Starting phenix.real_space_refine
on Sun Feb  8 03:41:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qoo_53265/02_2026/9qoo_53265.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qoo_53265/02_2026/9qoo_53265.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qoo_53265/02_2026/9qoo_53265.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qoo_53265/02_2026/9qoo_53265.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qoo_53265/02_2026/9qoo_53265.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qoo_53265/02_2026/9qoo_53265.map"
  }
  resolution = 3.3
  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
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.026 sd=   0.603
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      93      5.16       5
     C   12851      2.51       5
     N    3625      2.21       5
     O    3930      1.98       5
     H   18702      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 39201
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 9392
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 924, 9392
          Classifications: {'peptide': 924}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 881}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 1860
          Unresolved non-hydrogen angles: 2400
          Unresolved non-hydrogen dihedrals: 1527
          Unresolved non-hydrogen chiralities: 206
          Planarities with less than four sites: {'GLN:plan1': 36, 'GLU:plan': 48, 'ASP:plan': 24, 'ARG:plan': 22, 'PHE:plan': 33, 'HIS:plan': 16, 'TYR:plan': 13, 'TRP:plan': 10, 'ASN:plan1': 17}
          Unresolved non-hydrogen planarities: 1028
    Chain: "B"
      Number of atoms: 1033
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 1033
          Classifications: {'peptide': 61}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 59}
    Chain: "C"
      Number of atoms: 1476
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 1476
          Classifications: {'peptide': 90}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 88}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 20
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "D"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 70, 726
          Classifications: {'peptide': 70}
          Link IDs: {'TRANS': 69}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 179
          Unresolved non-hydrogen angles: 226
          Unresolved non-hydrogen dihedrals: 144
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'PHE:plan': 3, 'ASP:plan': 2, 'ARG:plan': 5, 'GLN:plan1': 2, 'GLU:plan': 9, 'TYR:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 110
    Chain: "F"
      Number of atoms: 3776
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 242, 3776
          Classifications: {'peptide': 242}
          Link IDs: {'PTRANS': 5, 'TRANS': 236}
    Chain: "G"
      Number of atoms: 3781
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 242, 3781
          Classifications: {'peptide': 242}
          Link IDs: {'PTRANS': 8, 'TRANS': 233}
    Chain: "I"
      Number of atoms: 321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 321
          Classifications: {'peptide': 45}
          Link IDs: {'TRANS': 44}
          Unresolved non-hydrogen bonds: 167
          Unresolved non-hydrogen angles: 210
          Unresolved non-hydrogen dihedrals: 136
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 4, 'GLN:plan1': 2, 'GLU:plan': 9, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 102
    Chain: "O"
      Number of atoms: 3609
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 3609
          Classifications: {'peptide': 231}
          Link IDs: {'PTRANS': 10, 'TRANS': 220}
    Chain: "P"
      Number of atoms: 3928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 248, 3928
          Classifications: {'peptide': 248}
          Link IDs: {'PTRANS': 5, 'TRANS': 242}
    Chain: "Q"
      Number of atoms: 3765
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 3765
          Classifications: {'peptide': 237}
          Link IDs: {'PTRANS': 6, 'TRANS': 230}
    Chain: "R"
      Number of atoms: 3686
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 241, 3686
          Classifications: {'peptide': 241}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 232}
    Chain: "S"
      Number of atoms: 3708
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 3708
          Classifications: {'peptide': 236}
          Link IDs: {'PTRANS': 9, 'TRANS': 226}
  Time building chain proxies: 6.69, per 1000 atoms: 0.17
  Number of scatterers: 39201
  At special positions: 0
  Unit cell: (127.27, 168.74, 140.14, 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      93     16.00
     O    3930      8.00
     N    3625      7.00
     C   12851      6.00
     H   18702      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  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.29
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  5666 Ramachandran restraints generated.
    2833 Oldfield, 0 Emsley, 2833 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5406

  Finding SS restraints...
    Secondary structure from input PDB file:
      125 helices and 16 sheets defined
      60.1% alpha, 10.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 33
      removed outlier: 3.606A  pdb=" N   LEU A  33 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 51
    Processing helix  chain 'A' and resid 55 through 66
    Processing helix  chain 'A' and resid 70 through 89
    Processing helix  chain 'A' and resid 102 through 113
    Processing helix  chain 'A' and resid 114 through 117
    Processing helix  chain 'A' and resid 121 through 138
      removed outlier: 3.743A  pdb=" N   TRP A 138 " --> pdb=" O   ALA A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 157
      removed outlier: 4.297A  pdb=" N   ASN A 149 " --> pdb=" O   PRO A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 176
      removed outlier: 3.917A  pdb=" N   GLU A 172 " --> pdb=" O   ARG A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 199
      removed outlier: 4.040A  pdb=" N   VAL A 185 " --> pdb=" O   GLN A 181 " (cutoff:3.500A)
      Proline residue:  A 187  - end of helix
      Proline residue:  A 191  - end of helix
    Processing helix  chain 'A' and resid 204 through 224
    Processing helix  chain 'A' and resid 225 through 229
    Processing helix  chain 'A' and resid 230 through 253
      Proline residue:  A 239  - end of helix
    Processing helix  chain 'A' and resid 261 through 279
    Processing helix  chain 'A' and resid 280 through 282
      No H-bonds generated for 'chain 'A' and resid 280 through 282'
    Processing helix  chain 'A' and resid 283 through 306
      removed outlier: 3.722A  pdb=" N   GLN A 288 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   GLN A 289 " --> pdb=" O   SER A 285 " (cutoff:3.500A)
      Proline residue:  A 292  - end of helix
      removed outlier: 4.011A  pdb=" N   ALA A 302 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
      removed outlier: 4.853A  pdb=" N   ALA A 303 " --> pdb=" O   THR A 299 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   PHE A 304 " --> pdb=" O   GLU A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 346
    Processing helix  chain 'A' and resid 347 through 355
      removed outlier: 3.601A  pdb=" N   LYS A 350 " --> pdb=" O   SER A 347 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   SER A 351 " --> pdb=" O   LYS A 348 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   VAL A 353 " --> pdb=" O   LYS A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 368
    Processing helix  chain 'A' and resid 371 through 381
    Processing helix  chain 'A' and resid 381 through 389
      removed outlier: 3.741A  pdb=" N   GLU A 387 " --> pdb=" O   GLN A 383 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   GLU A 389 " --> pdb=" O   PHE A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 410
    Processing helix  chain 'A' and resid 414 through 416
      No H-bonds generated for 'chain 'A' and resid 414 through 416'
    Processing helix  chain 'A' and resid 417 through 438
    Processing helix  chain 'A' and resid 440 through 447
    Processing helix  chain 'A' and resid 448 through 467
      removed outlier: 3.879A  pdb=" N   LEU A 452 " --> pdb=" O   GLU A 448 " (cutoff:3.500A)
      removed outlier: 5.603A  pdb=" N   ALA A 459 " --> pdb=" O   GLY A 455 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   ILE A 460 " --> pdb=" O   SER A 456 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ILE A 461 " --> pdb=" O   VAL A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 480
    Processing helix  chain 'A' and resid 482 through 488
    Processing helix  chain 'A' and resid 491 through 496
    Processing helix  chain 'A' and resid 496 through 506
      removed outlier: 3.888A  pdb=" N   TRP A 500 " --> pdb=" O   GLY A 496 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ARG A 504 " --> pdb=" O   TRP A 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 507 through 509
      No H-bonds generated for 'chain 'A' and resid 507 through 509'
    Processing helix  chain 'A' and resid 510 through 525
    Processing helix  chain 'A' and resid 530 through 550
      removed outlier: 3.785A  pdb=" N   ASP A 546 " --> pdb=" O   TRP A 542 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   VAL A 550 " --> pdb=" O   ASP A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 558
      removed outlier: 3.687A  pdb=" N   HIS A 555 " --> pdb=" O   GLU A 552 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 573
    Processing helix  chain 'A' and resid 574 through 576
      No H-bonds generated for 'chain 'A' and resid 574 through 576'
    Processing helix  chain 'A' and resid 577 through 592
    Processing helix  chain 'A' and resid 594 through 616
      removed outlier: 5.133A  pdb=" N   SER A 603 " --> pdb=" O   ALA A 599 " (cutoff:3.500A)
      removed outlier: 5.747A  pdb=" N   LYS A 604 " --> pdb=" O   SER A 600 " (cutoff:3.500A)
      Proline residue:  A 607  - end of helix
      removed outlier: 3.553A  pdb=" N   TYR A 616 " --> pdb=" O   ILE A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 635
    Processing helix  chain 'A' and resid 636 through 638
      No H-bonds generated for 'chain 'A' and resid 636 through 638'
    Processing helix  chain 'A' and resid 639 through 657
      Proline residue:  A 649  - end of helix
      removed outlier: 3.859A  pdb=" N   MET A 655 " --> pdb=" O   LEU A 651 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 681
      removed outlier: 3.891A  pdb=" N   ASP A 672 " --> pdb=" O   ALA A 668 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   THR A 681 " --> pdb=" O   VAL A 677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 692
      removed outlier: 3.944A  pdb=" N   ILE A 690 " --> pdb=" O   SER A 686 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 692 through 704
      removed outlier: 3.648A  pdb=" N   LEU A 702 " --> pdb=" O   ALA A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 731
      removed outlier: 7.189A  pdb=" N   GLU A 726 " --> pdb=" O   SER A 722 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   GLN A 727 " --> pdb=" O   VAL A 723 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 738 through 751
      removed outlier: 3.696A  pdb=" N   TYR A 742 " --> pdb=" O   ASN A 738 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LEU A 751 " --> pdb=" O   VAL A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 758 through 761
    Processing helix  chain 'A' and resid 762 through 779
      removed outlier: 3.728A  pdb=" N   LEU A 766 " --> pdb=" O   PHE A 762 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLY A 775 " --> pdb=" O   ILE A 771 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   ARG A 776 " --> pdb=" O   SER A 772 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   GLU A 777 " --> pdb=" O   LYS A 773 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 781 through 796
      removed outlier: 3.783A  pdb=" N   ILE A 785 " --> pdb=" O   ASN A 781 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU A 786 " --> pdb=" O   LEU A 782 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   GLN A 795 " --> pdb=" O   SER A 791 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 798 through 815
      removed outlier: 3.508A  pdb=" N   MET A 802 " --> pdb=" O   THR A 798 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   GLN A 803 " --> pdb=" O   LEU A 799 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   SER A 804 " --> pdb=" O   SER A 800 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   LEU A 805 " --> pdb=" O   VAL A 801 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   PHE A 809 " --> pdb=" O   LEU A 805 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LEU A 812 " --> pdb=" O   VAL A 808 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 816 through 827
      removed outlier: 3.543A  pdb=" N   LEU A 820 " --> pdb=" O   GLN A 816 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 834 through 845
    Processing helix  chain 'A' and resid 846 through 850
    Processing helix  chain 'A' and resid 852 through 874
      removed outlier: 4.732A  pdb=" N   ASN A 872 " --> pdb=" O   GLN A 868 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 912 through 929
      removed outlier: 3.883A  pdb=" N   ILE A 922 " --> pdb=" O   LEU A 918 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   LEU A 925 " --> pdb=" O   ILE A 921 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 930 through 932
      No H-bonds generated for 'chain 'A' and resid 930 through 932'
    Processing helix  chain 'A' and resid 993 through 996
    Processing helix  chain 'A' and resid 997 through 1002
      removed outlier: 3.627A  pdb=" N   GLN A1001 " --> pdb=" O   ASP A 997 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1003 through 1010
    Processing helix  chain 'A' and resid 1011 through 1016
      removed outlier: 4.281A  pdb=" N   ALA A1016 " --> pdb=" O   LEU A1012 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1019 through 1025
    Processing helix  chain 'A' and resid 1026 through 1028
      No H-bonds generated for 'chain 'A' and resid 1026 through 1028'
    Processing helix  chain 'A' and resid 1029 through 1039
      removed outlier: 3.611A  pdb=" N   GLN A1037 " --> pdb=" O   ARG A1033 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 194
      removed outlier: 3.736A  pdb=" N   MET B 149 " --> pdb=" O   ARG B 145 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ARG B 153 " --> pdb=" O   MET B 149 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   LEU B 154 " --> pdb=" O   ILE B 150 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   GLU B 168 " --> pdb=" O   GLU B 164 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ILE B 169 " --> pdb=" O   GLU B 165 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ALA B 180 " --> pdb=" O   GLU B 176 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ARG B 192 " --> pdb=" O   GLN B 188 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 77 through 93
    Processing helix  chain 'C' and resid 94 through 97
    Processing helix  chain 'C' and resid 143 through 188
      removed outlier: 3.982A  pdb=" N   MET C 149 " --> pdb=" O   ARG C 145 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLU C 167 " --> pdb=" O   ARG C 163 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   GLU C 168 " --> pdb=" O   GLU C 164 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ILE C 169 " --> pdb=" O   GLU C 165 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ASN C 171 " --> pdb=" O   GLU C 167 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 69 through 73
      removed outlier: 3.557A  pdb=" N   VAL D  72 " --> pdb=" O   PHE D  69 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 77 through 96
    Processing helix  chain 'D' and resid 143 through 182
      removed outlier: 3.654A  pdb=" N   GLU D 159 " --> pdb=" O   LEU D 155 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   GLU D 160 " --> pdb=" O   LYS D 156 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   LYS D 161 " --> pdb=" O   GLU D 157 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   VAL D 162 " --> pdb=" O   ARG D 158 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLU D 176 " --> pdb=" O   THR D 172 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   VAL D 182 " --> pdb=" O   TYR D 178 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 20 through 33
      removed outlier: 3.615A  pdb=" N   GLU F  24 " --> pdb=" O   VAL F  20 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   SER F  33 " --> pdb=" O   ALA F  29 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 80 through 103
      removed outlier: 3.511A  pdb=" N   GLY F 103 " --> pdb=" O   ARG F  99 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 107 through 122
      removed outlier: 3.858A  pdb=" N   ASP F 113 " --> pdb=" O   LYS F 109 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ALA F 116 " --> pdb=" O   ALA F 112 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   TYR F 122 " --> pdb=" O   TYR F 118 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 168 through 177
    Processing helix  chain 'F' and resid 178 through 179
      No H-bonds generated for 'chain 'F' and resid 178 through 179'
    Processing helix  chain 'F' and resid 180 through 184
      removed outlier: 3.598A  pdb=" N   MET F 184 " --> pdb=" O   MET F 181 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 185 through 200
      removed outlier: 4.256A  pdb=" N   LYS F 191 " --> pdb=" O   ARG F 187 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 228 through 242
    Processing helix  chain 'G' and resid 22 through 33
      removed outlier: 3.665A  pdb=" N   GLU G  26 " --> pdb=" O   LEU G  22 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   ASN G  33 " --> pdb=" O   PHE G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 34 through 36
      No H-bonds generated for 'chain 'G' and resid 34 through 36'
    Processing helix  chain 'G' and resid 83 through 106
    Processing helix  chain 'G' and resid 110 through 126
      removed outlier: 3.602A  pdb=" N   VAL G 124 " --> pdb=" O   ASP G 120 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   TYR G 125 " --> pdb=" O   ILE G 121 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   THR G 126 " --> pdb=" O   SER G 122 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 171 through 185
      removed outlier: 3.760A  pdb=" N   SER G 177 " --> pdb=" O   THR G 173 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   PHE G 178 " --> pdb=" O   GLU G 174 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 190 through 207
    Processing helix  chain 'G' and resid 231 through 243
    Processing helix  chain 'I' and resid 143 through 182
      removed outlier: 4.297A  pdb=" N   GLU I 164 " --> pdb=" O   GLU I 160 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   GLU I 165 " --> pdb=" O   LYS I 161 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   VAL I 182 " --> pdb=" O   TYR I 178 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 183 through 185
      No H-bonds generated for 'chain 'I' and resid 183 through 185'
    Processing helix  chain 'O' and resid 19 through 30
    Processing helix  chain 'O' and resid 79 through 101
      removed outlier: 3.547A  pdb=" N   ARG O  83 " --> pdb=" O   GLY O  79 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   VAL O  84 " --> pdb=" O   PRO O  80 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   LEU O  85 " --> pdb=" O   ASP O  81 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 105 through 120
      removed outlier: 3.636A  pdb=" N   TYR O 120 " --> pdb=" O   VAL O 116 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 165 through 177
      removed outlier: 3.681A  pdb=" N   GLY O 169 " --> pdb=" O   ASN O 165 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 182 through 196
      removed outlier: 3.554A  pdb=" N   GLU O 196 " --> pdb=" O   LEU O 192 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 203 through 207
      removed outlier: 4.173A  pdb=" N   ILE O 207 " --> pdb=" O   GLU O 204 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 221 through 231
      removed outlier: 3.802A  pdb=" N   ASP O 227 " --> pdb=" O   THR O 223 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   TYR O 228 " --> pdb=" O   GLU O 224 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ALA O 231 " --> pdb=" O   ASP O 227 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 18 through 29
    Processing helix  chain 'P' and resid 79 through 102
      removed outlier: 4.213A  pdb=" N   VAL P  85 " --> pdb=" O   SER P  81 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 106 through 121
      removed outlier: 3.911A  pdb=" N   TYR P 121 " --> pdb=" O   ILE P 117 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 167 through 179
      removed outlier: 3.651A  pdb=" N   GLN P 177 " --> pdb=" O   SER P 173 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 185 through 201
    Processing helix  chain 'P' and resid 207 through 209
      No H-bonds generated for 'chain 'P' and resid 207 through 209'
    Processing helix  chain 'P' and resid 229 through 246
    Processing helix  chain 'Q' and resid 17 through 27
    Processing helix  chain 'Q' and resid 55 through 60
      removed outlier: 3.906A  pdb=" N   VAL Q  59 " --> pdb=" O   ASP Q  55 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 76 through 98
    Processing helix  chain 'Q' and resid 103 through 121
      removed outlier: 3.627A  pdb=" N   ILE Q 107 " --> pdb=" O   THR Q 103 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 164 through 176
    Processing helix  chain 'Q' and resid 179 through 182
    Processing helix  chain 'Q' and resid 183 through 196
    Processing helix  chain 'Q' and resid 221 through 237
    Processing helix  chain 'R' and resid 5 through 9
    Processing helix  chain 'R' and resid 21 through 33
      removed outlier: 4.035A  pdb=" N   LYS R  32 " --> pdb=" O   ILE R  28 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   LEU R  33 " --> pdb=" O   GLU R  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 60 through 64
      removed outlier: 3.572A  pdb=" N   ILE R  64 " --> pdb=" O   PRO R  61 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 81 through 104
      removed outlier: 3.630A  pdb=" N   ALA R  85 " --> pdb=" O   LEU R  81 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LYS R  86 " --> pdb=" O   ILE R  82 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   THR R  87 " --> pdb=" O   ALA R  83 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   LEU R  88 " --> pdb=" O   ASP R  84 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 108 through 119
      removed outlier: 4.016A  pdb=" N   LEU R 119 " --> pdb=" O   ALA R 115 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 173 through 183
      removed outlier: 3.620A  pdb=" N   SER R 179 " --> pdb=" O   GLU R 175 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 190 through 206
    Processing helix  chain 'R' and resid 230 through 239
      removed outlier: 3.849A  pdb=" N   VAL R 237 " --> pdb=" O   GLU R 233 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LYS R 239 " --> pdb=" O   GLU R 235 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 19 through 30
      removed outlier: 3.517A  pdb=" N   GLU S  23 " --> pdb=" O   ILE S  19 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ALA S  28 " --> pdb=" O   TYR S  24 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   VAL S  29 " --> pdb=" O   ALA S  25 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LYS S  30 " --> pdb=" O   MET S  26 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 77 through 99
    Processing helix  chain 'S' and resid 104 through 118
      removed outlier: 3.773A  pdb=" N   SER S 110 " --> pdb=" O   SER S 106 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ILE S 118 " --> pdb=" O   SER S 114 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 119 through 121
      No H-bonds generated for 'chain 'S' and resid 119 through 121'
    Processing helix  chain 'S' and resid 165 through 175
    Processing helix  chain 'S' and resid 175 through 180
      removed outlier: 4.070A  pdb=" N   PHE S 179 " --> pdb=" O   HIS S 175 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   MET S 180 " --> pdb=" O   MET S 176 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 175 through 180'
    Processing helix  chain 'S' and resid 183 through 198
      removed outlier: 3.942A  pdb=" N   THR S 198 " --> pdb=" O   ALA S 194 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 229 through 234
    Processing sheet with id=AA1, first strand: chain 'F' and resid 162 through 165
    Processing sheet with id=AA2, first strand: chain 'F' and resid 66 through 68
      removed outlier: 3.735A  pdb=" N   GLY F 138 " --> pdb=" O   GLY F  74 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ALA F  76 " --> pdb=" O   MET F 136 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLN F 147 " --> pdb=" O   SER F 139 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'G' and resid 165 through 169
      removed outlier: 6.507A  pdb=" N   THR G  38 " --> pdb=" O   GLN G  53 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLN G  53 " --> pdb=" O   THR G  38 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'G' and resid 79 through 82
    Processing sheet with id=AA5, first strand: chain 'O' and resid 12 through 13
      removed outlier: 3.654A  pdb=" N   LYS O  17 " --> pdb=" O   SER O  13 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'O' and resid 159 through 162
      removed outlier: 3.571A  pdb=" N   ASN O 213 " --> pdb=" O   GLY O 216 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'O' and resid 65 through 66
      removed outlier: 4.156A  pdb=" N   SER O 132 " --> pdb=" O   SER O  76 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLY O 137 " --> pdb=" O   TYR O 144 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'P' and resid 161 through 164
      removed outlier: 3.644A  pdb=" N   THR P 217 " --> pdb=" O   VAL P 224 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'P' and resid 65 through 67
    Processing sheet with id=AB1, first strand: chain 'Q' and resid 10 through 11
    Processing sheet with id=AB2, first strand: chain 'Q' and resid 158 through 161
      removed outlier: 3.641A  pdb=" N   GLY Q  34 " --> pdb=" O   ASN Q 159 " (cutoff:3.500A)
      removed outlier: 5.295A  pdb=" N   ARG Q 212 " --> pdb=" O   SER Q 216 " (cutoff:3.500A)
      removed outlier: 5.641A  pdb=" N   SER Q 216 " --> pdb=" O   ARG Q 212 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'Q' and resid 63 through 64
    Processing sheet with id=AB4, first strand: chain 'R' and resid 167 through 170
    Processing sheet with id=AB5, first strand: chain 'R' and resid 67 through 71
      removed outlier: 6.452A  pdb=" N   ILE R  74 " --> pdb=" O   ILE R  70 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LEU R 142 " --> pdb=" O   ALA R  77 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ASP R 147 " --> pdb=" O   GLY R 150 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'S' and resid 158 through 161
    Processing sheet with id=AB7, first strand: chain 'S' and resid 63 through 67
      removed outlier: 6.072A  pdb=" N   ILE S  63 " --> pdb=" O   ILE S  74 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   ILE S  74 " --> pdb=" O   ILE S  63 " (cutoff:3.500A)
      removed outlier: 5.565A  pdb=" N   HIS S  65 " --> pdb=" O   ILE S  72 " (cutoff:3.500A)
      removed outlier: 5.719A  pdb=" N   ILE S  72 " --> pdb=" O   HIS S  65 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   ILE S 144 " --> pdb=" O   CYS S 156 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   ASN S 152 " --> pdb=" O   CYS S 148 " (cutoff:3.500A)

