping.
Residue THR  319 is missing expected H atoms. Skipping.
Residue ILE  320 is missing expected H atoms. Skipping.
Residue VAL  321 is missing expected H atoms. Skipping.
Residue ILE  322 is missing expected H atoms. Skipping.
Residue VAL  324 is missing expected H atoms. Skipping.
Residue TYR  326 is missing expected H atoms. Skipping.
Residue SER  331 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue ILE  335 is missing expected H atoms. Skipping.
Residue ILE  339 is missing expected H atoms. Skipping.
Residue MET  340 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue LYS  344 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  348 is missing expected H atoms. Skipping.
Residue LEU  351 is missing expected H atoms. Skipping.
Residue ILE  352 is missing expected H atoms. Skipping.
Residue THR  353 is missing expected H atoms. Skipping.
Residue VAL  354 is missing expected H atoms. Skipping.
Residue ILE  357 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LYS  361 is missing expected H atoms. Skipping.
Residue SER  363 is missing expected H atoms. Skipping.
Residue VAL  365 is missing expected H atoms. Skipping.
Residue ILE  367 is missing expected H atoms. Skipping.
Residue ALA  369 is missing expected H atoms. Skipping.
Residue SER  376 is missing expected H atoms. Skipping.
Residue TYR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue ILE  379 is missing expected H atoms. Skipping.
Residue ILE  380 is missing expected H atoms. Skipping.
Residue VAL  382 is missing expected H atoms. Skipping.
Residue LEU  387 is missing expected H atoms. Skipping.
Residue LYS  388 is missing expected H atoms. Skipping.
Residue LEU  389 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue LYS  394 is missing expected H atoms. Skipping.
Residue SER  396 is missing expected H atoms. Skipping.
Residue SER  397 is missing expected H atoms. Skipping.
Residue ILE  398 is missing expected H atoms. Skipping.
Residue MET  401 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue THR  404 is missing expected H atoms. Skipping.
Residue THR  405 is missing expected H atoms. Skipping.
Residue MET  406 is missing expected H atoms. Skipping.
Residue ALA  409 is missing expected H atoms. Skipping.
Residue LYS  410 is missing expected H atoms. Skipping.
Residue MET  412 is missing expected H atoms. Skipping.
Residue ALA  413 is missing expected H atoms. Skipping.
Residue ILE  414 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue ALA  419 is missing expected H atoms. Skipping.
Residue SER  424 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue VAL  428 is missing expected H atoms. Skipping.
Residue THR  430 is missing expected H atoms. Skipping.
Residue SER  431 is missing expected H atoms. Skipping.
Residue ILE  432 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue ALA  435 is missing expected H atoms. Skipping.
Residue LEU  436 is missing expected H atoms. Skipping.
Residue VAL  439 is missing expected H atoms. Skipping.
Residue ALA  442 is missing expected H atoms. Skipping.
Residue ILE  443 is missing expected H atoms. Skipping.
Residue TYR  444 is missing expected H atoms. Skipping.
Residue ALA  446 is missing expected H atoms. Skipping.
Residue ALA  447 is missing expected H atoms. Skipping.
Residue SER  449 is missing expected H atoms. Skipping.
Residue VAL  451 is missing expected H atoms. Skipping.
Residue SER  452 is missing expected H atoms. Skipping.
Residue ILE  454 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue ILE  457 is missing expected H atoms. Skipping.
Residue LEU  458 is missing expected H atoms. Skipping.
Residue ILE  459 is missing expected H atoms. Skipping.
Residue VAL  461 is missing expected H atoms. Skipping.
Residue ILE  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue THR  464 is missing expected H atoms. Skipping.
Residue ILE  466 is missing expected H atoms. Skipping.
Residue MET  468 is missing expected H atoms. Skipping.
Residue SER  470 is missing expected H atoms. Skipping.
Residue SER  472 is missing expected H atoms. Skipping.
Residue THR  473 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue LEU  475 is missing expected H atoms. Skipping.
Residue SER  476 is missing expected H atoms. Skipping.
Residue VAL  477 is missing expected H atoms. Skipping.
Residue SER  478 is missing expected H atoms. Skipping.
Residue LEU  479 is missing expected H atoms. Skipping.
Residue VAL  480 is missing expected H atoms. Skipping.
Residue LEU  481 is missing expected H atoms. Skipping.
Residue VAL  482 is missing expected H atoms. Skipping.
Residue VAL  484 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue LEU  487 is missing expected H atoms. Skipping.
Residue TYR  488 is missing expected H atoms. Skipping.
Residue LEU  489 is missing expected H atoms. Skipping.
Residue VAL  491 is missing expected H atoms. Skipping.
Residue MET  492 is missing expected H atoms. Skipping.
Residue VAL  493 is missing expected H atoms. Skipping.
Residue VAL    2 is missing expected H atoms. Skipping.
Residue ALA    3 is missing expected H atoms. Skipping.
Residue LEU    4 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue MET   10 is missing expected H atoms. Skipping.
Residue LEU   12 is missing expected H atoms. Skipping.
Residue THR   14 is missing expected H atoms. Skipping.
Residue ALA   15 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue THR   18 is missing expected H atoms. Skipping.
Residue MET   20 is missing expected H atoms. Skipping.
Residue SER   21 is missing expected H atoms. Skipping.
Residue SER   22 is missing expected H atoms. Skipping.
Residue ALA   25 is missing expected H atoms. Skipping.
Residue LYS   27 is missing expected H atoms. Skipping.
Residue ALA   29 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue ILE   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue THR   43 is missing expected H atoms. Skipping.
Residue ILE   44 is missing expected H atoms. Skipping.
Residue MET   45 is missing expected H atoms. Skipping.
Residue ALA   46 is missing expected H atoms. Skipping.
Residue ALA   47 is missing expected H atoms. Skipping.
Residue ILE   48 is missing expected H atoms. Skipping.
Residue LEU   49 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue TYR   51 is missing expected H atoms. Skipping.
Residue THR   52 is missing expected H atoms. Skipping.
Residue ILE   53 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue THR   56 is missing expected H atoms. Skipping.
Residue ALA   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue ILE   63 is missing expected H atoms. Skipping.
Residue ILE   65 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 THR   68 is missing expected H atoms. Skipping.
Residue ALA   69 is missing expected H atoms. Skipping.
Residue VAL   70 is missing expected H atoms. Skipping.
Residue ALA   71 is missing expected H atoms. Skipping.
Residue ILE    4 is missing expected H atoms. Skipping.
Residue ILE    6 is missing expected H atoms. Skipping.
Residue SER    7 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue VAL   15 is missing expected H atoms. Skipping.
Residue SER   16 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue VAL   21 is missing expected H atoms. Skipping.
Residue ILE   23 is missing expected H atoms. Skipping.
Residue VAL   24 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue SER   29 is missing expected H atoms. Skipping.
Residue VAL   31 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 MET   34 is missing expected H atoms. Skipping.
Residue ALA   35 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue THR   40 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue ILE   46 is missing expected H atoms. Skipping.
Residue THR   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue ALA   54 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue ILE   61 is missing expected H atoms. Skipping.
Residue ALA   63 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue LEU   65 is missing expected H atoms. Skipping.
Residue THR   66 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue THR   70 is missing expected H atoms. Skipping.
Residue SER   72 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue SER   81 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LYS   88 is missing expected H atoms. Skipping.
Residue VAL   91 is missing expected H atoms. Skipping.
Residue LYS   93 is missing expected H atoms. Skipping.
Residue SER   95 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue VAL   97 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue ILE  113 is missing expected H atoms. Skipping.
Residue VAL  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  117 is missing expected H atoms. Skipping.
Residue MET  118 is missing expected H atoms. Skipping.
Residue THR  120 is missing expected H atoms. Skipping.
Residue LYS  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  125 is missing expected H atoms. Skipping.
Residue LYS  126 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue VAL  129 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue TYR  137 is missing expected H atoms. Skipping.
Residue THR  138 is missing expected H atoms. Skipping.
Residue ILE  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue ILE  141 is missing expected H atoms. Skipping.
Residue THR  142 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue ALA  150 is missing expected H atoms. Skipping.
Residue VAL  151 is missing expected H atoms. Skipping.
Residue THR  155 is missing expected H atoms. Skipping.
Residue LYS  157 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Residue ILE  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue ILE  164 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue SER  169 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue ALA  173 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue THR  176 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue THR  182 is missing expected H atoms. Skipping.
Residue MET  183 is missing expected H atoms. Skipping.
Residue SER  186 is missing expected H atoms. Skipping.
Residue THR  189 is missing expected H atoms. Skipping.
Residue LEU  191 is missing expected H atoms. Skipping.
Residue MET  196 is missing expected H atoms. Skipping.
Residue VAL  197 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  201 is missing expected H atoms. Skipping.
Residue LYS  204 is missing expected H atoms. Skipping.
Residue ALA  205 is missing expected H atoms. Skipping.
Residue LEU  207 is missing expected H atoms. Skipping.