    1327 hydrogen bonds defined for protein.
    3822 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: 11.65

  Time building geometry restraints manager: 5.67 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 18663
        1.03 -     1.23: 43
        1.23 -     1.42: 8483
        1.42 -     1.62: 12175
        1.62 -     1.81: 147
  Bond restraints: 39511
  Sorted by residual:
  bond pdb=" N   GLY G   4 "
       pdb=" CA  GLY G   4 "
    ideal  model  delta    sigma   weight residual
    1.451  1.491 -0.040 1.60e-02 3.91e+03 6.11e+00
  bond pdb=" N   PHE B 142 "
       pdb=" CA  PHE B 142 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.07e+00
  bond pdb=" N   GLU O   2 "
       pdb=" CA  GLU O   2 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.97e+00
  bond pdb=" N   LEU D 141 "
       pdb=" CA  LEU D 141 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.97e+00
  bond pdb=" N   LEU I 141 "
       pdb=" CA  LEU I 141 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.93e+00
  ... (remaining 39506 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 69182
        1.38 -     2.77: 1722
        2.77 -     4.15: 162
        4.15 -     5.53: 22
        5.53 -     6.92: 3
  Bond angle restraints: 71091
  Sorted by residual:
  angle pdb=" N   GLN G 127 "
        pdb=" CA  GLN G 127 "
        pdb=" C   GLN G 127 "
      ideal   model   delta    sigma   weight residual
     114.56  109.92    4.64 1.27e+00 6.20e-01 1.34e+01
  angle pdb=" N   VAL A 185 "
        pdb=" CA  VAL A 185 "
        pdb=" C   VAL A 185 "
      ideal   model   delta    sigma   weight residual
     113.71  110.59    3.12 9.50e-01 1.11e+00 1.08e+01
  angle pdb=" N   TYR Q   3 "
        pdb=" CA  TYR Q   3 "
        pdb=" C   TYR Q   3 "
      ideal   model   delta    sigma   weight residual
     113.43  109.34    4.09 1.26e+00 6.30e-01 1.06e+01
  angle pdb=" N   GLN A 868 "
        pdb=" CA  GLN A 868 "
        pdb=" C   GLN A 868 "
      ideal   model   delta    sigma   weight residual
     113.01  109.40    3.61 1.20e+00 6.94e-01 9.06e+00
  angle pdb=" CA  ARG A 776 "
        pdb=" CB  ARG A 776 "
        pdb=" CG  ARG A 776 "
      ideal   model   delta    sigma   weight residual
     114.10  120.01   -5.91 2.00e+00 2.50e-01 8.73e+00
  ... (remaining 71086 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 16991
       17.99 -    35.98: 1330
       35.98 -    53.97: 467
       53.97 -    71.96: 123
       71.96 -    89.95: 44
  Dihedral angle restraints: 18955
    sinusoidal: 9681
      harmonic: 9274
  Sorted by residual:
  dihedral pdb=" CA  TYR O 120 "
           pdb=" C   TYR O 120 "
           pdb=" N   THR O 121 "
           pdb=" CA  THR O 121 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.77   22.23     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" CA  PHE G 210 "
           pdb=" C   PHE G 210 "
           pdb=" N   LYS G 211 "
           pdb=" CA  LYS G 211 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.90   19.10     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  ASN S   4 "
           pdb=" C   ASN S   4 "
           pdb=" N   GLN S   5 "
           pdb=" CA  GLN S   5 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.33  -18.67     0      5.00e+00 4.00e-02 1.39e+01
  ... (remaining 18952 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 2090
       0.029 -    0.058: 781
       0.058 -    0.087: 258
       0.087 -    0.116: 154
       0.116 -    0.145: 24
  Chirality restraints: 3307
  Sorted by residual:
  chirality pdb=" CA  ILE F   3 "
            pdb=" N   ILE F   3 "
            pdb=" C   ILE F   3 "
            pdb=" CB  ILE F   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.22e-01
  chirality pdb=" CA  ILE Q  40 "
            pdb=" N   ILE Q  40 "
            pdb=" C   ILE Q  40 "
            pdb=" CB  ILE Q  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.06e-01
  chirality pdb=" CA  ILE A 254 "
            pdb=" N   ILE A 254 "
            pdb=" C   ILE A 254 "
            pdb=" CB  ILE A 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.57e-01
  ... (remaining 3304 not shown)

  Planarity restraints: 6487
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 829 "    0.028 5.00e-02 4.00e+02   4.27e-02 2.92e+00
        pdb=" N   PRO A 830 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 830 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 830 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG F 114 "    0.122 9.50e-02 1.11e+02   4.09e-02 2.22e+00
        pdb=" NE  ARG F 114 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  ARG F 114 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG F 114 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG F 114 "    0.000 2.00e-02 2.50e+03
        pdb="HH11 ARG F 114 "   -0.003 2.00e-02 2.50e+03
        pdb="HH12 ARG F 114 "   -0.000 2.00e-02 2.50e+03
        pdb="HH21 ARG F 114 "   -0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG F 114 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 752 "    0.024 5.00e-02 4.00e+02   3.68e-02 2.16e+00
        pdb=" N   PRO A 753 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A 753 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 753 "    0.021 5.00e-02 4.00e+02
  ... (remaining 6484 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.11: 801
        2.11 -     2.74: 67017
        2.74 -     3.36: 110558
        3.36 -     3.98: 133438
        3.98 -     4.60: 212441
  Nonbonded interactions: 524255
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU Q 179 "
            pdb=" H   GLU Q 179 "
     model   vdw
     1.493 2.450
  nonbonded pdb=" HZ2 LYS Q 189 "
            pdb=" OE2 GLU Q 235 "
     model   vdw
     1.545 2.450
  nonbonded pdb=" O   GLN C  80 "
            pdb="HD21 ASN C  84 "
     model   vdw
     1.552 2.450
  nonbonded pdb=" OD2 ASP C 187 "
            pdb=" HH  TYR O  23 "
     model   vdw
     1.570 2.450
  nonbonded pdb=" H   PHE F  14 "
            pdb=" OE1 GLN G  24 "
     model   vdw
     1.571 2.450
  ... (remaining 524250 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.400
  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:             0.280
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.100
  Set scattering table:                    0.060
  Process input model:                     40.080
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5854
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  20809  Z= 0.140
  Angle     :  0.536   6.915  28272  Z= 0.302
  Chirality :  0.039   0.145   3307
  Planarity :  0.004   0.054   3731
  Dihedral  : 15.909  89.946   7236
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 18.51 %
    Favored  : 78.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.16), residues: 2833
  helix:  1.82 (0.14), residues: 1522
  sheet: -0.77 (0.27), residues: 345
  loop :  0.07 (0.21), residues: 966

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG F 114 
 TYR   0.013   0.001   TYR O  75 
 PHE   0.017   0.001   PHE P 124 
 TRP   0.012   0.001   TRP Q 156 
 HIS   0.004   0.001   HIS A 703 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (20809)
  covalent geometry    : angle       0.53574 (28272)
  hydrogen bonds       : bond        0.16615 ( 1327)
  hydrogen bonds       : angle       6.13075 ( 3822)