Residue VAL  208 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LEU  216 is missing expected H atoms. Skipping.
Residue LEU  218 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue ALA  224 is missing expected H atoms. Skipping.
Residue THR  226 is missing expected H atoms. Skipping.
Residue SER  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue THR  236 is missing expected H atoms. Skipping.
Residue LEU  237 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue THR  239 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue VAL  250 is missing expected H atoms. Skipping.
Residue VAL  251 is missing expected H atoms. Skipping.
Residue VAL  252 is missing expected H atoms. Skipping.
Residue LEU  253 is missing expected H atoms. Skipping.
Residue SER  255 is missing expected H atoms. Skipping.
Residue ALA  259 is missing expected H atoms. Skipping.
Residue MET  260 is missing expected H atoms. Skipping.
Residue THR  262 is missing expected H atoms. Skipping.
Residue ALA  263 is missing expected H atoms. Skipping.
Residue LEU  264 is missing expected H atoms. Skipping.
Residue THR  265 is missing expected H atoms. Skipping.
Residue ALA  267 is missing expected H atoms. Skipping.
Residue THR  268 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue SER  273 is missing expected H atoms. Skipping.
Residue SER  274 is missing expected H atoms. Skipping.
Residue LEU  277 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue LYS  284 is missing expected H atoms. Skipping.
Residue LEU  287 is missing expected H atoms. Skipping.
Residue MET  289 is missing expected H atoms. Skipping.
Residue LYS  291 is missing expected H atoms. Skipping.
Residue LEU  292 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue LYS  295 is missing expected H atoms. Skipping.
Residue MET  297 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue TYR  299 is missing expected H atoms. Skipping.
Residue SER  300 is missing expected H atoms. Skipping.
Residue MET  301 is missing expected H atoms. Skipping.
Residue THR  303 is missing expected H atoms. Skipping.
Residue LYS  305 is missing expected H atoms. Skipping.
Residue LYS  307 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue VAL  309 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue ILE  312 is missing expected H atoms. Skipping.
Residue ALA  313 is missing expected H atoms. Skipping.
Residue THR  315 is missing expected H atoms. Skipping.
Residue THR  319 is missing expected H atoms. Skipping.
Residue ILE  320 is missing expected H atoms. Skipping.
Residue VAL  321 is missing expected H atoms. Skipping.
Residue ILE  322 is missing expected H atoms. Skipping.
Residue VAL  324 is missing expected H atoms. Skipping.
Residue TYR  326 is missing expected H atoms. Skipping.
Residue SER  331 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue ILE  335 is missing expected H atoms. Skipping.
Residue ILE  339 is missing expected H atoms. Skipping.
Residue MET  340 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue LYS  344 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  348 is missing expected H atoms. Skipping.
Residue LEU  351 is missing expected H atoms. Skipping.
Residue ILE  352 is missing expected H atoms. Skipping.
Residue THR  353 is missing expected H atoms. Skipping.
Residue VAL  354 is missing expected H atoms. Skipping.
Residue ILE  357 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LYS  361 is missing expected H atoms. Skipping.
Residue SER  363 is missing expected H atoms. Skipping.
Residue VAL  365 is missing expected H atoms. Skipping.
Residue ILE  367 is missing expected H atoms. Skipping.
Residue ALA  369 is missing expected H atoms. Skipping.
Residue SER  376 is missing expected H atoms. Skipping.
Residue TYR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue ILE  379 is missing expected H atoms. Skipping.
Residue ILE  380 is missing expected H atoms. Skipping.
Residue VAL  382 is missing expected H atoms. Skipping.
Residue LEU  387 is missing expected H atoms. Skipping.
Residue LYS  388 is missing expected H atoms. Skipping.
Residue LEU  389 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue LYS  394 is missing expected H atoms. Skipping.
Residue SER  396 is missing expected H atoms. Skipping.
Residue SER  397 is missing expected H atoms. Skipping.
Residue ILE  398 is missing expected H atoms. Skipping.
Residue MET  401 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue THR  404 is missing expected H atoms. Skipping.
Residue THR  405 is missing expected H atoms. Skipping.
Residue MET  406 is missing expected H atoms. Skipping.
Residue ALA  409 is missing expected H atoms. Skipping.
Residue LYS  410 is missing expected H atoms. Skipping.
Residue MET  412 is missing expected H atoms. Skipping.
Residue ALA  413 is missing expected H atoms. Skipping.
Residue ILE  414 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue ALA  419 is missing expected H atoms. Skipping.
Residue SER  424 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue VAL  428 is missing expected H atoms. Skipping.
Residue THR  430 is missing expected H atoms. Skipping.
Residue SER  431 is missing expected H atoms. Skipping.
Residue ILE  432 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue ALA  435 is missing expected H atoms. Skipping.
Residue LEU  436 is missing expected H atoms. Skipping.
Residue VAL  439 is missing expected H atoms. Skipping.
Residue ALA  442 is missing expected H atoms. Skipping.
Residue ILE  443 is missing expected H atoms. Skipping.
Residue TYR  444 is missing expected H atoms. Skipping.
Residue ALA  446 is missing expected H atoms. Skipping.
Residue ALA  447 is missing expected H atoms. Skipping.
Residue SER  449 is missing expected H atoms. Skipping.
Residue VAL  451 is missing expected H atoms. Skipping.
Residue SER  452 is missing expected H atoms. Skipping.
Residue ILE  454 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue ILE  457 is missing expected H atoms. Skipping.
Residue LEU  458 is missing expected H atoms. Skipping.
Residue ILE  459 is missing expected H atoms. Skipping.
Residue VAL  461 is missing expected H atoms. Skipping.
Residue ILE  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue THR  464 is missing expected H atoms. Skipping.
Residue ILE  466 is missing expected H atoms. Skipping.
Residue MET  468 is missing expected H atoms. Skipping.
Residue SER  470 is missing expected H atoms. Skipping.
Residue SER  472 is missing expected H atoms. Skipping.
Residue THR  473 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue LEU  475 is missing expected H atoms. Skipping.
Residue SER  476 is missing expected H atoms. Skipping.
Residue VAL  477 is missing expected H atoms. Skipping.
Residue SER  478 is missing expected H atoms. Skipping.
Residue LEU  479 is missing expected H atoms. Skipping.
Residue VAL  480 is missing expected H atoms. Skipping.
Residue LEU  481 is missing expected H atoms. Skipping.
Residue VAL  482 is missing expected H atoms. Skipping.
Residue VAL  484 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue LEU  487 is missing expected H atoms. Skipping.
Residue TYR  488 is missing expected H atoms. Skipping.
Residue LEU  489 is missing expected H atoms. Skipping.
Residue VAL  491 is missing expected H atoms. Skipping.
Residue MET  492 is missing expected H atoms. Skipping.
Residue VAL  493 is missing expected H atoms. Skipping.
Residue VAL    2 is missing expected H atoms. Skipping.
Residue ALA    3 is missing expected H atoms. Skipping.
Residue LEU    4 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue MET   10 is missing expected H atoms. Skipping.
Residue LEU   12 is missing expected H atoms. Skipping.
Residue THR   14 is missing expected H atoms. Skipping.
Residue ALA   15 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue THR   18 is missing expected H atoms. Skipping.
Residue MET   20 is missing expected H atoms. Skipping.
Residue SER   21 is missing expected H atoms. Skipping.
Residue SER   22 is missing expected H atoms. Skipping.
Residue ALA   25 is missing expected H atoms. Skipping.
Residue LYS   27 is missing expected H atoms. Skipping.
Residue ALA   29 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue ILE   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue THR   43 is missing expected H atoms. Skipping.
Residue ILE   44 is missing expected H atoms. Skipping.
Residue MET   45 is missing expected H atoms. Skipping.
Residue ALA   46 is missing expected H atoms. Skipping.
Residue ALA   47 is missing expected H atoms. Skipping.
Residue ILE   48 is missing expected H atoms. Skipping.
Residue LEU   49 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue TYR   51 is missing expected H atoms. Skipping.
Residue THR   52 is missing expected H atoms. Skipping.
Residue ILE   53 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue THR   56 is missing expected H atoms. Skipping.
Residue ALA   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue ILE   63 is missing expected H atoms. Skipping.
Residue ILE   65 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 THR   68 is missing expected H atoms. Skipping.
Residue ALA   69 is missing expected H atoms. Skipping.
Residue VAL   70 is missing expected H atoms. Skipping.
Residue ALA   71 is missing expected H atoms. Skipping.
Evaluate side-chains
  276 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 250
  time to evaluate  : 1.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 26
  outliers final: 13
  residues processed: 261
  average time/residue: 0.2266
  time to fit residues: 82.8879
Evaluate side-chains
  257 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 244
  time to evaluate  : 1.038 
Switching outliers to nearest non-outliers
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 13
  outliers final: 2
  residues processed: 13
  average time/residue: 0.1839
  time to fit residues: 5.0651
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:   40.0000
   chunk 100 optimal weight:    9.9990
   chunk 103 optimal weight:   30.0000
   chunk 60 optimal weight:    6.9990
   chunk 43 optimal weight:   30.0000
   chunk 78 optimal weight:   20.0000
   chunk 30 optimal weight:   40.0000
   chunk 90 optimal weight:    1.9990
   chunk 95 optimal weight:   20.0000
   chunk 66 optimal weight:   20.0000
   chunk 106 optimal weight:   30.0000
   overall best weight:   11.7994

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

Flipped N/Q/H residues before XYZ refinement:
** A  27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 203 ASN
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 244 HIS
** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   7 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.5819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.041   8986  Z= 0.362
  Angle     :  0.853   8.640  12164  Z= 0.435
  Chirality :  0.049   0.335   1412
  Planarity :  0.005   0.035   1520
  Dihedral  :  7.301  71.218   1224
  Min Nonbonded Distance : 1.800

Molprobity Statistics.
  All-atom Clashscore : 77.90
  Ramachandran Plot:
    Outliers :  3.73 %
    Allowed  : 25.75 %
    Favored  : 70.52 %
  Rotamer Outliers :  2.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -4.89 (0.22), residues: 1126
  helix: -1.95 (0.26), residues: 302
  sheet: -1.84 (0.34), residues: 262
  loop : -4.90 (0.20), residues: 562

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE    4 is missing expected H atoms. Skipping.
Residue ILE    6 is missing expected H atoms. Skipping.
Residue SER    7 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue VAL   15 is missing expected H atoms. Skipping.
Residue SER   16 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue VAL   21 is missing expected H atoms. Skipping.
Residue ILE   23 is missing expected H atoms. Skipping.
Residue VAL   24 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue SER   29 is missing expected H atoms. Skipping.
Residue VAL   31 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 MET   34 is missing expected H atoms. Skipping.
Residue ALA   35 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue THR   40 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue ILE   46 is missing expected H atoms. Skipping.
Residue THR   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue ALA   54 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue ILE   61 is missing expected H atoms. Skipping.
Residue ALA   63 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue LEU   65 is missing expected H atoms. Skipping.
Residue THR   66 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue THR   70 is missing expected H atoms. Skipping.
Residue SER   72 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue SER   81 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LYS   88 is missing expected H atoms. Skipping.
Residue VAL   91 is missing expected H atoms. Skipping.
Residue LYS   93 is missing expected H atoms. Skipping.
Residue SER   95 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue VAL   97 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue ILE  113 is missing expected H atoms. Skipping.
Residue VAL  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  117 is missing expected H atoms. Skipping.
Residue MET  118 is missing expected H atoms. Skipping.
Residue THR  120 is missing expected H atoms. Skipping.
Residue LYS  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  125 is missing expected H atoms. Skipping.
Residue LYS  126 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue VAL  129 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue TYR  137 is missing expected H atoms. Skipping.
Residue THR  138 is missing expected H atoms. Skipping.
Residue ILE  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue ILE  141 is missing expected H atoms. Skipping.
Residue THR  142 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue ALA  150 is missing expected H atoms. Skipping.
Residue VAL  151 is missing expected H atoms. Skipping.
Residue THR  155 is missing expected H atoms. Skipping.
Residue LYS  157 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Residue ILE  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue ILE  164 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue SER  169 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue ALA  173 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue THR  176 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue THR  182 is missing expected H atoms. Skipping.
Residue MET  183 is missing expected H atoms. Skipping.
Residue SER  186 is missing expected H atoms. Skipping.
Residue THR  189 is missing expected H atoms. Skipping.
Residue LEU  191 is missing expected H atoms. Skipping.
Residue MET  196 is missing expected H atoms. Skipping.
Residue VAL  197 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  201 is missing expected H atoms. Skipping.
Residue LYS  204 is missing expected H atoms. Skipping.
Residue ALA  205 is missing expected H atoms. Skipping.
Residue LEU  207 is missing expected H atoms. Skipping.
Residue VAL  208 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LEU  216 is missing expected H atoms. Skipping.
Residue LEU  218 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue ALA  224 is missing expected H atoms. Skipping.
Residue THR  226 is missing expected H atoms. Skipping.
Residue SER  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue THR  236 is missing expected H atoms. Skipping.
Residue LEU  237 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue THR  239 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue VAL  250 is missing expected H atoms. Skipping.
Residue VAL  251 is missing expected H atoms. Skipping.
Residue VAL  252 is missing expected H atoms. Skipping.
Residue LEU  253 is missing expected H atoms. Skipping.
Residue SER  255 is missing expected H atoms. Skipping.
Residue ALA  259 is missing expected H atoms. Skipping.
Residue MET  260 is missing expected H atoms. Skipping.
Residue THR  262 is missing expected H atoms. Skipping.
Residue ALA  263 is missing expected H atoms. Skipping.
Residue LEU  264 is missing expected H atoms. Skipping.
Residue THR  265 is missing expected H atoms. Skipping.
Residue ALA  267 is missing expected H atoms. Skipping.
Residue THR  268 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue SER  273 is missing expected H atoms. Skipping.
Residue SER  274 is missing expected H atoms. Skipping.
Residue LEU  277 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue LYS  284 is missing expected H atoms. Skipping.
Residue LEU  287 is missing expected H atoms. Skipping.
Residue MET  289 is missing expected H atoms. Skipping.
Residue LYS  291 is missing expected H atoms. Skipping.
Residue LEU  292 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue LYS  295 is missing expected H atoms. Skipping.
Residue MET  297 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue TYR  299 is missing expected H atoms. Skipping.
Residue SER  300 is missing expected H atoms. Skipping.
Residue MET  301 is missing expected H atoms. Skipping.
Residue THR  303 is missing expected H atoms. Skipping.
Residue LYS  305 is missing expected H atoms. Skipping.
Residue LYS  307 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue VAL  309 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue ILE  312 is missing expected H atoms. Skipping.
Residue ALA  313 is missing expected H atoms. Skipping.
Residue THR  315 is missing expected H atoms. Skipping.
Residue THR  319 is missing expected H atoms. Skipping.
Residue ILE  320 is missing expected H atoms. Skipping.
Residue VAL  321 is missing expected H atoms. Skipping.
Residue ILE  322 is missing expected H atoms. Skipping.
Residue VAL  324 is missing expected H atoms. Skipping.
Residue TYR  326 is missing expected H atoms. Skipping.
Residue SER  331 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue ILE  335 is missing expected H atoms. Skipping.
Residue ILE  339 is missing expected H atoms. Skipping.
Residue MET  340 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue LYS  344 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  348 is missing expected H atoms. Skipping.
Residue LEU  351 is missing expected H atoms. Skipping.
Residue ILE  352 is missing expected H atoms. Skipping.
Residue THR  353 is missing expected H atoms. Skipping.
Residue VAL  354 is missing expected H atoms. Skipping.
Residue ILE  357 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LYS  361 is missing expected H atoms. Skipping.
Residue SER  363 is missing expected H atoms. Skipping.
Residue VAL  365 is missing expected H atoms. Skipping.
Residue ILE  367 is missing expected H atoms. Skipping.
Residue ALA  369 is missing expected H atoms. Skipping.
Residue SER  376 is missing expected H atoms. Skipping.
Residue TYR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue ILE  379 is missing expected H atoms. Skipping.
Residue ILE  380 is missing expected H atoms. Skipping.
Residue VAL  382 is missing expected H atoms. Skipping.
Residue LEU  387 is missing expected H atoms. Skipping.
Residue LYS  388 is missing expected H atoms. Skipping.
Residue LEU  389 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue LYS  394 is missing expected H atoms. Skipping.
Residue SER  396 is missing expected H atoms. Skipping.
Residue SER  397 is missing expected H atoms. Skipping.
Residue ILE  398 is missing expected H atoms. Skipping.
Residue MET  401 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue THR  404 is missing expected H atoms. Skipping.
Residue THR  405 is missing expected H atoms. Skipping.
Residue MET  406 is missing expected H atoms. Skipping.
Residue ALA  409 is missing expected H atoms. Skipping.
Residue LYS  410 is missing expected H atoms. Skipping.
Residue MET  412 is missing expected H atoms. Skipping.
Residue ALA  413 is missing expected H atoms. Skipping.
Residue ILE  414 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue ALA  419 is missing expected H atoms. Skipping.
Residue SER  424 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue VAL  428 is missing expected H atoms. Skipping.
Residue THR  430 is missing expected H atoms. Skipping.
Residue SER  431 is missing expected H atoms. Skipping.
Residue ILE  432 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue ALA  435 is missing expected H atoms. Skipping.
Residue LEU  436 is missing expected H atoms. Skipping.
Residue VAL  439 is missing expected H atoms. Skipping.
Residue ALA  442 is missing expected H atoms. Skipping.
Residue ILE  443 is missing expected H atoms. Skipping.
Residue TYR  444 is missing expected H atoms. Skipping.
Residue ALA  446 is missing expected H atoms. Skipping.
Residue ALA  447 is missing expected H atoms. Skipping.
Residue SER  449 is missing expected H atoms. Skipping.