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

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

  5666 Ramachandran restraints generated.
    2833 Oldfield, 0 Emsley, 2833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5666 Ramachandran restraints generated.
    2833 Oldfield, 0 Emsley, 2833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL   17 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue VAL   26 is missing expected H atoms. Skipping.
Residue THR   28 is missing expected H atoms. Skipping.
Residue LEU   29 is missing expected H atoms. Skipping.
Residue THR   30 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue LEU   33 is missing expected H atoms. Skipping.
Residue SER   34 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue VAL   39 is missing expected H atoms. Skipping.
Residue ILE   47 is missing expected H atoms. Skipping.
Residue LYS   48 is missing expected H atoms. Skipping.
Residue VAL   49 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue VAL   52 is missing expected H atoms. Skipping.
Residue THR   53 is missing expected H atoms. Skipping.
Residue VAL   58 is missing expected H atoms. Skipping.
Residue LEU   60 is missing expected H atoms. Skipping.
Residue LEU   63 is missing expected H atoms. Skipping.
Residue THR   64 is missing expected H atoms. Skipping.
Residue VAL   65 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ILE   73 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue SER   78 is missing expected H atoms. Skipping.
Residue VAL   79 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue LEU   81 is missing expected H atoms. Skipping.
Residue LYS   82 is missing expected H atoms. Skipping.
Residue TYR   84 is missing expected H atoms. Skipping.
Residue VAL   85 is missing expected H atoms. Skipping.
Residue THR   87 is missing expected H atoms. Skipping.
Residue SER   93 is missing expected H atoms. Skipping.
Residue LYS   95 is missing expected H atoms. Skipping.
Residue THR  101 is missing expected H atoms. Skipping.
Residue THR  102 is missing expected H atoms. Skipping.
Residue LYS  106 is missing expected H atoms. Skipping.
Residue ILE  107 is missing expected H atoms. Skipping.
Residue VAL  108 is missing expected H atoms. Skipping.
Residue ILE  109 is missing expected H atoms. Skipping.
Residue LEU  112 is missing expected H atoms. Skipping.
Residue LEU  113 is missing expected H atoms. Skipping.
Residue LEU  117 is missing expected H atoms. Skipping.
Residue SER  120 is missing expected H atoms. Skipping.
Residue ILE  121 is missing expected H atoms. Skipping.
Residue SER  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue VAL  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue SER  127 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue TYR  130 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue SER  133 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  147 is missing expected H atoms. Skipping.
Residue LEU  150 is missing expected H atoms. Skipping.
Residue LEU  151 is missing expected H atoms. Skipping.
Residue MET  152 is missing expected H atoms. Skipping.
Residue MET  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue VAL  156 is missing expected H atoms. Skipping.
Residue SER  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue VAL  163 is missing expected H atoms. Skipping.
Residue MET  167 is missing expected H atoms. Skipping.
Residue VAL  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue THR  174 is missing expected H atoms. Skipping.
Residue VAL  177 is missing expected H atoms. Skipping.
Residue THR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue MET  182 is missing expected H atoms. Skipping.
Residue LEU  184 is missing expected H atoms. Skipping.
Residue VAL  185 is missing expected H atoms. Skipping.
Residue VAL  188 is missing expected H atoms. Skipping.
Residue ILE  189 is missing expected H atoms. Skipping.
Residue LEU  190 is missing expected H atoms. Skipping.
Residue MET  193 is missing expected H atoms. Skipping.
Residue TYR  194 is missing expected H atoms. Skipping.
Residue LYS  195 is missing expected H atoms. Skipping.
Residue ILE  196 is missing expected H atoms. Skipping.
Residue THR  198 is missing expected H atoms. Skipping.
Residue MET  199 is missing expected H atoms. Skipping.
Residue VAL  202 is missing expected H atoms. Skipping.
Residue TYR  203 is missing expected H atoms. Skipping.
Residue ILE  205 is missing expected H atoms. Skipping.
Residue THR  207 is missing expected H atoms. Skipping.
Residue SER  209 is missing expected H atoms. Skipping.
Residue VAL  212 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue THR  216 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue MET  221 is missing expected H atoms. Skipping.
Residue ILE  222 is missing expected H atoms. Skipping.
Residue MET  225 is missing expected H atoms. Skipping.
Residue LEU  228 is missing expected H atoms. Skipping.
Residue LYS  230 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue VAL  235 is missing expected H atoms. Skipping.
Residue LEU  236 is missing expected H atoms. Skipping.
Residue ILE  237 is missing expected H atoms. Skipping.
Residue VAL  240 is missing expected H atoms. Skipping.
Residue VAL  241 is missing expected H atoms. Skipping.
Residue THR  245 is missing expected H atoms. Skipping.
Residue VAL  249 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue ILE  254 is missing expected H atoms. Skipping.
Residue THR  259 is missing expected H atoms. Skipping.
Residue SER  260 is missing expected H atoms. Skipping.
Residue SER  262 is missing expected H atoms. Skipping.
Residue LYS  265 is missing expected H atoms. Skipping.
Residue MET  266 is missing expected H atoms. Skipping.
Residue VAL  268 is missing expected H atoms. Skipping.
Residue LEU  269 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue VAL  272 is missing expected H atoms. Skipping.
Residue THR  273 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue VAL  276 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue MET  283 is missing expected H atoms. Skipping.
Residue VAL  284 is missing expected H atoms. Skipping.
Residue SER  285 is missing expected H atoms. Skipping.
Residue SER  286 is missing expected H atoms. Skipping.
Residue MET  287 is missing expected H atoms. Skipping.
Residue ILE  290 is missing expected H atoms. Skipping.
Residue LEU  291 is missing expected H atoms. Skipping.
Residue ILE  293 is missing expected H atoms. Skipping.
Residue VAL  294 is missing expected H atoms. Skipping.
Residue THR  297 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue THR  299 is missing expected H atoms. Skipping.
Residue SER  301 is missing expected H atoms. Skipping.
Residue TYR  305 is missing expected H atoms. Skipping.
Residue VAL  306 is missing expected H atoms. Skipping.
Residue THR  308 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue VAL  333 is missing expected H atoms. Skipping.
Residue SER  335 is missing expected H atoms. Skipping.
Residue ILE  336 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  344 is missing expected H atoms. Skipping.
Residue SER  347 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LYS  350 is missing expected H atoms. Skipping.
Residue SER  351 is missing expected H atoms. Skipping.
Residue THR  352 is missing expected H atoms. Skipping.
Residue VAL  353 is missing expected H atoms. Skipping.
Residue LYS  354 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LEU  357 is missing expected H atoms. Skipping.
Residue LEU  360 is missing expected H atoms. Skipping.
Residue ILE  361 is missing expected H atoms. Skipping.
Residue TYR  362 is missing expected H atoms. Skipping.
Residue TYR  363 is missing expected H atoms. Skipping.
Residue ILE  364 is missing expected H atoms. Skipping.
Residue ILE  365 is missing expected H atoms. Skipping.
Residue LEU  366 is missing expected H atoms. Skipping.
Residue TYR  367 is missing expected H atoms. Skipping.
Residue MET  368 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue THR  371 is missing expected H atoms. Skipping.
Residue ILE  375 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue VAL  377 is missing expected H atoms. Skipping.
Residue THR  379 is missing expected H atoms. Skipping.
Residue VAL  386 is missing expected H atoms. Skipping.
Residue THR  393 is missing expected H atoms. Skipping.
Residue SER  395 is missing expected H atoms. Skipping.
Residue TYR  396 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue VAL  398 is missing expected H atoms. Skipping.
Residue ILE  400 is missing expected H atoms. Skipping.
Residue LEU  405 is missing expected H atoms. Skipping.
Residue LEU  406 is missing expected H atoms. Skipping.
Residue LEU  407 is missing expected H atoms. Skipping.
Residue VAL  409 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue SER  417 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue THR  426 is missing expected H atoms. Skipping.
Residue LEU  429 is missing expected H atoms. Skipping.
Residue THR  435 is missing expected H atoms. Skipping.
Residue LYS  436 is missing expected H atoms. Skipping.
Residue SER  438 is missing expected H atoms. Skipping.
Residue THR  440 is missing expected H atoms. Skipping.
Residue LYS  445 is missing expected H atoms. Skipping.
Residue ILE  446 is missing expected H atoms. Skipping.
Residue MET  451 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue LEU  454 is missing expected H atoms. Skipping.
Residue SER  456 is missing expected H atoms. Skipping.
Residue VAL  457 is missing expected H atoms. Skipping.
Residue LYS  458 is missing expected H atoms. Skipping.
Residue ILE  460 is missing expected H atoms. Skipping.
Residue ILE  461 is missing expected H atoms. Skipping.
Residue THR  462 is missing expected H atoms. Skipping.
Residue SER  464 is missing expected H atoms. Skipping.
Residue VAL  465 is missing expected H atoms. Skipping.
Residue LYS  466 is missing expected H atoms. Skipping.
Residue ILE  470 is missing expected H atoms. Skipping.
Residue MET  474 is missing expected H atoms. Skipping.
Residue LEU  478 is missing expected H atoms. Skipping.
Residue THR  479 is missing expected H atoms. Skipping.
Residue VAL  481 is missing expected H atoms. Skipping.
Residue ILE  482 is missing expected H atoms. Skipping.
Residue LEU  483 is missing expected H atoms. Skipping.
Residue LEU  486 is missing expected H atoms. Skipping.
Residue LEU  488 is missing expected H atoms. Skipping.
Residue SER  489 is missing expected H atoms. Skipping.
Residue VAL  490 is missing expected H atoms. Skipping.
Residue SER  491 is missing expected H atoms. Skipping.
Residue LEU  494 is missing expected H atoms. Skipping.
Residue LEU  495 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  503 is missing expected H atoms. Skipping.
Residue THR  506 is missing expected H atoms. Skipping.
Residue VAL  507 is missing expected H atoms. Skipping.
Residue MET  509 is missing expected H atoms. Skipping.
Residue SER  510 is missing expected H atoms. Skipping.
Residue LEU  513 is missing expected H atoms. Skipping.
Residue ILE  514 is missing expected H atoms. Skipping.
Residue LEU  518 is missing expected H atoms. Skipping.
Residue THR  521 is missing expected H atoms. Skipping.
Residue VAL  522 is missing expected H atoms. Skipping.
Residue SER  523 is missing expected H atoms. Skipping.
Residue LEU  525 is missing expected H atoms. Skipping.
Residue THR  528 is missing expected H atoms. Skipping.
Residue SER  532 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  535 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  538 is missing expected H atoms. Skipping.
Residue ILE  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LEU  548 is missing expected H atoms. Skipping.
Residue LYS  549 is missing expected H atoms. Skipping.
Residue VAL  550 is missing expected H atoms. Skipping.
Residue SER  551 is missing expected H atoms. Skipping.
Residue SER  553 is missing expected H atoms. Skipping.
Residue THR  554 is missing expected H atoms. Skipping.
Residue VAL  556 is missing expected H atoms. Skipping.
Residue LEU  557 is missing expected H atoms. Skipping.
Residue LEU  561 is missing expected H atoms. Skipping.
Residue SER  563 is missing expected H atoms. Skipping.
Residue ILE  564 is missing expected H atoms. Skipping.
Residue LEU  565 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue LEU  571 is missing expected H atoms. Skipping.
Residue SER  576 is missing expected H atoms. Skipping.
Residue SER  577 is missing expected H atoms. Skipping.
Residue VAL  579 is missing expected H atoms. Skipping.
Residue LEU  580 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue VAL  583 is missing expected H atoms. Skipping.
Residue MET  584 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue LEU  587 is missing expected H atoms. Skipping.
Residue ILE  589 is missing expected H atoms. Skipping.
Residue VAL  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue VAL  593 is missing expected H atoms. Skipping.
Residue THR  598 is missing expected H atoms. Skipping.
Residue SER  600 is missing expected H atoms. Skipping.
Residue MET  601 is missing expected H atoms. Skipping.
Residue SER  603 is missing expected H atoms. Skipping.
Residue LYS  604 is missing expected H atoms. Skipping.
Residue ILE  605 is missing expected H atoms. Skipping.
Residue THR  609 is missing expected H atoms. Skipping.
Residue ILE  610 is missing expected H atoms. Skipping.
Residue ILE  612 is missing expected H atoms. Skipping.
Residue LEU  614 is missing expected H atoms. Skipping.
Residue LYS  615 is missing expected H atoms. Skipping.
Residue LEU  995 is missing expected H atoms. Skipping.
Residue LYS  996 is missing expected H atoms. Skipping.
Residue LEU  999 is missing expected H atoms. Skipping.
Residue TYR 1000 is missing expected H atoms. Skipping.
Residue ILE 1002 is missing expected H atoms. Skipping.
Residue LEU 1004 is missing expected H atoms. Skipping.
Residue TYR 1007 is missing expected H atoms. Skipping.
Residue LEU 1008 is missing expected H atoms. Skipping.
Residue THR 1009 is missing expected H atoms. Skipping.
Residue LEU 1012 is missing expected H atoms. Skipping.
Residue TYR 1021 is missing expected H atoms. Skipping.
Residue ILE 1022 is missing expected H atoms. Skipping.
Residue MET 1023 is missing expected H atoms. Skipping.
Residue SER 1025 is missing expected H atoms. Skipping.
Residue LEU 1028 is missing expected H atoms. Skipping.
Residue VAL 1035 is missing expected H atoms. Skipping.
Residue LEU 1036 is missing expected H atoms. Skipping.
Residue THR 1038 is missing expected H atoms. Skipping.
Residue ILE 1039 is missing expected H atoms. Skipping.
Residue VAL   72 is missing expected H atoms. Skipping.
Residue SER   73 is missing expected H atoms. Skipping.
Residue SER   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue THR   77 is missing expected H atoms. Skipping.
Residue VAL   72 is missing expected H atoms. Skipping.
Residue SER   73 is missing expected H atoms. Skipping.
Residue SER   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue THR   77 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  143 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue VAL  147 is missing expected H atoms. Skipping.
Residue MET  149 is missing expected H atoms. Skipping.
Residue ILE  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue VAL  162 is missing expected H atoms. Skipping.
Residue TYR  166 is missing expected H atoms. Skipping.
Residue ILE  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LEU  174 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  143 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue VAL  147 is missing expected H atoms. Skipping.
Residue MET  149 is missing expected H atoms. Skipping.
Residue ILE  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue VAL  162 is missing expected H atoms. Skipping.
Residue TYR  166 is missing expected H atoms. Skipping.
Residue ILE  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LEU  174 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue VAL  182 is missing expected H atoms. Skipping.
Residue LYS  183 is missing expected H atoms. Skipping.
Evaluate side-chains
  720 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 671
  time to evaluate  : 1.008 
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
   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
   revert: symmetry clash
REVERT: A  705 ASP cc_start: 0.6004 (t0) cc_final: 0.5774 (t0)
REVERT: A  815 THR cc_start: 0.6690 (m) cc_final: 0.6285 (p)
REVERT: A  843 TRP cc_start: 0.6111 (t60) cc_final: 0.5488 (t60)
REVERT: C   88 GLU cc_start: 0.5769 (mm-30) cc_final: 0.5332 (mm-30)
REVERT: F   53 VAL cc_start: 0.7834 (m) cc_final: 0.7497 (p)
REVERT: F  122 TYR cc_start: 0.6417 (m-80) cc_final: 0.6101 (m-80)
REVERT: F  191 LYS cc_start: 0.7888 (mtpt) cc_final: 0.7683 (mtmm)
REVERT: F  198 TYR cc_start: 0.7063 (m-80) cc_final: 0.6839 (m-80)
REVERT: G   30 LYS cc_start: 0.7536 (mttp) cc_final: 0.7202 (mtpp)
REVERT: G   34 GLN cc_start: 0.7800 (tp40) cc_final: 0.7580 (mm110)
REVERT: G  244 GLU cc_start: 0.5519 (pp20) cc_final: 0.5307 (pp20)
REVERT: P   12 PHE cc_start: 0.6089 (m-80) cc_final: 0.5491 (m-10)
REVERT: P  130 PHE cc_start: 0.6688 (m-80) cc_final: 0.5439 (m-80)
REVERT: Q   43 LEU cc_start: 0.6693 (mt) cc_final: 0.6462 (mp)
REVERT: R   28 ILE cc_start: 0.7205 (mm) cc_final: 0.6871 (mm)
REVERT: R   41 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6660 (tt0)
REVERT: R  111 SER cc_start: 0.7075 (m) cc_final: 0.6722 (m)
REVERT: R  154 PHE cc_start: 0.6822 (m-80) cc_final: 0.6551 (m-80)
REVERT: S  114 SER cc_start: 0.7754 (t) cc_final: 0.7513 (t)
REVERT: S  176 MET cc_start: 0.6910 (mtp) cc_final: 0.6620 (mtm)
REVERT: S  220 GLU cc_start: 0.5680 (mm-30) cc_final: 0.5394 (mm-30)
REVERT: S  224 TYR cc_start: 0.7515 (m-80) cc_final: 0.7312 (m-10)
  outliers start: 49
  outliers final: 17
  residues processed: 698
  average time/residue: 0.3667
  time to fit residues: 374.4916
Evaluate side-chains
  554 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 536
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  619 ASP
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  798 THR
Chi-restraints excluded: chain A residue  868 GLN
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain C residue  166 TYR
Chi-restraints excluded: chain F residue  206 ASP
Chi-restraints excluded: chain F residue  244 LYS
Chi-restraints excluded: chain G residue  240 VAL
Chi-restraints excluded: chain O residue  149 ASP
Chi-restraints excluded: chain P residue   82 ASP
Chi-restraints excluded: chain P residue  239 LYS
Chi-restraints excluded: chain Q residue  114 LEU
Chi-restraints excluded: chain Q residue  129 ILE
Chi-restraints excluded: chain R residue   41 GLN
Chi-restraints excluded: chain R residue   47 CYS
Chi-restraints excluded: chain S residue   53 GLN
Chi-restraints excluded: chain S residue  144 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 283
   random chunks:
   chunk 197 optimal weight:    0.9980
   chunk 215 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 132 optimal weight:    1.9990
   chunk 261 optimal weight:    0.9980
   chunk 248 optimal weight:    2.9990
   chunk 207 optimal weight:    0.7980
   chunk 155 optimal weight:    1.9990
   chunk 244 optimal weight:    0.4980
   chunk 183 optimal weight:    1.9990
   chunk 111 optimal weight:    9.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 730 GLN
A 910 ASN
D  84 ASN
D  87 GLN
Q  92 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.147576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.118838 restraints weight = 86223.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 1.76
r_work: 0.3356 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3237 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3227
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3227 r_free = 0.3227    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       23 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3226 r_free = 0.3226    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
r_final: 0.3226
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7012
moved from start:          0.3949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  20809  Z= 0.244
  Angle     :  0.682   9.516  28272  Z= 0.372
  Chirality :  0.045   0.249   3307
  Planarity :  0.005   0.049   3731
  Dihedral  :  5.772  84.387   3096
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 21.12 %
    Favored  : 75.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.02 (0.16), residues: 2833
  helix:  1.59 (0.13), residues: 1560
  sheet: -0.62 (0.26), residues: 359
  loop : -0.23 (0.21), residues: 914