Residue VAL  451 is missing expected H atoms. Skipping.
Residue SER  452 is missing expected H atoms. Skipping.
Residue ILE  454 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue ILE  457 is missing expected H atoms. Skipping.
Residue LEU  458 is missing expected H atoms. Skipping.
Residue ILE  459 is missing expected H atoms. Skipping.
Residue VAL  461 is missing expected H atoms. Skipping.
Residue ILE  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue THR  464 is missing expected H atoms. Skipping.
Residue ILE  466 is missing expected H atoms. Skipping.
Residue MET  468 is missing expected H atoms. Skipping.
Residue SER  470 is missing expected H atoms. Skipping.
Residue SER  472 is missing expected H atoms. Skipping.
Residue THR  473 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue LEU  475 is missing expected H atoms. Skipping.
Residue SER  476 is missing expected H atoms. Skipping.
Residue VAL  477 is missing expected H atoms. Skipping.
Residue SER  478 is missing expected H atoms. Skipping.
Residue LEU  479 is missing expected H atoms. Skipping.
Residue VAL  480 is missing expected H atoms. Skipping.
Residue LEU  481 is missing expected H atoms. Skipping.
Residue VAL  482 is missing expected H atoms. Skipping.
Residue VAL  484 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue LEU  487 is missing expected H atoms. Skipping.
Residue TYR  488 is missing expected H atoms. Skipping.
Residue LEU  489 is missing expected H atoms. Skipping.
Residue VAL  491 is missing expected H atoms. Skipping.
Residue MET  492 is missing expected H atoms. Skipping.
Residue VAL  493 is missing expected H atoms. Skipping.
Residue VAL    2 is missing expected H atoms. Skipping.
Residue ALA    3 is missing expected H atoms. Skipping.
Residue LEU    4 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue MET   10 is missing expected H atoms. Skipping.
Residue LEU   12 is missing expected H atoms. Skipping.
Residue THR   14 is missing expected H atoms. Skipping.
Residue ALA   15 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue THR   18 is missing expected H atoms. Skipping.
Residue MET   20 is missing expected H atoms. Skipping.
Residue SER   21 is missing expected H atoms. Skipping.
Residue SER   22 is missing expected H atoms. Skipping.
Residue ALA   25 is missing expected H atoms. Skipping.
Residue LYS   27 is missing expected H atoms. Skipping.
Residue ALA   29 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue ILE   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue THR   43 is missing expected H atoms. Skipping.
Residue ILE   44 is missing expected H atoms. Skipping.
Residue MET   45 is missing expected H atoms. Skipping.
Residue ALA   46 is missing expected H atoms. Skipping.
Residue ALA   47 is missing expected H atoms. Skipping.
Residue ILE   48 is missing expected H atoms. Skipping.
Residue LEU   49 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue TYR   51 is missing expected H atoms. Skipping.
Residue THR   52 is missing expected H atoms. Skipping.
Residue ILE   53 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue THR   56 is missing expected H atoms. Skipping.
Residue ALA   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue ILE   63 is missing expected H atoms. Skipping.
Residue ILE   65 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 THR   68 is missing expected H atoms. Skipping.
Residue ALA   69 is missing expected H atoms. Skipping.
Residue VAL   70 is missing expected H atoms. Skipping.
Residue ALA   71 is missing expected H atoms. Skipping.
Residue ILE    4 is missing expected H atoms. Skipping.
Residue ILE    6 is missing expected H atoms. Skipping.
Residue SER    7 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue VAL   15 is missing expected H atoms. Skipping.
Residue SER   16 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue VAL   21 is missing expected H atoms. Skipping.
Residue ILE   23 is missing expected H atoms. Skipping.
Residue VAL   24 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue SER   29 is missing expected H atoms. Skipping.
Residue VAL   31 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 MET   34 is missing expected H atoms. Skipping.
Residue ALA   35 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue THR   40 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue ILE   46 is missing expected H atoms. Skipping.
Residue THR   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue ALA   54 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue ILE   61 is missing expected H atoms. Skipping.
Residue ALA   63 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue LEU   65 is missing expected H atoms. Skipping.
Residue THR   66 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue THR   70 is missing expected H atoms. Skipping.
Residue SER   72 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue SER   81 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LYS   88 is missing expected H atoms. Skipping.
Residue VAL   91 is missing expected H atoms. Skipping.
Residue LYS   93 is missing expected H atoms. Skipping.
Residue SER   95 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue VAL   97 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue ILE  113 is missing expected H atoms. Skipping.
Residue VAL  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  117 is missing expected H atoms. Skipping.
Residue MET  118 is missing expected H atoms. Skipping.
Residue THR  120 is missing expected H atoms. Skipping.
Residue LYS  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  125 is missing expected H atoms. Skipping.
Residue LYS  126 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue VAL  129 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue TYR  137 is missing expected H atoms. Skipping.
Residue THR  138 is missing expected H atoms. Skipping.
Residue ILE  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue ILE  141 is missing expected H atoms. Skipping.
Residue THR  142 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue ALA  150 is missing expected H atoms. Skipping.
Residue VAL  151 is missing expected H atoms. Skipping.
Residue THR  155 is missing expected H atoms. Skipping.
Residue LYS  157 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Residue ILE  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue ILE  164 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue SER  169 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue ALA  173 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue THR  176 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue THR  182 is missing expected H atoms. Skipping.
Residue MET  183 is missing expected H atoms. Skipping.
Residue SER  186 is missing expected H atoms. Skipping.
Residue THR  189 is missing expected H atoms. Skipping.
Residue LEU  191 is missing expected H atoms. Skipping.
Residue MET  196 is missing expected H atoms. Skipping.
Residue VAL  197 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  201 is missing expected H atoms. Skipping.
Residue LYS  204 is missing expected H atoms. Skipping.
Residue ALA  205 is missing expected H atoms. Skipping.
Residue LEU  207 is missing expected H atoms. Skipping.
Residue VAL  208 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LEU  216 is missing expected H atoms. Skipping.
Residue LEU  218 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue ALA  224 is missing expected H atoms. Skipping.
Residue THR  226 is missing expected H atoms. Skipping.
Residue SER  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue THR  236 is missing expected H atoms. Skipping.
Residue LEU  237 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue THR  239 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue VAL  250 is missing expected H atoms. Skipping.
Residue VAL  251 is missing expected H atoms. Skipping.
Residue VAL  252 is missing expected H atoms. Skipping.
Residue LEU  253 is missing expected H atoms. Skipping.
Residue SER  255 is missing expected H atoms. Skipping.
Residue ALA  259 is missing expected H atoms. Skipping.
Residue MET  260 is missing expected H atoms. Skipping.
Residue THR  262 is missing expected H atoms. Skipping.
Residue ALA  263 is missing expected H atoms. Skipping.
Residue LEU  264 is missing expected H atoms. Skipping.
Residue THR  265 is missing expected H atoms. Skipping.
Residue ALA  267 is missing expected H atoms. Skipping.
Residue THR  268 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue SER  273 is missing expected H atoms. Skipping.
Residue SER  274 is missing expected H atoms. Skipping.
Residue LEU  277 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue LYS  284 is missing expected H atoms. Skipping.
Residue LEU  287 is missing expected H atoms. Skipping.
Residue MET  289 is missing expected H atoms. Skipping.
Residue LYS  291 is missing expected H atoms. Skipping.
Residue LEU  292 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue LYS  295 is missing expected H atoms. Skipping.
Residue MET  297 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue TYR  299 is missing expected H atoms. Skipping.
Residue SER  300 is missing expected H atoms. Skipping.
Residue MET  301 is missing expected H atoms. Skipping.
Residue THR  303 is missing expected H atoms. Skipping.
Residue LYS  305 is missing expected H atoms. Skipping.
Residue LYS  307 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue VAL  309 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue ILE  312 is missing expected H atoms. Skipping.
Residue ALA  313 is missing expected H atoms. Skipping.
Residue THR  315 is missing expected H atoms. Skipping.
Residue THR  319 is missing expected H atoms. Skipping.
Residue ILE  320 is missing expected H atoms. Skipping.
Residue VAL  321 is missing expected H atoms. Skipping.
Residue ILE  322 is missing expected H atoms. Skipping.
Residue VAL  324 is missing expected H atoms. Skipping.
Residue TYR  326 is missing expected H atoms. Skipping.
Residue SER  331 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue ILE  335 is missing expected H atoms. Skipping.
Residue ILE  339 is missing expected H atoms. Skipping.
Residue MET  340 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue LYS  344 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  348 is missing expected H atoms. Skipping.
Residue LEU  351 is missing expected H atoms. Skipping.
Residue ILE  352 is missing expected H atoms. Skipping.
Residue THR  353 is missing expected H atoms. Skipping.
Residue VAL  354 is missing expected H atoms. Skipping.
Residue ILE  357 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LYS  361 is missing expected H atoms. Skipping.
Residue SER  363 is missing expected H atoms. Skipping.
Residue VAL  365 is missing expected H atoms. Skipping.