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F  65 
 TYR   0.021   0.002   TYR B 200 
 PHE   0.022   0.002   PHE F  47 
 TRP   0.014   0.002   TRP F 215 
 HIS   0.010   0.002   HIS O  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00550 (20809)
  covalent geometry    : angle       0.68174 (28272)
  hydrogen bonds       : bond        0.04676 ( 1327)
  hydrogen bonds       : angle       4.56128 ( 3822)

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

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

  5666 Ramachandran restraints generated.
    2833 Oldfield, 0 Emsley, 2833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5666 Ramachandran restraints generated.
    2833 Oldfield, 0 Emsley, 2833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL   17 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue VAL   26 is missing expected H atoms. Skipping.
Residue THR   28 is missing expected H atoms. Skipping.
Residue LEU   29 is missing expected H atoms. Skipping.
Residue THR   30 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue LEU   33 is missing expected H atoms. Skipping.
Residue SER   34 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue VAL   39 is missing expected H atoms. Skipping.
Residue ILE   47 is missing expected H atoms. Skipping.
Residue LYS   48 is missing expected H atoms. Skipping.
Residue VAL   49 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue VAL   52 is missing expected H atoms. Skipping.
Residue THR   53 is missing expected H atoms. Skipping.
Residue VAL   58 is missing expected H atoms. Skipping.
Residue LEU   60 is missing expected H atoms. Skipping.
Residue LEU   63 is missing expected H atoms. Skipping.
Residue THR   64 is missing expected H atoms. Skipping.
Residue VAL   65 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ILE   73 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue SER   78 is missing expected H atoms. Skipping.
Residue VAL   79 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue LEU   81 is missing expected H atoms. Skipping.
Residue LYS   82 is missing expected H atoms. Skipping.
Residue TYR   84 is missing expected H atoms. Skipping.
Residue VAL   85 is missing expected H atoms. Skipping.
Residue THR   87 is missing expected H atoms. Skipping.
Residue SER   93 is missing expected H atoms. Skipping.
Residue LYS   95 is missing expected H atoms. Skipping.
Residue THR  101 is missing expected H atoms. Skipping.
Residue THR  102 is missing expected H atoms. Skipping.
Residue LYS  106 is missing expected H atoms. Skipping.
Residue ILE  107 is missing expected H atoms. Skipping.
Residue VAL  108 is missing expected H atoms. Skipping.
Residue ILE  109 is missing expected H atoms. Skipping.
Residue LEU  112 is missing expected H atoms. Skipping.
Residue LEU  113 is missing expected H atoms. Skipping.
Residue LEU  117 is missing expected H atoms. Skipping.
Residue SER  120 is missing expected H atoms. Skipping.
Residue ILE  121 is missing expected H atoms. Skipping.
Residue SER  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue VAL  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue SER  127 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue TYR  130 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue SER  133 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  147 is missing expected H atoms. Skipping.
Residue LEU  150 is missing expected H atoms. Skipping.
Residue LEU  151 is missing expected H atoms. Skipping.
Residue MET  152 is missing expected H atoms. Skipping.
Residue MET  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue VAL  156 is missing expected H atoms. Skipping.
Residue SER  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue VAL  163 is missing expected H atoms. Skipping.
Residue MET  167 is missing expected H atoms. Skipping.
Residue VAL  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue THR  174 is missing expected H atoms. Skipping.
Residue VAL  177 is missing expected H atoms. Skipping.
Residue THR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue MET  182 is missing expected H atoms. Skipping.
Residue LEU  184 is missing expected H atoms. Skipping.
Residue VAL  185 is missing expected H atoms. Skipping.
Residue VAL  188 is missing expected H atoms. Skipping.
Residue ILE  189 is missing expected H atoms. Skipping.
Residue LEU  190 is missing expected H atoms. Skipping.
Residue MET  193 is missing expected H atoms. Skipping.
Residue TYR  194 is missing expected H atoms. Skipping.
Residue LYS  195 is missing expected H atoms. Skipping.
Residue ILE  196 is missing expected H atoms. Skipping.
Residue THR  198 is missing expected H atoms. Skipping.
Residue MET  199 is missing expected H atoms. Skipping.
Residue VAL  202 is missing expected H atoms. Skipping.
Residue TYR  203 is missing expected H atoms. Skipping.
Residue ILE  205 is missing expected H atoms. Skipping.
Residue THR  207 is missing expected H atoms. Skipping.
Residue SER  209 is missing expected H atoms. Skipping.
Residue VAL  212 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue THR  216 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue MET  221 is missing expected H atoms. Skipping.
Residue ILE  222 is missing expected H atoms. Skipping.
Residue MET  225 is missing expected H atoms. Skipping.
Residue LEU  228 is missing expected H atoms. Skipping.
Residue LYS  230 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue VAL  235 is missing expected H atoms. Skipping.
Residue LEU  236 is missing expected H atoms. Skipping.
Residue ILE  237 is missing expected H atoms. Skipping.
Residue VAL  240 is missing expected H atoms. Skipping.
Residue VAL  241 is missing expected H atoms. Skipping.
Residue THR  245 is missing expected H atoms. Skipping.
Residue VAL  249 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue ILE  254 is missing expected H atoms. Skipping.
Residue THR  259 is missing expected H atoms. Skipping.
Residue SER  260 is missing expected H atoms. Skipping.
Residue SER  262 is missing expected H atoms. Skipping.
Residue LYS  265 is missing expected H atoms. Skipping.
Residue MET  266 is missing expected H atoms. Skipping.
Residue VAL  268 is missing expected H atoms. Skipping.
Residue LEU  269 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue VAL  272 is missing expected H atoms. Skipping.
Residue THR  273 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue VAL  276 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue MET  283 is missing expected H atoms. Skipping.
Residue VAL  284 is missing expected H atoms. Skipping.
Residue SER  285 is missing expected H atoms. Skipping.
Residue SER  286 is missing expected H atoms. Skipping.
Residue MET  287 is missing expected H atoms. Skipping.
Residue ILE  290 is missing expected H atoms. Skipping.
Residue LEU  291 is missing expected H atoms. Skipping.
Residue ILE  293 is missing expected H atoms. Skipping.
Residue VAL  294 is missing expected H atoms. Skipping.
Residue THR  297 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue THR  299 is missing expected H atoms. Skipping.
Residue SER  301 is missing expected H atoms. Skipping.
Residue TYR  305 is missing expected H atoms. Skipping.
Residue VAL  306 is missing expected H atoms. Skipping.
Residue THR  308 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue VAL  333 is missing expected H atoms. Skipping.
Residue SER  335 is missing expected H atoms. Skipping.
Residue ILE  336 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  344 is missing expected H atoms. Skipping.
Residue SER  347 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LYS  350 is missing expected H atoms. Skipping.
Residue SER  351 is missing expected H atoms. Skipping.
Residue THR  352 is missing expected H atoms. Skipping.
Residue VAL  353 is missing expected H atoms. Skipping.
Residue LYS  354 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LEU  357 is missing expected H atoms. Skipping.
Residue LEU  360 is missing expected H atoms. Skipping.
Residue ILE  361 is missing expected H atoms. Skipping.
Residue TYR  362 is missing expected H atoms. Skipping.
Residue TYR  363 is missing expected H atoms. Skipping.
Residue ILE  364 is missing expected H atoms. Skipping.
Residue ILE  365 is missing expected H atoms. Skipping.
Residue LEU  366 is missing expected H atoms. Skipping.
Residue TYR  367 is missing expected H atoms. Skipping.
Residue MET  368 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue THR  371 is missing expected H atoms. Skipping.
Residue ILE  375 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue VAL  377 is missing expected H atoms. Skipping.
Residue THR  379 is missing expected H atoms. Skipping.
Residue VAL  386 is missing expected H atoms. Skipping.
Residue THR  393 is missing expected H atoms. Skipping.
Residue SER  395 is missing expected H atoms. Skipping.
Residue TYR  396 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue VAL  398 is missing expected H atoms. Skipping.
Residue ILE  400 is missing expected H atoms. Skipping.
Residue LEU  405 is missing expected H atoms. Skipping.
Residue LEU  406 is missing expected H atoms. Skipping.
Residue LEU  407 is missing expected H atoms. Skipping.
Residue VAL  409 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue SER  417 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue THR  426 is missing expected H atoms. Skipping.
Residue LEU  429 is missing expected H atoms. Skipping.
Residue THR  435 is missing expected H atoms. Skipping.
Residue LYS  436 is missing expected H atoms. Skipping.
Residue SER  438 is missing expected H atoms. Skipping.
Residue THR  440 is missing expected H atoms. Skipping.
Residue LYS  445 is missing expected H atoms. Skipping.
Residue ILE  446 is missing expected H atoms. Skipping.
Residue MET  451 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue LEU  454 is missing expected H atoms. Skipping.
Residue SER  456 is missing expected H atoms. Skipping.
Residue VAL  457 is missing expected H atoms. Skipping.
Residue LYS  458 is missing expected H atoms. Skipping.
Residue ILE  460 is missing expected H atoms. Skipping.
Residue ILE  461 is missing expected H atoms. Skipping.
Residue THR  462 is missing expected H atoms. Skipping.
Residue SER  464 is missing expected H atoms. Skipping.
Residue VAL  465 is missing expected H atoms. Skipping.
Residue LYS  466 is missing expected H atoms. Skipping.
Residue ILE  470 is missing expected H atoms. Skipping.
Residue MET  474 is missing expected H atoms. Skipping.
Residue LEU  478 is missing expected H atoms. Skipping.
Residue THR  479 is missing expected H atoms. Skipping.
Residue VAL  481 is missing expected H atoms. Skipping.
Residue ILE  482 is missing expected H atoms. Skipping.
Residue LEU  483 is missing expected H atoms. Skipping.
Residue LEU  486 is missing expected H atoms. Skipping.
Residue LEU  488 is missing expected H atoms. Skipping.
Residue SER  489 is missing expected H atoms. Skipping.
Residue VAL  490 is missing expected H atoms. Skipping.
Residue SER  491 is missing expected H atoms. Skipping.
Residue LEU  494 is missing expected H atoms. Skipping.
Residue LEU  495 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  503 is missing expected H atoms. Skipping.
Residue THR  506 is missing expected H atoms. Skipping.
Residue VAL  507 is missing expected H atoms. Skipping.
Residue MET  509 is missing expected H atoms. Skipping.
Residue SER  510 is missing expected H atoms. Skipping.
Residue LEU  513 is missing expected H atoms. Skipping.
Residue ILE  514 is missing expected H atoms. Skipping.
Residue LEU  518 is missing expected H atoms. Skipping.
Residue THR  521 is missing expected H atoms. Skipping.
Residue VAL  522 is missing expected H atoms. Skipping.
Residue SER  523 is missing expected H atoms. Skipping.
Residue LEU  525 is missing expected H atoms. Skipping.
Residue THR  528 is missing expected H atoms. Skipping.
Residue SER  532 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  535 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  538 is missing expected H atoms. Skipping.
Residue ILE  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LEU  548 is missing expected H atoms. Skipping.
Residue LYS  549 is missing expected H atoms. Skipping.
Residue VAL  550 is missing expected H atoms. Skipping.
Residue SER  551 is missing expected H atoms. Skipping.
Residue SER  553 is missing expected H atoms. Skipping.
Residue THR  554 is missing expected H atoms. Skipping.
Residue VAL  556 is missing expected H atoms. Skipping.
Residue LEU  557 is missing expected H atoms. Skipping.
Residue LEU  561 is missing expected H atoms. Skipping.
Residue SER  563 is missing expected H atoms. Skipping.
Residue ILE  564 is missing expected H atoms. Skipping.
Residue LEU  565 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue LEU  571 is missing expected H atoms. Skipping.
Residue SER  576 is missing expected H atoms. Skipping.
Residue SER  577 is missing expected H atoms. Skipping.
Residue VAL  579 is missing expected H atoms. Skipping.
Residue LEU  580 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue VAL  583 is missing expected H atoms. Skipping.
Residue MET  584 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue LEU  587 is missing expected H atoms. Skipping.
Residue ILE  589 is missing expected H atoms. Skipping.
Residue VAL  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue VAL  593 is missing expected H atoms. Skipping.
Residue THR  598 is missing expected H atoms. Skipping.
Residue SER  600 is missing expected H atoms. Skipping.
Residue MET  601 is missing expected H atoms. Skipping.
Residue SER  603 is missing expected H atoms. Skipping.
Residue LYS  604 is missing expected H atoms. Skipping.
Residue ILE  605 is missing expected H atoms. Skipping.
Residue THR  609 is missing expected H atoms. Skipping.
Residue ILE  610 is missing expected H atoms. Skipping.
Residue ILE  612 is missing expected H atoms. Skipping.
Residue LEU  614 is missing expected H atoms. Skipping.
Residue LYS  615 is missing expected H atoms. Skipping.
Residue LEU  995 is missing expected H atoms. Skipping.
Residue LYS  996 is missing expected H atoms. Skipping.
Residue LEU  999 is missing expected H atoms. Skipping.
Residue TYR 1000 is missing expected H atoms. Skipping.
Residue ILE 1002 is missing expected H atoms. Skipping.
Residue LEU 1004 is missing expected H atoms. Skipping.
Residue TYR 1007 is missing expected H atoms. Skipping.
Residue LEU 1008 is missing expected H atoms. Skipping.
Residue THR 1009 is missing expected H atoms. Skipping.
Residue LEU 1012 is missing expected H atoms. Skipping.
Residue TYR 1021 is missing expected H atoms. Skipping.
Residue ILE 1022 is missing expected H atoms. Skipping.
Residue MET 1023 is missing expected H atoms. Skipping.
Residue SER 1025 is missing expected H atoms. Skipping.
Residue LEU 1028 is missing expected H atoms. Skipping.
Residue VAL 1035 is missing expected H atoms. Skipping.
Residue LEU 1036 is missing expected H atoms. Skipping.
Residue THR 1038 is missing expected H atoms. Skipping.
Residue ILE 1039 is missing expected H atoms. Skipping.
Residue VAL   72 is missing expected H atoms. Skipping.
Residue SER   73 is missing expected H atoms. Skipping.
Residue SER   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue THR   77 is missing expected H atoms. Skipping.
Residue VAL   72 is missing expected H atoms. Skipping.
Residue SER   73 is missing expected H atoms. Skipping.
Residue SER   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue THR   77 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  143 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue VAL  147 is missing expected H atoms. Skipping.
Residue MET  149 is missing expected H atoms. Skipping.
Residue ILE  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue VAL  162 is missing expected H atoms. Skipping.
Residue TYR  166 is missing expected H atoms. Skipping.
Residue ILE  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LEU  174 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  143 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue VAL  147 is missing expected H atoms. Skipping.
Residue MET  149 is missing expected H atoms. Skipping.
Residue ILE  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue VAL  162 is missing expected H atoms. Skipping.
Residue TYR  166 is missing expected H atoms. Skipping.
Residue ILE  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LEU  174 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue VAL  182 is missing expected H atoms. Skipping.
Residue LYS  183 is missing expected H atoms. Skipping.
Evaluate side-chains
  687 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 616
  time to evaluate  : 0.846 
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
   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: A  699 GLN cc_start: 0.6801 (mm-40) cc_final: 0.6239 (mm110)
REVERT: A  705 ASP cc_start: 0.7403 (t0) cc_final: 0.7091 (t0)
REVERT: A  742 TYR cc_start: 0.5185 (m-80) cc_final: 0.4342 (m-10)
REVERT: A  757 GLU cc_start: 0.6760 (pm20) cc_final: 0.6344 (pm20)
REVERT: A  777 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7759 (mt-10)
REVERT: A  815 THR cc_start: 0.6554 (m) cc_final: 0.5992 (p)
REVERT: A  821 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6553 (mm)
REVERT: A  843 TRP cc_start: 0.6475 (t60) cc_final: 0.6269 (t60)
REVERT: A  846 ARG cc_start: 0.8561 (ttm110) cc_final: 0.8333 (ttm110)
REVERT: B  149 MET cc_start: 0.5706 (mtp) cc_final: 0.5234 (mtp)
REVERT: B  190 MET cc_start: 0.7301 (tmm) cc_final: 0.7095 (tmm)
REVERT: C  146 GLN cc_start: 0.6248 (mp10) cc_final: 0.5925 (mp10)
REVERT: C  169 ILE cc_start: 0.7710 (tp) cc_final: 0.7467 (tp)
REVERT: F  114 ARG cc_start: 0.7648 (mmm-85) cc_final: 0.7328 (mtp85)
REVERT: F  241 GLU cc_start: 0.6430 (pp20) cc_final: 0.5997 (pp20)
REVERT: O  133 LEU cc_start: 0.7555 (mp) cc_final: 0.7264 (mt)
REVERT: O  175 LYS cc_start: 0.8705 (ttmt) cc_final: 0.8472 (ttmm)
REVERT: O  180 ASP cc_start: 0.7437 (p0) cc_final: 0.7127 (p0)
REVERT: O  212 CYS cc_start: 0.7237 (p) cc_final: 0.6991 (p)
REVERT: P    8 ARG cc_start: 0.7519 (ttm110) cc_final: 0.7144 (ttm-80)
REVERT: P   70 GLU cc_start: 0.7671 (tt0) cc_final: 0.7450 (tt0)
REVERT: P  178 ASP cc_start: 0.7012 (m-30) cc_final: 0.6660 (t0)
REVERT: P  181 GLU cc_start: 0.7372 (tp30) cc_final: 0.7108 (tp30)
REVERT: P  231 LYS cc_start: 0.8016 (tttt) cc_final: 0.7726 (mtpp)
REVERT: P  236 LEU cc_start: 0.7472 (mp) cc_final: 0.7239 (mp)
REVERT: P  237 ILE cc_start: 0.7977 (mt) cc_final: 0.7773 (tt)
REVERT: P  239 LYS cc_start: 0.6365 (OUTLIER) cc_final: 0.6144 (mtpp)
REVERT: Q   23 GLN cc_start: 0.7323 (tm-30) cc_final: 0.7088 (tm-30)
REVERT: Q   45 VAL cc_start: 0.7617 (OUTLIER) cc_final: 0.7305 (t)
REVERT: Q   62 ILE cc_start: 0.7478 (OUTLIER) cc_final: 0.6977 (mt)
REVERT: Q   99 GLU cc_start: 0.7860 (mp0) cc_final: 0.7626 (mp0)
REVERT: R  111 SER cc_start: 0.8004 (m) cc_final: 0.7602 (m)
REVERT: R  118 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7800 (t0)
REVERT: R  133 MET cc_start: 0.7096 (mmt) cc_final: 0.6617 (mmt)
REVERT: R  141 LEU cc_start: 0.7878 (mt) cc_final: 0.7660 (mp)
REVERT: R  156 MET cc_start: 0.7596 (tmm) cc_final: 0.7383 (tmm)
REVERT: R  197 SER cc_start: 0.8881 (t) cc_final: 0.8467 (m)
REVERT: S  144 ILE cc_start: 0.6775 (OUTLIER) cc_final: 0.6424 (tt)
REVERT: S  153 TYR cc_start: 0.7976 (p90) cc_final: 0.7474 (p90)
  outliers start: 71
  outliers final: 39
  residues processed: 654
  average time/residue: 0.3729
  time to fit residues: 354.3660
Evaluate side-chains
  614 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 569
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  821 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  928 VAL
Chi-restraints excluded: chain C residue  166 TYR
Chi-restraints excluded: chain F residue   17 ASP
Chi-restraints excluded: chain F residue   56 LYS
Chi-restraints excluded: chain F residue  123 THR
Chi-restraints excluded: chain F residue  156 VAL
Chi-restraints excluded: chain F residue  199 ILE
Chi-restraints excluded: chain F residue  244 LYS
Chi-restraints excluded: chain G residue    6 SER
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue  126 THR
Chi-restraints excluded: chain G residue  181 LYS
Chi-restraints excluded: chain G residue  211 LYS
Chi-restraints excluded: chain G residue  240 VAL
Chi-restraints excluded: chain O residue   28 VAL
Chi-restraints excluded: chain O residue  126 VAL
Chi-restraints excluded: chain O residue  151 SER
Chi-restraints excluded: chain O residue  224 GLU
Chi-restraints excluded: chain P residue    9 THR
Chi-restraints excluded: chain P residue   11 ILE
Chi-restraints excluded: chain P residue   54 LYS
Chi-restraints excluded: chain P residue  134 LEU
Chi-restraints excluded: chain P residue  239 LYS
Chi-restraints excluded: chain Q residue   45 VAL
Chi-restraints excluded: chain Q residue   58 THR
Chi-restraints excluded: chain Q residue   62 ILE
Chi-restraints excluded: chain Q residue   98 VAL
Chi-restraints excluded: chain Q residue  129 ILE
Chi-restraints excluded: chain Q residue  147 THR
Chi-restraints excluded: chain Q residue  191 VAL
Chi-restraints excluded: chain R residue   35 SER
Chi-restraints excluded: chain R residue   43 SER
Chi-restraints excluded: chain R residue   47 CYS
Chi-restraints excluded: chain R residue   74 ILE
Chi-restraints excluded: chain R residue  113 THR
Chi-restraints excluded: chain R residue  118 ASN
Chi-restraints excluded: chain S residue    9 ASP
Chi-restraints excluded: chain S residue   38 LEU
Chi-restraints excluded: chain S residue   53 GLN
Chi-restraints excluded: chain S residue  144 ILE
Chi-restraints excluded: chain S residue  177 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 283
   random chunks:
   chunk 183 optimal weight:    1.9990
   chunk 196 optimal weight:    2.9990
   chunk 215 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 234 optimal weight:    1.9990
   chunk 246 optimal weight:    0.9990
   chunk 180 optimal weight:    0.8980
   chunk 266 optimal weight:    0.9990
   chunk 193 optimal weight:    1.9990
   chunk 94 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0070
   overall best weight:    0.6800

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

Flipped N/Q/H residues before XYZ refinement:
A 803 GLN
A 910 ASN
D  84 ASN
G  92 GLN
G 224 ASN
O 147 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.147207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.118001 restraints weight = 86013.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 1.78
r_work: 0.3363 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3241 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3231
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       39 |
|-----------------------------------------------------------------------------|
r_final: 0.3230
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7182
moved from start:          0.5122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.093  20809  Z= 0.156
  Angle     :  0.550   6.205  28272  Z= 0.295
  Chirality :  0.040   0.152   3307
  Planarity :  0.005   0.073   3731
  Dihedral  :  4.891  48.281   3076
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 21.88 %
    Favored  : 74.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.46 (0.16), residues: 2833
  helix:  2.00 (0.14), residues: 1554
  sheet: -0.54 (0.27), residues: 350
  loop : -0.09 (0.21), residues: 929

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG F 187 
 TYR   0.017   0.001   TYR P 143 
 PHE   0.014   0.001   PHE R 226 
 TRP   0.011   0.001   TRP Q 156 
 HIS   0.007   0.001   HIS B 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (20809)
  covalent geometry    : angle       0.54981 (28272)
  hydrogen bonds       : bond        0.04327 ( 1327)
  hydrogen bonds       : angle       4.15699 ( 3822)