Residue ILE  367 is missing expected H atoms. Skipping.
Residue ALA  369 is missing expected H atoms. Skipping.
Residue SER  376 is missing expected H atoms. Skipping.
Residue TYR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue ILE  379 is missing expected H atoms. Skipping.
Residue ILE  380 is missing expected H atoms. Skipping.
Residue VAL  382 is missing expected H atoms. Skipping.
Residue LEU  387 is missing expected H atoms. Skipping.
Residue LYS  388 is missing expected H atoms. Skipping.
Residue LEU  389 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue LYS  394 is missing expected H atoms. Skipping.
Residue SER  396 is missing expected H atoms. Skipping.
Residue SER  397 is missing expected H atoms. Skipping.
Residue ILE  398 is missing expected H atoms. Skipping.
Residue MET  401 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue THR  404 is missing expected H atoms. Skipping.
Residue THR  405 is missing expected H atoms. Skipping.
Residue MET  406 is missing expected H atoms. Skipping.
Residue ALA  409 is missing expected H atoms. Skipping.
Residue LYS  410 is missing expected H atoms. Skipping.
Residue MET  412 is missing expected H atoms. Skipping.
Residue ALA  413 is missing expected H atoms. Skipping.
Residue ILE  414 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue ALA  419 is missing expected H atoms. Skipping.
Residue SER  424 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue VAL  428 is missing expected H atoms. Skipping.
Residue THR  430 is missing expected H atoms. Skipping.
Residue SER  431 is missing expected H atoms. Skipping.
Residue ILE  432 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue ALA  435 is missing expected H atoms. Skipping.
Residue LEU  436 is missing expected H atoms. Skipping.
Residue VAL  439 is missing expected H atoms. Skipping.
Residue ALA  442 is missing expected H atoms. Skipping.
Residue ILE  443 is missing expected H atoms. Skipping.
Residue TYR  444 is missing expected H atoms. Skipping.
Residue ALA  446 is missing expected H atoms. Skipping.
Residue ALA  447 is missing expected H atoms. Skipping.
Residue SER  449 is missing expected H atoms. Skipping.
Residue VAL  451 is missing expected H atoms. Skipping.
Residue SER  452 is missing expected H atoms. Skipping.
Residue ILE  454 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue ILE  457 is missing expected H atoms. Skipping.
Residue LEU  458 is missing expected H atoms. Skipping.
Residue ILE  459 is missing expected H atoms. Skipping.
Residue VAL  461 is missing expected H atoms. Skipping.
Residue ILE  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue THR  464 is missing expected H atoms. Skipping.
Residue ILE  466 is missing expected H atoms. Skipping.
Residue MET  468 is missing expected H atoms. Skipping.
Residue SER  470 is missing expected H atoms. Skipping.
Residue SER  472 is missing expected H atoms. Skipping.
Residue THR  473 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue LEU  475 is missing expected H atoms. Skipping.
Residue SER  476 is missing expected H atoms. Skipping.
Residue VAL  477 is missing expected H atoms. Skipping.
Residue SER  478 is missing expected H atoms. Skipping.
Residue LEU  479 is missing expected H atoms. Skipping.
Residue VAL  480 is missing expected H atoms. Skipping.
Residue LEU  481 is missing expected H atoms. Skipping.
Residue VAL  482 is missing expected H atoms. Skipping.
Residue VAL  484 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue LEU  487 is missing expected H atoms. Skipping.
Residue TYR  488 is missing expected H atoms. Skipping.
Residue LEU  489 is missing expected H atoms. Skipping.
Residue VAL  491 is missing expected H atoms. Skipping.
Residue MET  492 is missing expected H atoms. Skipping.
Residue VAL  493 is missing expected H atoms. Skipping.
Residue VAL    2 is missing expected H atoms. Skipping.
Residue ALA    3 is missing expected H atoms. Skipping.
Residue LEU    4 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue MET   10 is missing expected H atoms. Skipping.
Residue LEU   12 is missing expected H atoms. Skipping.
Residue THR   14 is missing expected H atoms. Skipping.
Residue ALA   15 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue THR   18 is missing expected H atoms. Skipping.
Residue MET   20 is missing expected H atoms. Skipping.
Residue SER   21 is missing expected H atoms. Skipping.
Residue SER   22 is missing expected H atoms. Skipping.
Residue ALA   25 is missing expected H atoms. Skipping.
Residue LYS   27 is missing expected H atoms. Skipping.
Residue ALA   29 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue ILE   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue THR   43 is missing expected H atoms. Skipping.
Residue ILE   44 is missing expected H atoms. Skipping.
Residue MET   45 is missing expected H atoms. Skipping.
Residue ALA   46 is missing expected H atoms. Skipping.
Residue ALA   47 is missing expected H atoms. Skipping.
Residue ILE   48 is missing expected H atoms. Skipping.
Residue LEU   49 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue TYR   51 is missing expected H atoms. Skipping.
Residue THR   52 is missing expected H atoms. Skipping.
Residue ILE   53 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue THR   56 is missing expected H atoms. Skipping.
Residue ALA   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue ILE   63 is missing expected H atoms. Skipping.
Residue ILE   65 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 THR   68 is missing expected H atoms. Skipping.
Residue ALA   69 is missing expected H atoms. Skipping.
Residue VAL   70 is missing expected H atoms. Skipping.
Residue ALA   71 is missing expected H atoms. Skipping.
Evaluate side-chains
  265 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 242
  time to evaluate  : 1.015 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 23
  outliers final: 14
  residues processed: 253
  average time/residue: 0.2212
  time to fit residues: 79.2142
Evaluate side-chains
  251 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 237
  time to evaluate  : 1.088 
Switching outliers to nearest non-outliers
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 14
  outliers final: 2
  residues processed: 14
  average time/residue: 0.1124
  time to fit residues: 4.1898
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:   10.0000
   chunk 50 optimal weight:   20.0000
   chunk 73 optimal weight:    5.9990
   chunk 111 optimal weight:    9.9990
   chunk 102 optimal weight:    5.9990
   chunk 88 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   chunk 68 optimal weight:    6.9990
   chunk 54 optimal weight:   20.0000
   chunk 70 optimal weight:    0.5980
   chunk 94 optimal weight:    4.9990
   overall best weight:    4.9188

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

Flipped N/Q/H residues before XYZ refinement:
** A  27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 203 ASN
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.6075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8986  Z= 0.202
  Angle     :  0.735   9.559  12164  Z= 0.373
  Chirality :  0.045   0.250   1412
  Planarity :  0.004   0.035   1520
  Dihedral  :  6.818  67.066   1224
  Min Nonbonded Distance : 1.822

Molprobity Statistics.
  All-atom Clashscore : 71.84
  Ramachandran Plot:
    Outliers :  3.82 %
    Allowed  : 19.36 %
    Favored  : 76.82 %
  Rotamer Outliers :  0.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -4.61 (0.22), residues: 1126
  helix: -1.58 (0.27), residues: 306
  sheet: -1.78 (0.33), residues: 264
  loop : -4.78 (0.20), residues: 556

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE    4 is missing expected H atoms. Skipping.
Residue ILE    6 is missing expected H atoms. Skipping.
Residue SER    7 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue VAL   15 is missing expected H atoms. Skipping.
Residue SER   16 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue VAL   21 is missing expected H atoms. Skipping.
Residue ILE   23 is missing expected H atoms. Skipping.
Residue VAL   24 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue SER   29 is missing expected H atoms. Skipping.
Residue VAL   31 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 MET   34 is missing expected H atoms. Skipping.
Residue ALA   35 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue THR   40 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue ILE   46 is missing expected H atoms. Skipping.
Residue THR   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue ALA   54 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue ILE   61 is missing expected H atoms. Skipping.
Residue ALA   63 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue LEU   65 is missing expected H atoms. Skipping.
Residue THR   66 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue THR   70 is missing expected H atoms. Skipping.
Residue SER   72 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue SER   81 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LYS   88 is missing expected H atoms. Skipping.
Residue VAL   91 is missing expected H atoms. Skipping.
Residue LYS   93 is missing expected H atoms. Skipping.
Residue SER   95 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue VAL   97 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue ILE  113 is missing expected H atoms. Skipping.
Residue VAL  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  117 is missing expected H atoms. Skipping.
Residue MET  118 is missing expected H atoms. Skipping.
Residue THR  120 is missing expected H atoms. Skipping.
Residue LYS  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  125 is missing expected H atoms. Skipping.
Residue LYS  126 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue VAL  129 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue TYR  137 is missing expected H atoms. Skipping.
Residue THR  138 is missing expected H atoms. Skipping.
Residue ILE  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue ILE  141 is missing expected H atoms. Skipping.
Residue THR  142 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue ALA  150 is missing expected H atoms. Skipping.
Residue VAL  151 is missing expected H atoms. Skipping.
Residue THR  155 is missing expected H atoms. Skipping.
Residue LYS  157 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Residue ILE  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue ILE  164 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue SER  169 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue ALA  173 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue THR  176 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue THR  182 is missing expected H atoms. Skipping.