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

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

  5666 Ramachandran restraints generated.
    2833 Oldfield, 0 Emsley, 2833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5666 Ramachandran restraints generated.
    2833 Oldfield, 0 Emsley, 2833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL   17 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue VAL   26 is missing expected H atoms. Skipping.
Residue THR   28 is missing expected H atoms. Skipping.
Residue LEU   29 is missing expected H atoms. Skipping.
Residue THR   30 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue LEU   33 is missing expected H atoms. Skipping.
Residue SER   34 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue VAL   39 is missing expected H atoms. Skipping.
Residue ILE   47 is missing expected H atoms. Skipping.
Residue LYS   48 is missing expected H atoms. Skipping.
Residue VAL   49 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue VAL   52 is missing expected H atoms. Skipping.
Residue THR   53 is missing expected H atoms. Skipping.
Residue VAL   58 is missing expected H atoms. Skipping.
Residue LEU   60 is missing expected H atoms. Skipping.
Residue LEU   63 is missing expected H atoms. Skipping.
Residue THR   64 is missing expected H atoms. Skipping.
Residue VAL   65 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ILE   73 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue SER   78 is missing expected H atoms. Skipping.
Residue VAL   79 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue LEU   81 is missing expected H atoms. Skipping.
Residue LYS   82 is missing expected H atoms. Skipping.
Residue TYR   84 is missing expected H atoms. Skipping.
Residue VAL   85 is missing expected H atoms. Skipping.
Residue THR   87 is missing expected H atoms. Skipping.
Residue SER   93 is missing expected H atoms. Skipping.
Residue LYS   95 is missing expected H atoms. Skipping.
Residue THR  101 is missing expected H atoms. Skipping.
Residue THR  102 is missing expected H atoms. Skipping.
Residue LYS  106 is missing expected H atoms. Skipping.
Residue ILE  107 is missing expected H atoms. Skipping.
Residue VAL  108 is missing expected H atoms. Skipping.
Residue ILE  109 is missing expected H atoms. Skipping.
Residue LEU  112 is missing expected H atoms. Skipping.
Residue LEU  113 is missing expected H atoms. Skipping.
Residue LEU  117 is missing expected H atoms. Skipping.
Residue SER  120 is missing expected H atoms. Skipping.
Residue ILE  121 is missing expected H atoms. Skipping.
Residue SER  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue VAL  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue SER  127 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue TYR  130 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue SER  133 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  147 is missing expected H atoms. Skipping.
Residue LEU  150 is missing expected H atoms. Skipping.
Residue LEU  151 is missing expected H atoms. Skipping.
Residue MET  152 is missing expected H atoms. Skipping.
Residue MET  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue VAL  156 is missing expected H atoms. Skipping.
Residue SER  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue VAL  163 is missing expected H atoms. Skipping.
Residue MET  167 is missing expected H atoms. Skipping.
Residue VAL  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue THR  174 is missing expected H atoms. Skipping.
Residue VAL  177 is missing expected H atoms. Skipping.
Residue THR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue MET  182 is missing expected H atoms. Skipping.
Residue LEU  184 is missing expected H atoms. Skipping.
Residue VAL  185 is missing expected H atoms. Skipping.
Residue VAL  188 is missing expected H atoms. Skipping.
Residue ILE  189 is missing expected H atoms. Skipping.
Residue LEU  190 is missing expected H atoms. Skipping.
Residue MET  193 is missing expected H atoms. Skipping.
Residue TYR  194 is missing expected H atoms. Skipping.
Residue LYS  195 is missing expected H atoms. Skipping.
Residue ILE  196 is missing expected H atoms. Skipping.
Residue THR  198 is missing expected H atoms. Skipping.
Residue MET  199 is missing expected H atoms. Skipping.
Residue VAL  202 is missing expected H atoms. Skipping.
Residue TYR  203 is missing expected H atoms. Skipping.
Residue ILE  205 is missing expected H atoms. Skipping.
Residue THR  207 is missing expected H atoms. Skipping.
Residue SER  209 is missing expected H atoms. Skipping.
Residue VAL  212 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue THR  216 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue MET  221 is missing expected H atoms. Skipping.
Residue ILE  222 is missing expected H atoms. Skipping.
Residue MET  225 is missing expected H atoms. Skipping.
Residue LEU  228 is missing expected H atoms. Skipping.
Residue LYS  230 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue VAL  235 is missing expected H atoms. Skipping.
Residue LEU  236 is missing expected H atoms. Skipping.
Residue ILE  237 is missing expected H atoms. Skipping.
Residue VAL  240 is missing expected H atoms. Skipping.
Residue VAL  241 is missing expected H atoms. Skipping.
Residue THR  245 is missing expected H atoms. Skipping.
Residue VAL  249 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue ILE  254 is missing expected H atoms. Skipping.
Residue THR  259 is missing expected H atoms. Skipping.
Residue SER  260 is missing expected H atoms. Skipping.
Residue SER  262 is missing expected H atoms. Skipping.
Residue LYS  265 is missing expected H atoms. Skipping.
Residue MET  266 is missing expected H atoms. Skipping.
Residue VAL  268 is missing expected H atoms. Skipping.
Residue LEU  269 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue VAL  272 is missing expected H atoms. Skipping.
Residue THR  273 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue VAL  276 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue MET  283 is missing expected H atoms. Skipping.
Residue VAL  284 is missing expected H atoms. Skipping.
Residue SER  285 is missing expected H atoms. Skipping.
Residue SER  286 is missing expected H atoms. Skipping.
Residue MET  287 is missing expected H atoms. Skipping.
Residue ILE  290 is missing expected H atoms. Skipping.
Residue LEU  291 is missing expected H atoms. Skipping.
Residue ILE  293 is missing expected H atoms. Skipping.
Residue VAL  294 is missing expected H atoms. Skipping.
Residue THR  297 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue THR  299 is missing expected H atoms. Skipping.
Residue SER  301 is missing expected H atoms. Skipping.
Residue TYR  305 is missing expected H atoms. Skipping.
Residue VAL  306 is missing expected H atoms. Skipping.
Residue THR  308 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue VAL  333 is missing expected H atoms. Skipping.
Residue SER  335 is missing expected H atoms. Skipping.
Residue ILE  336 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  344 is missing expected H atoms. Skipping.
Residue SER  347 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LYS  350 is missing expected H atoms. Skipping.
Residue SER  351 is missing expected H atoms. Skipping.
Residue THR  352 is missing expected H atoms. Skipping.
Residue VAL  353 is missing expected H atoms. Skipping.
Residue LYS  354 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LEU  357 is missing expected H atoms. Skipping.
Residue LEU  360 is missing expected H atoms. Skipping.
Residue ILE  361 is missing expected H atoms. Skipping.
Residue TYR  362 is missing expected H atoms. Skipping.
Residue TYR  363 is missing expected H atoms. Skipping.
Residue ILE  364 is missing expected H atoms. Skipping.
Residue ILE  365 is missing expected H atoms. Skipping.
Residue LEU  366 is missing expected H atoms. Skipping.
Residue TYR  367 is missing expected H atoms. Skipping.
Residue MET  368 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue THR  371 is missing expected H atoms. Skipping.
Residue ILE  375 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue VAL  377 is missing expected H atoms. Skipping.
Residue THR  379 is missing expected H atoms. Skipping.
Residue VAL  386 is missing expected H atoms. Skipping.
Residue THR  393 is missing expected H atoms. Skipping.
Residue SER  395 is missing expected H atoms. Skipping.
Residue TYR  396 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue VAL  398 is missing expected H atoms. Skipping.
Residue ILE  400 is missing expected H atoms. Skipping.
Residue LEU  405 is missing expected H atoms. Skipping.
Residue LEU  406 is missing expected H atoms. Skipping.
Residue LEU  407 is missing expected H atoms. Skipping.
Residue VAL  409 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue SER  417 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue THR  426 is missing expected H atoms. Skipping.
Residue LEU  429 is missing expected H atoms. Skipping.
Residue THR  435 is missing expected H atoms. Skipping.
Residue LYS  436 is missing expected H atoms. Skipping.
Residue SER  438 is missing expected H atoms. Skipping.
Residue THR  440 is missing expected H atoms. Skipping.
Residue LYS  445 is missing expected H atoms. Skipping.
Residue ILE  446 is missing expected H atoms. Skipping.
Residue MET  451 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue LEU  454 is missing expected H atoms. Skipping.
Residue SER  456 is missing expected H atoms. Skipping.
Residue VAL  457 is missing expected H atoms. Skipping.
Residue LYS  458 is missing expected H atoms. Skipping.
Residue ILE  460 is missing expected H atoms. Skipping.
Residue ILE  461 is missing expected H atoms. Skipping.
Residue THR  462 is missing expected H atoms. Skipping.
Residue SER  464 is missing expected H atoms. Skipping.
Residue VAL  465 is missing expected H atoms. Skipping.
Residue LYS  466 is missing expected H atoms. Skipping.
Residue ILE  470 is missing expected H atoms. Skipping.
Residue MET  474 is missing expected H atoms. Skipping.
Residue LEU  478 is missing expected H atoms. Skipping.
Residue THR  479 is missing expected H atoms. Skipping.
Residue VAL  481 is missing expected H atoms. Skipping.
Residue ILE  482 is missing expected H atoms. Skipping.
Residue LEU  483 is missing expected H atoms. Skipping.
Residue LEU  486 is missing expected H atoms. Skipping.
Residue LEU  488 is missing expected H atoms. Skipping.
Residue SER  489 is missing expected H atoms. Skipping.
Residue VAL  490 is missing expected H atoms. Skipping.
Residue SER  491 is missing expected H atoms. Skipping.
Residue LEU  494 is missing expected H atoms. Skipping.
Residue LEU  495 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  503 is missing expected H atoms. Skipping.
Residue THR  506 is missing expected H atoms. Skipping.
Residue VAL  507 is missing expected H atoms. Skipping.
Residue MET  509 is missing expected H atoms. Skipping.
Residue SER  510 is missing expected H atoms. Skipping.
Residue LEU  513 is missing expected H atoms. Skipping.
Residue ILE  514 is missing expected H atoms. Skipping.
Residue LEU  518 is missing expected H atoms. Skipping.
Residue THR  521 is missing expected H atoms. Skipping.
Residue VAL  522 is missing expected H atoms. Skipping.
Residue SER  523 is missing expected H atoms. Skipping.
Residue LEU  525 is missing expected H atoms. Skipping.
Residue THR  528 is missing expected H atoms. Skipping.
Residue SER  532 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  535 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  538 is missing expected H atoms. Skipping.
Residue ILE  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LEU  548 is missing expected H atoms. Skipping.
Residue LYS  549 is missing expected H atoms. Skipping.
Residue VAL  550 is missing expected H atoms. Skipping.
Residue SER  551 is missing expected H atoms. Skipping.
Residue SER  553 is missing expected H atoms. Skipping.
Residue THR  554 is missing expected H atoms. Skipping.
Residue VAL  556 is missing expected H atoms. Skipping.
Residue LEU  557 is missing expected H atoms. Skipping.
Residue LEU  561 is missing expected H atoms. Skipping.
Residue SER  563 is missing expected H atoms. Skipping.
Residue ILE  564 is missing expected H atoms. Skipping.
Residue LEU  565 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue LEU  571 is missing expected H atoms. Skipping.
Residue SER  576 is missing expected H atoms. Skipping.
Residue SER  577 is missing expected H atoms. Skipping.
Residue VAL  579 is missing expected H atoms. Skipping.
Residue LEU  580 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue VAL  583 is missing expected H atoms. Skipping.
Residue MET  584 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue LEU  587 is missing expected H atoms. Skipping.
Residue ILE  589 is missing expected H atoms. Skipping.
Residue VAL  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue VAL  593 is missing expected H atoms. Skipping.
Residue THR  598 is missing expected H atoms. Skipping.
Residue SER  600 is missing expected H atoms. Skipping.
Residue MET  601 is missing expected H atoms. Skipping.
Residue SER  603 is missing expected H atoms. Skipping.
Residue LYS  604 is missing expected H atoms. Skipping.
Residue ILE  605 is missing expected H atoms. Skipping.
Residue THR  609 is missing expected H atoms. Skipping.
Residue ILE  610 is missing expected H atoms. Skipping.
Residue ILE  612 is missing expected H atoms. Skipping.
Residue LEU  614 is missing expected H atoms. Skipping.
Residue LYS  615 is missing expected H atoms. Skipping.
Residue LEU  995 is missing expected H atoms. Skipping.
Residue LYS  996 is missing expected H atoms. Skipping.
Residue LEU  999 is missing expected H atoms. Skipping.
Residue TYR 1000 is missing expected H atoms. Skipping.
Residue ILE 1002 is missing expected H atoms. Skipping.
Residue LEU 1004 is missing expected H atoms. Skipping.
Residue TYR 1007 is missing expected H atoms. Skipping.
Residue LEU 1008 is missing expected H atoms. Skipping.
Residue THR 1009 is missing expected H atoms. Skipping.
Residue LEU 1012 is missing expected H atoms. Skipping.
Residue TYR 1021 is missing expected H atoms. Skipping.
Residue ILE 1022 is missing expected H atoms. Skipping.
Residue MET 1023 is missing expected H atoms. Skipping.
Residue SER 1025 is missing expected H atoms. Skipping.
Residue LEU 1028 is missing expected H atoms. Skipping.
Residue VAL 1035 is missing expected H atoms. Skipping.
Residue LEU 1036 is missing expected H atoms. Skipping.
Residue THR 1038 is missing expected H atoms. Skipping.
Residue ILE 1039 is missing expected H atoms. Skipping.
Residue VAL   72 is missing expected H atoms. Skipping.
Residue SER   73 is missing expected H atoms. Skipping.
Residue SER   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue THR   77 is missing expected H atoms. Skipping.
Residue VAL   72 is missing expected H atoms. Skipping.
Residue SER   73 is missing expected H atoms. Skipping.
Residue SER   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue THR   77 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  143 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue VAL  147 is missing expected H atoms. Skipping.
Residue MET  149 is missing expected H atoms. Skipping.
Residue ILE  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue VAL  162 is missing expected H atoms. Skipping.
Residue TYR  166 is missing expected H atoms. Skipping.
Residue ILE  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LEU  174 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  143 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue VAL  147 is missing expected H atoms. Skipping.
Residue MET  149 is missing expected H atoms. Skipping.
Residue ILE  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue VAL  162 is missing expected H atoms. Skipping.
Residue TYR  166 is missing expected H atoms. Skipping.
Residue ILE  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LEU  174 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue VAL  182 is missing expected H atoms. Skipping.
Residue LYS  183 is missing expected H atoms. Skipping.
Evaluate side-chains
  650 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 588
  time to evaluate  : 1.081 
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
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  705 ASP cc_start: 0.7506 (t0) cc_final: 0.7306 (t0)
REVERT: A  710 MET cc_start: 0.7807 (mtm) cc_final: 0.7554 (mtm)
REVERT: A  757 GLU cc_start: 0.6667 (pm20) cc_final: 0.6223 (pm20)
REVERT: A  777 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7746 (mt-10)
REVERT: A  821 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6559 (mm)
REVERT: A  842 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7318 (mm-30)
REVERT: A  846 ARG cc_start: 0.8516 (ttm110) cc_final: 0.8235 (ttm110)
REVERT: B  149 MET cc_start: 0.5607 (mtp) cc_final: 0.5173 (mtp)
REVERT: B  188 GLN cc_start: 0.7571 (tp40) cc_final: 0.7144 (tp40)
REVERT: B  190 MET cc_start: 0.7387 (tmm) cc_final: 0.7150 (tmm)
REVERT: C  146 GLN cc_start: 0.6345 (mp10) cc_final: 0.6056 (mp10)
REVERT: F   42 LYS cc_start: 0.8156 (tttp) cc_final: 0.7814 (tttp)
REVERT: F   51 LYS cc_start: 0.6791 (ttmm) cc_final: 0.6489 (mtpp)
REVERT: F  114 ARG cc_start: 0.7881 (mmm-85) cc_final: 0.7565 (mtp85)
REVERT: F  236 GLU cc_start: 0.7151 (tt0) cc_final: 0.6917 (mt-10)
REVERT: F  241 GLU cc_start: 0.6502 (pp20) cc_final: 0.6050 (pp20)
REVERT: G  117 ARG cc_start: 0.7627 (mmm-85) cc_final: 0.7373 (mmm160)
REVERT: G  118 ILE cc_start: 0.7331 (mm) cc_final: 0.7076 (mt)
REVERT: O   70 HIS cc_start: 0.7814 (p-80) cc_final: 0.7402 (p-80)
REVERT: O  100 TYR cc_start: 0.7940 (m-10) cc_final: 0.7724 (m-10)
REVERT: O  109 LEU cc_start: 0.7214 (tt) cc_final: 0.6828 (tp)
REVERT: O  133 LEU cc_start: 0.7949 (mp) cc_final: 0.7669 (mp)
REVERT: O  175 LYS cc_start: 0.8827 (ttmt) cc_final: 0.8595 (ttmm)
REVERT: O  180 ASP cc_start: 0.7119 (p0) cc_final: 0.6907 (p0)
REVERT: P    8 ARG cc_start: 0.7493 (ttm110) cc_final: 0.7281 (ttm-80)
REVERT: P   15 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6517 (mt-10)
REVERT: P   19 TYR cc_start: 0.8242 (m-10) cc_final: 0.7895 (m-10)
REVERT: P  153 SER cc_start: 0.7581 (p) cc_final: 0.7217 (t)
REVERT: P  166 ASN cc_start: 0.7929 (t0) cc_final: 0.7572 (t0)
REVERT: P  178 ASP cc_start: 0.7366 (m-30) cc_final: 0.7052 (t0)
REVERT: P  181 GLU cc_start: 0.7833 (tp30) cc_final: 0.7506 (tp30)
REVERT: P  231 LYS cc_start: 0.8214 (tttt) cc_final: 0.7968 (mtpp)
REVERT: P  232 GLU cc_start: 0.6778 (mm-30) cc_final: 0.6564 (mp0)
REVERT: P  234 GLU cc_start: 0.7587 (tp30) cc_final: 0.7263 (tp30)
REVERT: P  239 LYS cc_start: 0.6448 (OUTLIER) cc_final: 0.6206 (mtpp)
REVERT: Q   66 ASP cc_start: 0.7673 (t70) cc_final: 0.7385 (t0)
REVERT: Q   67 ASP cc_start: 0.8152 (m-30) cc_final: 0.7823 (m-30)
REVERT: Q  124 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7536 (mtt90)
REVERT: Q  143 ARG cc_start: 0.7789 (mtp85) cc_final: 0.7587 (mtp85)
REVERT: Q  197 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7210 (mt-10)
REVERT: Q  225 ILE cc_start: 0.7586 (mt) cc_final: 0.7366 (mm)
REVERT: R  111 SER cc_start: 0.8017 (m) cc_final: 0.7798 (t)
REVERT: R  133 MET cc_start: 0.7547 (mmt) cc_final: 0.7276 (mmt)
REVERT: R  156 MET cc_start: 0.7637 (tmm) cc_final: 0.7322 (tmm)
REVERT: R  170 ILE cc_start: 0.7764 (tp) cc_final: 0.7558 (tp)
REVERT: R  192 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8128 (mtpp)
REVERT: R  197 SER cc_start: 0.9035 (t) cc_final: 0.8746 (m)
REVERT: S   35 THR cc_start: 0.7973 (p) cc_final: 0.7738 (p)
REVERT: S   80 ASP cc_start: 0.7605 (m-30) cc_final: 0.7319 (m-30)
REVERT: S  144 ILE cc_start: 0.7072 (OUTLIER) cc_final: 0.6771 (tt)
  outliers start: 62
  outliers final: 44
  residues processed: 609
  average time/residue: 0.3631
  time to fit residues: 321.5392
Evaluate side-chains
  621 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 572
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain A residue  814 HIS
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  821 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain C residue  166 TYR
Chi-restraints excluded: chain F residue   55 SER
Chi-restraints excluded: chain F residue  119 VAL
Chi-restraints excluded: chain F residue  123 THR
Chi-restraints excluded: chain F residue  156 VAL
Chi-restraints excluded: chain F residue  244 LYS
Chi-restraints excluded: chain G residue    6 SER
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue  108 GLU
Chi-restraints excluded: chain G residue  192 GLU
Chi-restraints excluded: chain G residue  211 LYS
Chi-restraints excluded: chain G residue  235 ILE
Chi-restraints excluded: chain G residue  240 VAL
Chi-restraints excluded: chain O residue   28 VAL
Chi-restraints excluded: chain O residue   50 LYS
Chi-restraints excluded: chain O residue  126 VAL
Chi-restraints excluded: chain O residue  224 GLU
Chi-restraints excluded: chain P residue    9 THR
Chi-restraints excluded: chain P residue   11 ILE
Chi-restraints excluded: chain P residue   54 LYS
Chi-restraints excluded: chain P residue  239 LYS
Chi-restraints excluded: chain Q residue   58 THR
Chi-restraints excluded: chain Q residue   96 LEU
Chi-restraints excluded: chain Q residue  124 ARG
Chi-restraints excluded: chain Q residue  129 ILE
Chi-restraints excluded: chain Q residue  137 ASP
Chi-restraints excluded: chain Q residue  147 THR
Chi-restraints excluded: chain Q residue  191 VAL
Chi-restraints excluded: chain Q residue  206 ILE
Chi-restraints excluded: chain Q residue  207 GLU
Chi-restraints excluded: chain Q residue  219 ILE
Chi-restraints excluded: chain R residue   47 CYS
Chi-restraints excluded: chain R residue  165 CYS
Chi-restraints excluded: chain R residue  189 MET
Chi-restraints excluded: chain R residue  192 LYS
Chi-restraints excluded: chain R residue  238 ILE
Chi-restraints excluded: chain S residue   30 LYS
Chi-restraints excluded: chain S residue   38 LEU
Chi-restraints excluded: chain S residue   53 GLN
Chi-restraints excluded: chain S residue  144 ILE
Chi-restraints excluded: chain S residue  147 THR
Chi-restraints excluded: chain S residue  177 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 283
   random chunks:
   chunk 212 optimal weight:    0.6980
   chunk 226 optimal weight:    0.9980
   chunk 94 optimal weight:    2.9990
   chunk 207 optimal weight:    2.9990
   chunk 174 optimal weight:    0.9980
   chunk 59 optimal weight:    9.9990
   chunk 148 optimal weight:    0.9980
   chunk 27 optimal weight:    0.3980
   chunk 244 optimal weight:    1.9990
   chunk 10 optimal weight:   20.0000
   chunk 227 optimal weight:    0.3980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
O 165 ASN
P  53 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.146659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.117512 restraints weight = 86389.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 1.77
r_work: 0.3363 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3241 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3195
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       39 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
r_final: 0.3195
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.5952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070  20809  Z= 0.157
  Angle     :  0.534   6.019  28272  Z= 0.287
  Chirality :  0.039   0.168   3307
  Planarity :  0.004   0.042   3731
  Dihedral  :  4.817  48.489   3076
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 22.04 %
    Favored  : 74.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.53 (0.16), residues: 2833
  helix:  2.08 (0.14), residues: 1556
  sheet: -0.52 (0.26), residues: 351
  loop : -0.11 (0.21), residues: 926

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F 223 
 TYR   0.012   0.001   TYR B 200 
 PHE   0.016   0.001   PHE C 184 
 TRP   0.011   0.001   TRP P 139 
 HIS   0.007   0.001   HIS B 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (20809)
  covalent geometry    : angle       0.53414 (28272)
  hydrogen bonds       : bond        0.03696 ( 1327)
  hydrogen bonds       : angle       4.00314 ( 3822)

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

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

  5666 Ramachandran restraints generated.
    2833 Oldfield, 0 Emsley, 2833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5666 Ramachandran restraints generated.
    2833 Oldfield, 0 Emsley, 2833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL   17 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue VAL   26 is missing expected H atoms. Skipping.
Residue THR   28 is missing expected H atoms. Skipping.
Residue LEU   29 is missing expected H atoms. Skipping.
Residue THR   30 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue LEU   33 is missing expected H atoms. Skipping.
Residue SER   34 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue VAL   39 is missing expected H atoms. Skipping.
Residue ILE   47 is missing expected H atoms. Skipping.
Residue LYS   48 is missing expected H atoms. Skipping.
Residue VAL   49 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue VAL   52 is missing expected H atoms. Skipping.
Residue THR   53 is missing expected H atoms. Skipping.
Residue VAL   58 is missing expected H atoms. Skipping.
Residue LEU   60 is missing expected H atoms. Skipping.
Residue LEU   63 is missing expected H atoms. Skipping.
Residue THR   64 is missing expected H atoms. Skipping.
Residue VAL   65 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ILE   73 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue SER   78 is missing expected H atoms. Skipping.
Residue VAL   79 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue LEU   81 is missing expected H atoms. Skipping.
Residue LYS   82 is missing expected H atoms. Skipping.
Residue TYR   84 is missing expected H atoms. Skipping.
Residue VAL   85 is missing expected H atoms. Skipping.
Residue THR   87 is missing expected H atoms. Skipping.
Residue SER   93 is missing expected H atoms. Skipping.
Residue LYS   95 is missing expected H atoms. Skipping.
Residue THR  101 is missing expected H atoms. Skipping.
Residue THR  102 is missing expected H atoms. Skipping.
Residue LYS  106 is missing expected H atoms. Skipping.
Residue ILE  107 is missing expected H atoms. Skipping.
Residue VAL  108 is missing expected H atoms. Skipping.
Residue ILE  109 is missing expected H atoms. Skipping.
Residue LEU  112 is missing expected H atoms. Skipping.
Residue LEU  113 is missing expected H atoms. Skipping.
Residue LEU  117 is missing expected H atoms. Skipping.
Residue SER  120 is missing expected H atoms. Skipping.
Residue ILE  121 is missing expected H atoms. Skipping.
Residue SER  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue VAL  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue SER  127 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue TYR  130 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue SER  133 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  147 is missing expected H atoms. Skipping.
Residue LEU  150 is missing expected H atoms. Skipping.
Residue LEU  151 is missing expected H atoms. Skipping.
Residue MET  152 is missing expected H atoms. Skipping.
Residue MET  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue VAL  156 is missing expected H atoms. Skipping.
Residue SER  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue VAL  163 is missing expected H atoms. Skipping.
Residue MET  167 is missing expected H atoms. Skipping.
Residue VAL  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue THR  174 is missing expected H atoms. Skipping.
Residue VAL  177 is missing expected H atoms. Skipping.
Residue THR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue MET  182 is missing expected H atoms. Skipping.
Residue LEU  184 is missing expected H atoms. Skipping.
Residue VAL  185 is missing expected H atoms. Skipping.
Residue VAL  188 is missing expected H atoms. Skipping.
Residue ILE  189 is missing expected H atoms. Skipping.
Residue LEU  190 is missing expected H atoms. Skipping.
Residue MET  193 is missing expected H atoms. Skipping.
Residue TYR  194 is missing expected H atoms. Skipping.
Residue LYS  195 is missing expected H atoms. Skipping.
Residue ILE  196 is missing expected H atoms. Skipping.
Residue THR  198 is missing expected H atoms. Skipping.
Residue MET  199 is missing expected H atoms. Skipping.
Residue VAL  202 is missing expected H atoms. Skipping.
Residue TYR  203 is missing expected H atoms. Skipping.
Residue ILE  205 is missing expected H atoms. Skipping.
Residue THR  207 is missing expected H atoms. Skipping.
Residue SER  209 is missing expected H atoms. Skipping.
Residue VAL  212 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue THR  216 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue MET  221 is missing expected H atoms. Skipping.
Residue ILE  222 is missing expected H atoms. Skipping.
Residue MET  225 is missing expected H atoms. Skipping.
Residue LEU  228 is missing expected H atoms. Skipping.
Residue LYS  230 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue VAL  235 is missing expected H atoms. Skipping.
Residue LEU  236 is missing expected H atoms. Skipping.
Residue ILE  237 is missing expected H atoms. Skipping.
Residue VAL  240 is missing expected H atoms. Skipping.
Residue VAL  241 is missing expected H atoms. Skipping.
Residue THR  245 is missing expected H atoms. Skipping.
Residue VAL  249 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue ILE  254 is missing expected H atoms. Skipping.
Residue THR  259 is missing expected H atoms. Skipping.
Residue SER  260 is missing expected H atoms. Skipping.
Residue SER  262 is missing expected H atoms. Skipping.
Residue LYS  265 is missing expected H atoms. Skipping.
Residue MET  266 is missing expected H atoms. Skipping.
Residue VAL  268 is missing expected H atoms. Skipping.
Residue LEU  269 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue VAL  272 is missing expected H atoms. Skipping.
Residue THR  273 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue VAL  276 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue MET  283 is missing expected H atoms. Skipping.
Residue VAL  284 is missing expected H atoms. Skipping.
Residue SER  285 is missing expected H atoms. Skipping.
Residue SER  286 is missing expected H atoms. Skipping.
Residue MET  287 is missing expected H atoms. Skipping.
Residue ILE  290 is missing expected H atoms. Skipping.
Residue LEU  291 is missing expected H atoms. Skipping.
Residue ILE  293 is missing expected H atoms. Skipping.
Residue VAL  294 is missing expected H atoms. Skipping.
Residue THR  297 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue THR  299 is missing expected H atoms. Skipping.
Residue SER  301 is missing expected H atoms. Skipping.
Residue TYR  305 is missing expected H atoms. Skipping.
Residue VAL  306 is missing expected H atoms. Skipping.
Residue THR  308 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue VAL  333 is missing expected H atoms. Skipping.
Residue SER  335 is missing expected H atoms. Skipping.
Residue ILE  336 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  344 is missing expected H atoms. Skipping.
Residue SER  347 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LYS  350 is missing expected H atoms. Skipping.
Residue SER  351 is missing expected H atoms. Skipping.
Residue THR  352 is missing expected H atoms. Skipping.
Residue VAL  353 is missing expected H atoms. Skipping.
Residue LYS  354 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LEU  357 is missing expected H atoms. Skipping.
Residue LEU  360 is missing expected H atoms. Skipping.
Residue ILE  361 is missing expected H atoms. Skipping.
Residue TYR  362 is missing expected H atoms. Skipping.
Residue TYR  363 is missing expected H atoms. Skipping.
Residue ILE  364 is missing expected H atoms. Skipping.
Residue ILE  365 is missing expected H atoms. Skipping.
Residue LEU  366 is missing expected H atoms. Skipping.
Residue TYR  367 is missing expected H atoms. Skipping.
Residue MET  368 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue THR  371 is missing expected H atoms. Skipping.
Residue ILE  375 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue VAL  377 is missing expected H atoms. Skipping.
Residue THR  379 is missing expected H atoms. Skipping.
Residue VAL  386 is missing expected H atoms. Skipping.
Residue THR  393 is missing expected H atoms. Skipping.
Residue SER  395 is missing expected H atoms. Skipping.
Residue TYR  396 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue VAL  398 is missing expected H atoms. Skipping.
Residue ILE  400 is missing expected H atoms. Skipping.
Residue LEU  405 is missing expected H atoms. Skipping.
Residue LEU  406 is missing expected H atoms. Skipping.
Residue LEU  407 is missing expected H atoms. Skipping.
Residue VAL  409 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue SER  417 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue THR  426 is missing expected H atoms. Skipping.
Residue LEU  429 is missing expected H atoms. Skipping.
Residue THR  435 is missing expected H atoms. Skipping.
Residue LYS  436 is missing expected H atoms. Skipping.
Residue SER  438 is missing expected H atoms. Skipping.
Residue THR  440 is missing expected H atoms. Skipping.
Residue LYS  445 is missing expected H atoms. Skipping.
Residue ILE  446 is missing expected H atoms. Skipping.
Residue MET  451 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue LEU  454 is missing expected H atoms. Skipping.
Residue SER  456 is missing expected H atoms. Skipping.
Residue VAL  457 is missing expected H atoms. Skipping.
Residue LYS  458 is missing expected H atoms. Skipping.
Residue ILE  460 is missing expected H atoms. Skipping.
Residue ILE  461 is missing expected H atoms. Skipping.
Residue THR  462 is missing expected H atoms. Skipping.
Residue SER  464 is missing expected H atoms. Skipping.
Residue VAL  465 is missing expected H atoms. Skipping.
Residue LYS  466 is missing expected H atoms. Skipping.
Residue ILE  470 is missing expected H atoms. Skipping.
Residue MET  474 is missing expected H atoms. Skipping.
Residue LEU  478 is missing expected H atoms. Skipping.
Residue THR  479 is missing expected H atoms. Skipping.
Residue VAL  481 is missing expected H atoms. Skipping.
Residue ILE  482 is missing expected H atoms. Skipping.
Residue LEU  483 is missing expected H atoms. Skipping.
Residue LEU  486 is missing expected H atoms. Skipping.
Residue LEU  488 is missing expected H atoms. Skipping.
Residue SER  489 is missing expected H atoms. Skipping.
Residue VAL  490 is missing expected H atoms. Skipping.
Residue SER  491 is missing expected H atoms. Skipping.
Residue LEU  494 is missing expected H atoms. Skipping.
Residue LEU  495 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  503 is missing expected H atoms. Skipping.
Residue THR  506 is missing expected H atoms. Skipping.
Residue VAL  507 is missing expected H atoms. Skipping.
Residue MET  509 is missing expected H atoms. Skipping.
Residue SER  510 is missing expected H atoms. Skipping.
Residue LEU  513 is missing expected H atoms. Skipping.
Residue ILE  514 is missing expected H atoms. Skipping.
Residue LEU  518 is missing expected H atoms. Skipping.
Residue THR  521 is missing expected H atoms. Skipping.
Residue VAL  522 is missing expected H atoms. Skipping.
Residue SER  523 is missing expected H atoms. Skipping.
Residue LEU  525 is missing expected H atoms. Skipping.
Residue THR  528 is missing expected H atoms. Skipping.
Residue SER  532 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  535 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  538 is missing expected H atoms. Skipping.
Residue ILE  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LEU  548 is missing expected H atoms. Skipping.
Residue LYS  549 is missing expected H atoms. Skipping.
Residue VAL  550 is missing expected H atoms. Skipping.
Residue SER  551 is missing expected H atoms. Skipping.
Residue SER  553 is missing expected H atoms. Skipping.
Residue THR  554 is missing expected H atoms. Skipping.
Residue VAL  556 is missing expected H atoms. Skipping.
Residue LEU  557 is missing expected H atoms. Skipping.
Residue LEU  561 is missing expected H atoms. Skipping.
Residue SER  563 is missing expected H atoms. Skipping.
Residue ILE  564 is missing expected H atoms. Skipping.
Residue LEU  565 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue LEU  571 is missing expected H atoms. Skipping.
Residue SER  576 is missing expected H atoms. Skipping.
Residue SER  577 is missing expected H atoms. Skipping.
Residue VAL  579 is missing expected H atoms. Skipping.
Residue LEU  580 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue VAL  583 is missing expected H atoms. Skipping.
Residue MET  584 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue LEU  587 is missing expected H atoms. Skipping.
Residue ILE  589 is missing expected H atoms. Skipping.
Residue VAL  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue VAL  593 is missing expected H atoms. Skipping.
Residue THR  598 is missing expected H atoms. Skipping.
Residue SER  600 is missing expected H atoms. Skipping.
Residue MET  601 is missing expected H atoms. Skipping.
Residue SER  603 is missing expected H atoms. Skipping.
Residue LYS  604 is missing expected H atoms. Skipping.
Residue ILE  605 is missing expected H atoms. Skipping.
Residue THR  609 is missing expected H atoms. Skipping.
Residue ILE  610 is missing expected H atoms. Skipping.
Residue ILE  612 is missing expected H atoms. Skipping.
Residue LEU  614 is missing expected H atoms. Skipping.
Residue LYS  615 is missing expected H atoms. Skipping.
Residue LEU  995 is missing expected H atoms. Skipping.
Residue LYS  996 is missing expected H atoms. Skipping.
Residue LEU  999 is missing expected H atoms. Skipping.
Residue TYR 1000 is missing expected H atoms. Skipping.
Residue ILE 1002 is missing expected H atoms. Skipping.
Residue LEU 1004 is missing expected H atoms. Skipping.
Residue TYR 1007 is missing expected H atoms. Skipping.
Residue LEU 1008 is missing expected H atoms. Skipping.
Residue THR 1009 is missing expected H atoms. Skipping.
Residue LEU 1012 is missing expected H atoms. Skipping.
Residue TYR 1021 is missing expected H atoms. Skipping.
Residue ILE 1022 is missing expected H atoms. Skipping.
Residue MET 1023 is missing expected H atoms. Skipping.
Residue SER 1025 is missing expected H atoms. Skipping.
Residue LEU 1028 is missing expected H atoms. Skipping.
Residue VAL 1035 is missing expected H atoms. Skipping.
Residue LEU 1036 is missing expected H atoms. Skipping.
Residue THR 1038 is missing expected H atoms. Skipping.
Residue ILE 1039 is missing expected H atoms. Skipping.
Residue VAL   72 is missing expected H atoms. Skipping.
Residue SER   73 is missing expected H atoms. Skipping.
Residue SER   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue THR   77 is missing expected H atoms. Skipping.
Residue VAL   72 is missing expected H atoms. Skipping.
Residue SER   73 is missing expected H atoms. Skipping.
Residue SER   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue THR   77 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  143 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue VAL  147 is missing expected H atoms. Skipping.
Residue MET  149 is missing expected H atoms. Skipping.
Residue ILE  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue VAL  162 is missing expected H atoms. Skipping.
Residue TYR  166 is missing expected H atoms. Skipping.
Residue ILE  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LEU  174 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  143 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue VAL  147 is missing expected H atoms. Skipping.
Residue MET  149 is missing expected H atoms. Skipping.
Residue ILE  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue VAL  162 is missing expected H atoms. Skipping.
Residue TYR  166 is missing expected H atoms. Skipping.
Residue ILE  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LEU  174 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue VAL  182 is missing expected H atoms. Skipping.
Residue LYS  183 is missing expected H atoms. Skipping.
Evaluate side-chains
  656 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 594
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: 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: A  661 LYS cc_start: 0.8687 (tmmt) cc_final: 0.8372 (tmmt)
REVERT: A  699 GLN cc_start: 0.6891 (mm-40) cc_final: 0.6683 (mm-40)
REVERT: A  705 ASP cc_start: 0.7392 (t0) cc_final: 0.7108 (t0)
REVERT: A  710 MET cc_start: 0.7803 (mtm) cc_final: 0.7511 (mtm)
REVERT: A  757 GLU cc_start: 0.7179 (pm20) cc_final: 0.6680 (pm20)
REVERT: A  798 THR cc_start: 0.7375 (t) cc_final: 0.7109 (p)
REVERT: A  821 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6546 (mm)
REVERT: A  842 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7209 (mm-30)
REVERT: A  846 ARG cc_start: 0.8546 (ttm110) cc_final: 0.8242 (ttm110)
REVERT: B  149 MET cc_start: 0.5553 (mtp) cc_final: 0.5098 (mtp)
REVERT: B  158 ARG cc_start: 0.7932 (tpp-160) cc_final: 0.7433 (tpm170)
REVERT: B  188 GLN cc_start: 0.7736 (tp40) cc_final: 0.7150 (tp40)
REVERT: C  161 LYS cc_start: 0.6538 (mtmt) cc_final: 0.6226 (mmmt)
REVERT: F   42 LYS cc_start: 0.8302 (tttp) cc_final: 0.7973 (tttp)
REVERT: F  236 GLU cc_start: 0.7508 (tt0) cc_final: 0.7237 (mt-10)
REVERT: G  118 ILE cc_start: 0.7610 (mm) cc_final: 0.7344 (mt)
REVERT: O   23 TYR cc_start: 0.7067 (m-10) cc_final: 0.6830 (m-10)
REVERT: O  109 LEU cc_start: 0.7342 (tt) cc_final: 0.7067 (tp)
REVERT: O  175 LYS cc_start: 0.8901 (ttmt) cc_final: 0.8650 (ttmm)
REVERT: P    8 ARG cc_start: 0.7688 (ttm110) cc_final: 0.7345 (ttm-80)
REVERT: P   15 GLU cc_start: 0.7294 (mt-10) cc_final: 0.7085 (mt-10)
REVERT: P  153 SER cc_start: 0.7901 (p) cc_final: 0.7665 (t)
REVERT: P  166 ASN cc_start: 0.7998 (t0) cc_final: 0.7738 (t0)
REVERT: P  178 ASP cc_start: 0.7534 (m-30) cc_final: 0.7157 (t0)
REVERT: P  181 GLU cc_start: 0.7942 (tp30) cc_final: 0.7624 (tp30)
REVERT: P  222 LYS cc_start: 0.8322 (mmmt) cc_final: 0.7934 (mmmt)
REVERT: P  231 LYS cc_start: 0.8275 (tttt) cc_final: 0.8001 (mtpp)
REVERT: P  234 GLU cc_start: 0.7645 (tp30) cc_final: 0.7323 (tp30)
REVERT: P  239 LYS cc_start: 0.6754 (OUTLIER) cc_final: 0.6534 (mtpp)
REVERT: Q   62 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7613 (mt)
REVERT: Q   67 ASP cc_start: 0.8335 (m-30) cc_final: 0.8129 (m-30)
REVERT: Q  197 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7392 (mt-10)
REVERT: Q  227 LYS cc_start: 0.7246 (tmmt) cc_final: 0.6918 (ttmt)
REVERT: R  111 SER cc_start: 0.8009 (m) cc_final: 0.7803 (t)
REVERT: R  114 GLN cc_start: 0.8510 (tt0) cc_final: 0.8310 (tt0)
REVERT: R  117 SER cc_start: 0.8106 (t) cc_final: 0.7694 (t)
REVERT: R  119 LEU cc_start: 0.8603 (tp) cc_final: 0.8377 (tt)
REVERT: R  156 MET cc_start: 0.7545 (tmm) cc_final: 0.7324 (tmm)
REVERT: R  197 SER cc_start: 0.9237 (t) cc_final: 0.8985 (m)
REVERT: S   27 GLU cc_start: 0.8129 (tp30) cc_final: 0.7848 (tp30)
REVERT: S   29 VAL cc_start: 0.8462 (m) cc_final: 0.8253 (p)
REVERT: S  122 ARG cc_start: 0.8238 (mtp85) cc_final: 0.7927 (mtp-110)
REVERT: S  144 ILE cc_start: 0.7296 (OUTLIER) cc_final: 0.7066 (mm)
  outliers start: 62
  outliers final: 38
  residues processed: 623
  average time/residue: 0.3620
  time to fit residues: 327.9408
Evaluate side-chains
  595 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 553
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  821 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain C residue  166 TYR
Chi-restraints excluded: chain C residue  177 GLN
Chi-restraints excluded: chain F residue   30 VAL
Chi-restraints excluded: chain F residue   55 SER
Chi-restraints excluded: chain F residue   56 LYS
Chi-restraints excluded: chain F residue  119 VAL
Chi-restraints excluded: chain F residue  123 THR
Chi-restraints excluded: chain F residue  156 VAL
Chi-restraints excluded: chain F residue  244 LYS
Chi-restraints excluded: chain G residue  211 LYS
Chi-restraints excluded: chain G residue  240 VAL
Chi-restraints excluded: chain O residue   28 VAL
Chi-restraints excluded: chain O residue  119 GLU
Chi-restraints excluded: chain O residue  126 VAL
Chi-restraints excluded: chain O residue  224 GLU
Chi-restraints excluded: chain P residue    9 THR
Chi-restraints excluded: chain P residue   11 ILE
Chi-restraints excluded: chain P residue   54 LYS
Chi-restraints excluded: chain P residue  117 ILE
Chi-restraints excluded: chain P residue  122 THR
Chi-restraints excluded: chain P residue  239 LYS
Chi-restraints excluded: chain Q residue   58 THR
Chi-restraints excluded: chain Q residue   62 ILE
Chi-restraints excluded: chain Q residue  129 ILE
Chi-restraints excluded: chain Q residue  147 THR
Chi-restraints excluded: chain Q residue  191 VAL
Chi-restraints excluded: chain Q residue  196 LEU
Chi-restraints excluded: chain R residue   35 SER
Chi-restraints excluded: chain R residue   47 CYS
Chi-restraints excluded: chain R residue   62 SER
Chi-restraints excluded: chain R residue  165 CYS
Chi-restraints excluded: chain R residue  189 MET
Chi-restraints excluded: chain R residue  238 ILE
Chi-restraints excluded: chain S residue   38 LEU
Chi-restraints excluded: chain S residue   53 GLN
Chi-restraints excluded: chain S residue  144 ILE
Chi-restraints excluded: chain S residue  227 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 283
   random chunks:
   chunk 253 optimal weight:    2.9990
   chunk 100 optimal weight:    5.9990
   chunk 30 optimal weight:   10.0000
   chunk 120 optimal weight:    1.9990
   chunk 221 optimal weight:    1.9990
   chunk 224 optimal weight:    0.9980
   chunk 98 optimal weight:    9.9990
   chunk 263 optimal weight:    2.9990
   chunk 137 optimal weight:    2.9990
   chunk 275 optimal weight:    0.6980
   chunk 42 optimal weight:    5.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
C  97 HIS
** P 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 182 GLN
S  21 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.145492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.115733 restraints weight = 85806.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 1.84
r_work: 0.3278 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3144 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3153
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
r_final: 0.3153
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.7191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.068  20809  Z= 0.309
  Angle     :  0.626   6.096  28272  Z= 0.344
  Chirality :  0.043   0.156   3307
  Planarity :  0.005   0.068   3731
  Dihedral  :  5.185  47.936   3076
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 22.58 %
    Favored  : 73.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.16), residues: 2833
  helix:  1.77 (0.14), residues: 1541
  sheet: -0.87 (0.26), residues: 361
  loop : -0.48 (0.20), residues: 931