Residue MET  183 is missing expected H atoms. Skipping.
Residue SER  186 is missing expected H atoms. Skipping.
Residue THR  189 is missing expected H atoms. Skipping.
Residue LEU  191 is missing expected H atoms. Skipping.
Residue MET  196 is missing expected H atoms. Skipping.
Residue VAL  197 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  201 is missing expected H atoms. Skipping.
Residue LYS  204 is missing expected H atoms. Skipping.
Residue ALA  205 is missing expected H atoms. Skipping.
Residue LEU  207 is missing expected H atoms. Skipping.
Residue VAL  208 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LEU  216 is missing expected H atoms. Skipping.
Residue LEU  218 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue ALA  224 is missing expected H atoms. Skipping.
Residue THR  226 is missing expected H atoms. Skipping.
Residue SER  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue THR  236 is missing expected H atoms. Skipping.
Residue LEU  237 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue THR  239 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue VAL  250 is missing expected H atoms. Skipping.
Residue VAL  251 is missing expected H atoms. Skipping.
Residue VAL  252 is missing expected H atoms. Skipping.
Residue LEU  253 is missing expected H atoms. Skipping.
Residue SER  255 is missing expected H atoms. Skipping.
Residue ALA  259 is missing expected H atoms. Skipping.
Residue MET  260 is missing expected H atoms. Skipping.
Residue THR  262 is missing expected H atoms. Skipping.
Residue ALA  263 is missing expected H atoms. Skipping.
Residue LEU  264 is missing expected H atoms. Skipping.
Residue THR  265 is missing expected H atoms. Skipping.
Residue ALA  267 is missing expected H atoms. Skipping.
Residue THR  268 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue SER  273 is missing expected H atoms. Skipping.
Residue SER  274 is missing expected H atoms. Skipping.
Residue LEU  277 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue LYS  284 is missing expected H atoms. Skipping.
Residue LEU  287 is missing expected H atoms. Skipping.
Residue MET  289 is missing expected H atoms. Skipping.
Residue LYS  291 is missing expected H atoms. Skipping.
Residue LEU  292 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue LYS  295 is missing expected H atoms. Skipping.
Residue MET  297 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue TYR  299 is missing expected H atoms. Skipping.
Residue SER  300 is missing expected H atoms. Skipping.
Residue MET  301 is missing expected H atoms. Skipping.
Residue THR  303 is missing expected H atoms. Skipping.
Residue LYS  305 is missing expected H atoms. Skipping.
Residue LYS  307 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue VAL  309 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue ILE  312 is missing expected H atoms. Skipping.
Residue ALA  313 is missing expected H atoms. Skipping.
Residue THR  315 is missing expected H atoms. Skipping.
Residue THR  319 is missing expected H atoms. Skipping.
Residue ILE  320 is missing expected H atoms. Skipping.
Residue VAL  321 is missing expected H atoms. Skipping.
Residue ILE  322 is missing expected H atoms. Skipping.
Residue VAL  324 is missing expected H atoms. Skipping.
Residue TYR  326 is missing expected H atoms. Skipping.
Residue SER  331 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue ILE  335 is missing expected H atoms. Skipping.
Residue ILE  339 is missing expected H atoms. Skipping.
Residue MET  340 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue LYS  344 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  348 is missing expected H atoms. Skipping.
Residue LEU  351 is missing expected H atoms. Skipping.
Residue ILE  352 is missing expected H atoms. Skipping.
Residue THR  353 is missing expected H atoms. Skipping.
Residue VAL  354 is missing expected H atoms. Skipping.
Residue ILE  357 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LYS  361 is missing expected H atoms. Skipping.
Residue SER  363 is missing expected H atoms. Skipping.
Residue VAL  365 is missing expected H atoms. Skipping.
Residue ILE  367 is missing expected H atoms. Skipping.
Residue ALA  369 is missing expected H atoms. Skipping.
Residue SER  376 is missing expected H atoms. Skipping.
Residue TYR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue ILE  379 is missing expected H atoms. Skipping.
Residue ILE  380 is missing expected H atoms. Skipping.
Residue VAL  382 is missing expected H atoms. Skipping.
Residue LEU  387 is missing expected H atoms. Skipping.
Residue LYS  388 is missing expected H atoms. Skipping.
Residue LEU  389 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue LYS  394 is missing expected H atoms. Skipping.
Residue SER  396 is missing expected H atoms. Skipping.
Residue SER  397 is missing expected H atoms. Skipping.
Residue ILE  398 is missing expected H atoms. Skipping.
Residue MET  401 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue THR  404 is missing expected H atoms. Skipping.
Residue THR  405 is missing expected H atoms. Skipping.
Residue MET  406 is missing expected H atoms. Skipping.
Residue ALA  409 is missing expected H atoms. Skipping.
Residue LYS  410 is missing expected H atoms. Skipping.
Residue MET  412 is missing expected H atoms. Skipping.
Residue ALA  413 is missing expected H atoms. Skipping.
Residue ILE  414 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue ALA  419 is missing expected H atoms. Skipping.
Residue SER  424 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue VAL  428 is missing expected H atoms. Skipping.
Residue THR  430 is missing expected H atoms. Skipping.
Residue SER  431 is missing expected H atoms. Skipping.
Residue ILE  432 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue ALA  435 is missing expected H atoms. Skipping.
Residue LEU  436 is missing expected H atoms. Skipping.
Residue VAL  439 is missing expected H atoms. Skipping.
Residue ALA  442 is missing expected H atoms. Skipping.
Residue ILE  443 is missing expected H atoms. Skipping.
Residue TYR  444 is missing expected H atoms. Skipping.
Residue ALA  446 is missing expected H atoms. Skipping.
Residue ALA  447 is missing expected H atoms. Skipping.
Residue SER  449 is missing expected H atoms. Skipping.
Residue VAL  451 is missing expected H atoms. Skipping.
Residue SER  452 is missing expected H atoms. Skipping.
Residue ILE  454 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue ILE  457 is missing expected H atoms. Skipping.
Residue LEU  458 is missing expected H atoms. Skipping.
Residue ILE  459 is missing expected H atoms. Skipping.
Residue VAL  461 is missing expected H atoms. Skipping.
Residue ILE  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue THR  464 is missing expected H atoms. Skipping.
Residue ILE  466 is missing expected H atoms. Skipping.
Residue MET  468 is missing expected H atoms. Skipping.
Residue SER  470 is missing expected H atoms. Skipping.
Residue SER  472 is missing expected H atoms. Skipping.
Residue THR  473 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue LEU  475 is missing expected H atoms. Skipping.
Residue SER  476 is missing expected H atoms. Skipping.
Residue VAL  477 is missing expected H atoms. Skipping.
Residue SER  478 is missing expected H atoms. Skipping.
Residue LEU  479 is missing expected H atoms. Skipping.
Residue VAL  480 is missing expected H atoms. Skipping.
Residue LEU  481 is missing expected H atoms. Skipping.
Residue VAL  482 is missing expected H atoms. Skipping.
Residue VAL  484 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue LEU  487 is missing expected H atoms. Skipping.
Residue TYR  488 is missing expected H atoms. Skipping.
Residue LEU  489 is missing expected H atoms. Skipping.
Residue VAL  491 is missing expected H atoms. Skipping.
Residue MET  492 is missing expected H atoms. Skipping.
Residue VAL  493 is missing expected H atoms. Skipping.
Residue VAL    2 is missing expected H atoms. Skipping.
Residue ALA    3 is missing expected H atoms. Skipping.
Residue LEU    4 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue MET   10 is missing expected H atoms. Skipping.
Residue LEU   12 is missing expected H atoms. Skipping.
Residue THR   14 is missing expected H atoms. Skipping.
Residue ALA   15 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue THR   18 is missing expected H atoms. Skipping.
Residue MET   20 is missing expected H atoms. Skipping.
Residue SER   21 is missing expected H atoms. Skipping.
Residue SER   22 is missing expected H atoms. Skipping.
Residue ALA   25 is missing expected H atoms. Skipping.
Residue LYS   27 is missing expected H atoms. Skipping.
Residue ALA   29 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue ILE   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue THR   43 is missing expected H atoms. Skipping.
Residue ILE   44 is missing expected H atoms. Skipping.
Residue MET   45 is missing expected H atoms. Skipping.
Residue ALA   46 is missing expected H atoms. Skipping.
Residue ALA   47 is missing expected H atoms. Skipping.
Residue ILE   48 is missing expected H atoms. Skipping.
Residue LEU   49 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue TYR   51 is missing expected H atoms. Skipping.
Residue THR   52 is missing expected H atoms. Skipping.
Residue ILE   53 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue THR   56 is missing expected H atoms. Skipping.
Residue ALA   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue ILE   63 is missing expected H atoms. Skipping.
Residue ILE   65 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 THR   68 is missing expected H atoms. Skipping.
Residue ALA   69 is missing expected H atoms. Skipping.
Residue VAL   70 is missing expected H atoms. Skipping.
Residue ALA   71 is missing expected H atoms. Skipping.
Residue ILE    4 is missing expected H atoms. Skipping.
Residue ILE    6 is missing expected H atoms. Skipping.
Residue SER    7 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue VAL   15 is missing expected H atoms. Skipping.
Residue SER   16 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue VAL   21 is missing expected H atoms. Skipping.
Residue ILE   23 is missing expected H atoms. Skipping.
Residue VAL   24 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue SER   29 is missing expected H atoms. Skipping.
Residue VAL   31 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 MET   34 is missing expected H atoms. Skipping.
Residue ALA   35 is missing expected H atoms. Skipping.
Residue LYS   36 is missing expected H atoms. Skipping.
Residue LYS   38 is missing expected H atoms. Skipping.
Residue THR   40 is missing expected H atoms. Skipping.
Residue LEU   41 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue ILE   46 is missing expected H atoms. Skipping.
Residue THR   48 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue LYS   51 is missing expected H atoms. Skipping.
Residue ALA   54 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue LEU   56 is missing expected H atoms. Skipping.
Residue LYS   58 is missing expected H atoms. Skipping.
Residue TYR   59 is missing expected H atoms. Skipping.
Residue ILE   61 is missing expected H atoms. Skipping.
Residue ALA   63 is missing expected H atoms. Skipping.
Residue LYS   64 is missing expected H atoms. Skipping.
Residue LEU   65 is missing expected H atoms. Skipping.
Residue THR   66 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue THR   69 is missing expected H atoms. Skipping.
Residue THR   70 is missing expected H atoms. Skipping.
Residue SER   72 is missing expected H atoms. Skipping.
Residue THR   76 is missing expected H atoms. Skipping.
Residue SER   81 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LYS   88 is missing expected H atoms. Skipping.
Residue VAL   91 is missing expected H atoms. Skipping.
Residue LYS   93 is missing expected H atoms. Skipping.
Residue SER   95 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue VAL   97 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue LYS  110 is missing expected H atoms. Skipping.
Residue ILE  113 is missing expected H atoms. Skipping.
Residue VAL  114 is missing expected H atoms. Skipping.
Residue THR  115 is missing expected H atoms. Skipping.
Residue ALA  117 is missing expected H atoms. Skipping.
Residue MET  118 is missing expected H atoms. Skipping.
Residue THR  120 is missing expected H atoms. Skipping.
Residue LYS  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue MET  125 is missing expected H atoms. Skipping.
Residue LYS  126 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue VAL  129 is missing expected H atoms. Skipping.
Residue VAL  130 is missing expected H atoms. Skipping.
Residue LEU  135 is missing expected H atoms. Skipping.
Residue TYR  137 is missing expected H atoms. Skipping.
Residue THR  138 is missing expected H atoms. Skipping.
Residue ILE  139 is missing expected H atoms. Skipping.
Residue VAL  140 is missing expected H atoms. Skipping.
Residue ILE  141 is missing expected H atoms. Skipping.
Residue THR  142 is missing expected H atoms. Skipping.
Residue SER  145 is missing expected H atoms. Skipping.
Residue ALA  150 is missing expected H atoms. Skipping.
Residue VAL  151 is missing expected H atoms. Skipping.
Residue THR  155 is missing expected H atoms. Skipping.
Residue LYS  157 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Residue ILE  162 is missing expected H atoms. Skipping.
Residue LYS  163 is missing expected H atoms. Skipping.
Residue ILE  164 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue SER  168 is missing expected H atoms. Skipping.
Residue SER  169 is missing expected H atoms. Skipping.
Residue ILE  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue ALA  173 is missing expected H atoms. Skipping.
Residue LEU  175 is missing expected H atoms. Skipping.
Residue THR  176 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Residue THR  182 is missing expected H atoms. Skipping.
Residue MET  183 is missing expected H atoms. Skipping.
Residue SER  186 is missing expected H atoms. Skipping.
Residue THR  189 is missing expected H atoms. Skipping.
Residue LEU  191 is missing expected H atoms. Skipping.
Residue MET  196 is missing expected H atoms. Skipping.
Residue VAL  197 is missing expected H atoms. Skipping.
Residue LEU  198 is missing expected H atoms. Skipping.
Residue LEU  199 is missing expected H atoms. Skipping.
Residue MET  201 is missing expected H atoms. Skipping.
Residue LYS  204 is missing expected H atoms. Skipping.
Residue ALA  205 is missing expected H atoms. Skipping.
Residue LEU  207 is missing expected H atoms. Skipping.
Residue VAL  208 is missing expected H atoms. Skipping.
Residue LEU  214 is missing expected H atoms. Skipping.
Residue LEU  216 is missing expected H atoms. Skipping.
Residue LEU  218 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue ALA  224 is missing expected H atoms. Skipping.
Residue THR  226 is missing expected H atoms. Skipping.
Residue SER  229 is missing expected H atoms. Skipping.
Residue ILE  232 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue THR  236 is missing expected H atoms. Skipping.
Residue LEU  237 is missing expected H atoms. Skipping.
Residue VAL  238 is missing expected H atoms. Skipping.
Residue THR  239 is missing expected H atoms. Skipping.
Residue LYS  241 is missing expected H atoms. Skipping.
Residue ALA  245 is missing expected H atoms. Skipping.
Residue LYS  246 is missing expected H atoms. Skipping.
Residue LYS  247 is missing expected H atoms. Skipping.
Residue VAL  250 is missing expected H atoms. Skipping.
Residue VAL  251 is missing expected H atoms. Skipping.
Residue VAL  252 is missing expected H atoms. Skipping.
Residue LEU  253 is missing expected H atoms. Skipping.
Residue SER  255 is missing expected H atoms. Skipping.
Residue ALA  259 is missing expected H atoms. Skipping.
Residue MET  260 is missing expected H atoms. Skipping.
Residue THR  262 is missing expected H atoms. Skipping.
Residue ALA  263 is missing expected H atoms. Skipping.
Residue LEU  264 is missing expected H atoms. Skipping.
Residue THR  265 is missing expected H atoms. Skipping.
Residue ALA  267 is missing expected H atoms. Skipping.
Residue THR  268 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue MET  272 is missing expected H atoms. Skipping.
Residue SER  273 is missing expected H atoms. Skipping.
Residue SER  274 is missing expected H atoms. Skipping.
Residue LEU  277 is missing expected H atoms. Skipping.
Residue LEU  278 is missing expected H atoms. Skipping.
Residue THR  280 is missing expected H atoms. Skipping.
Residue LEU  283 is missing expected H atoms. Skipping.
Residue LYS  284 is missing expected H atoms. Skipping.
Residue LEU  287 is missing expected H atoms. Skipping.
Residue MET  289 is missing expected H atoms. Skipping.
Residue LYS  291 is missing expected H atoms. Skipping.
Residue LEU  292 is missing expected H atoms. Skipping.
Residue LEU  294 is missing expected H atoms. Skipping.
Residue LYS  295 is missing expected H atoms. Skipping.
Residue MET  297 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue TYR  299 is missing expected H atoms. Skipping.
Residue SER  300 is missing expected H atoms. Skipping.
Residue MET  301 is missing expected H atoms. Skipping.
Residue THR  303 is missing expected H atoms. Skipping.
Residue LYS  305 is missing expected H atoms. Skipping.
Residue LYS  307 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue VAL  309 is missing expected H atoms. Skipping.
Residue LYS  310 is missing expected H atoms. Skipping.
Residue ILE  312 is missing expected H atoms. Skipping.
Residue ALA  313 is missing expected H atoms. Skipping.
Residue THR  315 is missing expected H atoms. Skipping.
Residue THR  319 is missing expected H atoms. Skipping.
Residue ILE  320 is missing expected H atoms. Skipping.
Residue VAL  321 is missing expected H atoms. Skipping.
Residue ILE  322 is missing expected H atoms. Skipping.
Residue VAL  324 is missing expected H atoms. Skipping.
Residue TYR  326 is missing expected H atoms. Skipping.
Residue SER  331 is missing expected H atoms. Skipping.
Residue LYS  334 is missing expected H atoms. Skipping.
Residue ILE  335 is missing expected H atoms. Skipping.
Residue ILE  339 is missing expected H atoms. Skipping.
Residue MET  340 is missing expected H atoms. Skipping.
Residue LEU  342 is missing expected H atoms. Skipping.
Residue LYS  344 is missing expected H atoms. Skipping.
Residue VAL  347 is missing expected H atoms. Skipping.
Residue LEU  348 is missing expected H atoms. Skipping.
Residue LEU  351 is missing expected H atoms. Skipping.
Residue ILE  352 is missing expected H atoms. Skipping.
Residue THR  353 is missing expected H atoms. Skipping.
Residue VAL  354 is missing expected H atoms. Skipping.
Residue ILE  357 is missing expected H atoms. Skipping.
Residue VAL  358 is missing expected H atoms. Skipping.
Residue THR  359 is missing expected H atoms. Skipping.
Residue LYS  361 is missing expected H atoms. Skipping.
Residue SER  363 is missing expected H atoms. Skipping.
Residue VAL  365 is missing expected H atoms. Skipping.
Residue ILE  367 is missing expected H atoms. Skipping.
Residue ALA  369 is missing expected H atoms. Skipping.
Residue SER  376 is missing expected H atoms. Skipping.
Residue TYR  377 is missing expected H atoms. Skipping.
Residue ILE  378 is missing expected H atoms. Skipping.
Residue ILE  379 is missing expected H atoms. Skipping.
Residue ILE  380 is missing expected H atoms. Skipping.
Residue VAL  382 is missing expected H atoms. Skipping.
Residue LEU  387 is missing expected H atoms. Skipping.
Residue LYS  388 is missing expected H atoms. Skipping.
Residue LEU  389 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue LYS  394 is missing expected H atoms. Skipping.
Residue SER  396 is missing expected H atoms. Skipping.
Residue SER  397 is missing expected H atoms. Skipping.
Residue ILE  398 is missing expected H atoms. Skipping.
Residue MET  401 is missing expected H atoms. Skipping.
Residue ILE  402 is missing expected H atoms. Skipping.
Residue THR  404 is missing expected H atoms. Skipping.
Residue THR  405 is missing expected H atoms. Skipping.
Residue MET  406 is missing expected H atoms. Skipping.
Residue ALA  409 is missing expected H atoms. Skipping.
Residue LYS  410 is missing expected H atoms. Skipping.
Residue MET  412 is missing expected H atoms. Skipping.
Residue ALA  413 is missing expected H atoms. Skipping.
Residue ILE  414 is missing expected H atoms. Skipping.
Residue LEU  415 is missing expected H atoms. Skipping.
Residue THR  418 is missing expected H atoms. Skipping.
Residue ALA  419 is missing expected H atoms. Skipping.
Residue SER  424 is missing expected H atoms. Skipping.
Residue LEU  425 is missing expected H atoms. Skipping.
Residue VAL  428 is missing expected H atoms. Skipping.
Residue THR  430 is missing expected H atoms. Skipping.
Residue SER  431 is missing expected H atoms. Skipping.
Residue ILE  432 is missing expected H atoms. Skipping.
Residue LYS  434 is missing expected H atoms. Skipping.
Residue ALA  435 is missing expected H atoms. Skipping.
Residue LEU  436 is missing expected H atoms. Skipping.
Residue VAL  439 is missing expected H atoms. Skipping.
Residue ALA  442 is missing expected H atoms. Skipping.
Residue ILE  443 is missing expected H atoms. Skipping.
Residue TYR  444 is missing expected H atoms. Skipping.
Residue ALA  446 is missing expected H atoms. Skipping.
Residue ALA  447 is missing expected H atoms. Skipping.
Residue SER  449 is missing expected H atoms. Skipping.
Residue VAL  451 is missing expected H atoms. Skipping.
Residue SER  452 is missing expected H atoms. Skipping.
Residue ILE  454 is missing expected H atoms. Skipping.
Residue MET  455 is missing expected H atoms. Skipping.
Residue LYS  456 is missing expected H atoms. Skipping.
Residue ILE  457 is missing expected H atoms. Skipping.
Residue LEU  458 is missing expected H atoms. Skipping.
Residue ILE  459 is missing expected H atoms. Skipping.
Residue VAL  461 is missing expected H atoms. Skipping.
Residue ILE  462 is missing expected H atoms. Skipping.
Residue ILE  463 is missing expected H atoms. Skipping.
Residue THR  464 is missing expected H atoms. Skipping.
Residue ILE  466 is missing expected H atoms. Skipping.
Residue MET  468 is missing expected H atoms. Skipping.
Residue SER  470 is missing expected H atoms. Skipping.
Residue SER  472 is missing expected H atoms. Skipping.
Residue THR  473 is missing expected H atoms. Skipping.
Residue SER  474 is missing expected H atoms. Skipping.
Residue LEU  475 is missing expected H atoms. Skipping.
Residue SER  476 is missing expected H atoms. Skipping.
Residue VAL  477 is missing expected H atoms. Skipping.
Residue SER  478 is missing expected H atoms. Skipping.
Residue LEU  479 is missing expected H atoms. Skipping.
Residue VAL  480 is missing expected H atoms. Skipping.
Residue LEU  481 is missing expected H atoms. Skipping.
Residue VAL  482 is missing expected H atoms. Skipping.
Residue VAL  484 is missing expected H atoms. Skipping.
Residue VAL  485 is missing expected H atoms. Skipping.
Residue THR  486 is missing expected H atoms. Skipping.
Residue LEU  487 is missing expected H atoms. Skipping.
Residue TYR  488 is missing expected H atoms. Skipping.
Residue LEU  489 is missing expected H atoms. Skipping.
Residue VAL  491 is missing expected H atoms. Skipping.
Residue MET  492 is missing expected H atoms. Skipping.
Residue VAL  493 is missing expected H atoms. Skipping.
Residue VAL    2 is missing expected H atoms. Skipping.
Residue ALA    3 is missing expected H atoms. Skipping.
Residue LEU    4 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL    8 is missing expected H atoms. Skipping.
Residue MET   10 is missing expected H atoms. Skipping.
Residue LEU   12 is missing expected H atoms. Skipping.
Residue THR   14 is missing expected H atoms. Skipping.
Residue ALA   15 is missing expected H atoms. Skipping.
Residue THR   16 is missing expected H atoms. Skipping.
Residue THR   18 is missing expected H atoms. Skipping.
Residue MET   20 is missing expected H atoms. Skipping.
Residue SER   21 is missing expected H atoms. Skipping.
Residue SER   22 is missing expected H atoms. Skipping.
Residue ALA   25 is missing expected H atoms. Skipping.
Residue LYS   27 is missing expected H atoms. Skipping.
Residue ALA   29 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue THR   34 is missing expected H atoms. Skipping.
Residue ILE   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue THR   43 is missing expected H atoms. Skipping.
Residue ILE   44 is missing expected H atoms. Skipping.
Residue MET   45 is missing expected H atoms. Skipping.
Residue ALA   46 is missing expected H atoms. Skipping.
Residue ALA   47 is missing expected H atoms. Skipping.
Residue ILE   48 is missing expected H atoms. Skipping.
Residue LEU   49 is missing expected H atoms. Skipping.
Residue ALA   50 is missing expected H atoms. Skipping.
Residue TYR   51 is missing expected H atoms. Skipping.
Residue THR   52 is missing expected H atoms. Skipping.
Residue ILE   53 is missing expected H atoms. Skipping.
Residue THR   55 is missing expected H atoms. Skipping.
Residue THR   56 is missing expected H atoms. Skipping.
Residue ALA   61 is missing expected H atoms. Skipping.
Residue LEU   62 is missing expected H atoms. Skipping.
Residue ILE   63 is missing expected H atoms. Skipping.
Residue ILE   65 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 THR   68 is missing expected H atoms. Skipping.
Residue ALA   69 is missing expected H atoms. Skipping.
Residue VAL   70 is missing expected H atoms. Skipping.
Residue ALA   71 is missing expected H atoms. Skipping.
Evaluate side-chains
  259 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 250
  time to evaluate  : 1.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 7
  residues processed: 255
  average time/residue: 0.2212
  time to fit residues: 79.8852
Evaluate side-chains
  242 residues out of total 954 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 235
  time to evaluate  : 1.023 
Switching outliers to nearest non-outliers
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 2
  residues processed: 7
  average time/residue: 0.0967
  time to fit residues: 2.6974
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 81 optimal weight:    8.9990
   chunk 13 optimal weight:    0.0370
   chunk 24 optimal weight:    6.9990
   chunk 88 optimal weight:    6.9990
   chunk 37 optimal weight:   20.0000
   chunk 91 optimal weight:    4.9990
   chunk 11 optimal weight:    7.9990
   chunk 16 optimal weight:    2.9990
   chunk 78 optimal weight:   20.0000
   chunk 5 optimal weight:    1.9990
   overall best weight:    2.1864

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

Flipped N/Q/H residues before XYZ refinement:
** A  27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 203 ASN
A 244 HIS
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 203 ASN
** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 248 GLN
** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.152343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.142253 restraints weight = 21257.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.144990 restraints weight = 10642.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.146820 restraints weight = 6252.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start:          0.6281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.048   8986  Z= 0.164
  Angle     :  0.693   9.613  12164  Z= 0.351
  Chirality :  0.044   0.355   1412
  Planarity :  0.004   0.038   1520
  Dihedral  :  6.408  63.190   1224
  Min Nonbonded Distance : 1.839

Molprobity Statistics.
  All-atom Clashscore : 69.59
  Ramachandran Plot:
    Outliers :  3.55 %
    Allowed  : 18.38 %
    Favored  : 78.06 %
  Rotamer Outliers :  1.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -4.35 (0.23), residues: 1126
  helix: -1.13 (0.28), residues: 302
  sheet: -1.90 (0.34), residues: 240
  loop : -4.52 (0.20), residues: 584

===============================================================================
Job complete
usr+sys time: 2275.72 seconds
wall clock time: 42 minutes 23.12 seconds (2543.12 seconds total)