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG Q  57 
 TYR   0.021   0.002   TYR O 120 
 PHE   0.022   0.002   PHE S 154 
 TRP   0.015   0.002   TRP P 139 
 HIS   0.008   0.002   HIS B 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00700 (20809)
  covalent geometry    : angle       0.62561 (28272)
  hydrogen bonds       : bond        0.04741 ( 1327)
  hydrogen bonds       : angle       4.30636 ( 3822)

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

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

  5666 Ramachandran restraints generated.
    2833 Oldfield, 0 Emsley, 2833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5666 Ramachandran restraints generated.
    2833 Oldfield, 0 Emsley, 2833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL   17 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue VAL   26 is missing expected H atoms. Skipping.
Residue THR   28 is missing expected H atoms. Skipping.
Residue LEU   29 is missing expected H atoms. Skipping.
Residue THR   30 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue LEU   33 is missing expected H atoms. Skipping.
Residue SER   34 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue VAL   39 is missing expected H atoms. Skipping.
Residue ILE   47 is missing expected H atoms. Skipping.
Residue LYS   48 is missing expected H atoms. Skipping.
Residue VAL   49 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue VAL   52 is missing expected H atoms. Skipping.
Residue THR   53 is missing expected H atoms. Skipping.
Residue VAL   58 is missing expected H atoms. Skipping.
Residue LEU   60 is missing expected H atoms. Skipping.
Residue LEU   63 is missing expected H atoms. Skipping.
Residue THR   64 is missing expected H atoms. Skipping.
Residue VAL   65 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ILE   73 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue SER   78 is missing expected H atoms. Skipping.
Residue VAL   79 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue LEU   81 is missing expected H atoms. Skipping.
Residue LYS   82 is missing expected H atoms. Skipping.
Residue TYR   84 is missing expected H atoms. Skipping.
Residue VAL   85 is missing expected H atoms. Skipping.
Residue THR   87 is missing expected H atoms. Skipping.
Residue SER   93 is missing expected H atoms. Skipping.
Residue LYS   95 is missing expected H atoms. Skipping.
Residue THR  101 is missing expected H atoms. Skipping.
Residue THR  102 is missing expected H atoms. Skipping.
Residue LYS  106 is missing expected H atoms. Skipping.
Residue ILE  107 is missing expected H atoms. Skipping.
Residue VAL  108 is missing expected H atoms. Skipping.
Residue ILE  109 is missing expected H atoms. Skipping.
Residue LEU  112 is missing expected H atoms. Skipping.
Residue LEU  113 is missing expected H atoms. Skipping.
Residue LEU  117 is missing expected H atoms. Skipping.
Residue SER  120 is missing expected H atoms. Skipping.
Residue ILE  121 is missing expected H atoms. Skipping.
Residue SER  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue VAL  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue SER  127 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue TYR  130 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue SER  133 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  147 is missing expected H atoms. Skipping.
Residue LEU  150 is missing expected H atoms. Skipping.
Residue LEU  151 is missing expected H atoms. Skipping.
Residue MET  152 is missing expected H atoms. Skipping.
Residue MET  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue VAL  156 is missing expected H atoms. Skipping.
Residue SER  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue VAL  163 is missing expected H atoms. Skipping.
Residue MET  167 is missing expected H atoms. Skipping.
Residue VAL  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue THR  174 is missing expected H atoms. Skipping.
Residue VAL  177 is missing expected H atoms. Skipping.
Residue THR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue MET  182 is missing expected H atoms. Skipping.
Residue LEU  184 is missing expected H atoms. Skipping.
Residue VAL  185 is missing expected H atoms. Skipping.
Residue VAL  188 is missing expected H atoms. Skipping.
Residue ILE  189 is missing expected H atoms. Skipping.
Residue LEU  190 is missing expected H atoms. Skipping.
Residue MET  193 is missing expected H atoms. Skipping.
Residue TYR  194 is missing expected H atoms. Skipping.
Residue LYS  195 is missing expected H atoms. Skipping.
Residue ILE  196 is missing expected H atoms. Skipping.
Residue THR  198 is missing expected H atoms. Skipping.
Residue MET  199 is missing expected H atoms. Skipping.
Residue VAL  202 is missing expected H atoms. Skipping.
Residue TYR  203 is missing expected H atoms. Skipping.
Residue ILE  205 is missing expected H atoms. Skipping.
Residue THR  207 is missing expected H atoms. Skipping.
Residue SER  209 is missing expected H atoms. Skipping.
Residue VAL  212 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue THR  216 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue MET  221 is missing expected H atoms. Skipping.
Residue ILE  222 is missing expected H atoms. Skipping.
Residue MET  225 is missing expected H atoms. Skipping.
Residue LEU  228 is missing expected H atoms. Skipping.
Residue LYS  230 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue VAL  235 is missing expected H atoms. Skipping.
Residue LEU  236 is missing expected H atoms. Skipping.
Residue ILE  237 is missing expected H atoms. Skipping.
Residue VAL  240 is missing expected H atoms. Skipping.
Residue VAL  241 is missing expected H atoms. Skipping.
Residue THR  245 is missing expected H atoms. Skipping.
Residue VAL  249 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue ILE  254 is missing expected H atoms. Skipping.
Residue THR  259 is missing expected H atoms. Skipping.
Residue SER  260 is missing expected H atoms. Skipping.
Residue SER  262 is missing expected H atoms. Skipping.
Residue LYS  265 is missing expected H atoms. Skipping.
Residue MET  266 is missing expected H atoms. Skipping.
Residue VAL  268 is missing expected H atoms. Skipping.
Residue LEU  269 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue VAL  272 is missing expected H atoms. Skipping.
Residue THR  273 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue VAL  276 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue MET  283 is missing expected H atoms. Skipping.
Residue VAL  284 is missing expected H atoms. Skipping.
Residue SER  285 is missing expected H atoms. Skipping.
Residue SER  286 is missing expected H atoms. Skipping.
Residue MET  287 is missing expected H atoms. Skipping.
Residue ILE  290 is missing expected H atoms. Skipping.
Residue LEU  291 is missing expected H atoms. Skipping.
Residue ILE  293 is missing expected H atoms. Skipping.
Residue VAL  294 is missing expected H atoms. Skipping.
Residue THR  297 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue THR  299 is missing expected H atoms. Skipping.
Residue SER  301 is missing expected H atoms. Skipping.
Residue TYR  305 is missing expected H atoms. Skipping.
Residue VAL  306 is missing expected H atoms. Skipping.
Residue THR  308 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue VAL  333 is missing expected H atoms. Skipping.
Residue SER  335 is missing expected H atoms. Skipping.
Residue ILE  336 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  344 is missing expected H atoms. Skipping.
Residue SER  347 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LYS  350 is missing expected H atoms. Skipping.
Residue SER  351 is missing expected H atoms. Skipping.
Residue THR  352 is missing expected H atoms. Skipping.
Residue VAL  353 is missing expected H atoms. Skipping.
Residue LYS  354 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LEU  357 is missing expected H atoms. Skipping.
Residue LEU  360 is missing expected H atoms. Skipping.
Residue ILE  361 is missing expected H atoms. Skipping.
Residue TYR  362 is missing expected H atoms. Skipping.
Residue TYR  363 is missing expected H atoms. Skipping.
Residue ILE  364 is missing expected H atoms. Skipping.
Residue ILE  365 is missing expected H atoms. Skipping.
Residue LEU  366 is missing expected H atoms. Skipping.
Residue TYR  367 is missing expected H atoms. Skipping.
Residue MET  368 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue THR  371 is missing expected H atoms. Skipping.
Residue ILE  375 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue VAL  377 is missing expected H atoms. Skipping.
Residue THR  379 is missing expected H atoms. Skipping.
Residue VAL  386 is missing expected H atoms. Skipping.
Residue THR  393 is missing expected H atoms. Skipping.
Residue SER  395 is missing expected H atoms. Skipping.
Residue TYR  396 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue VAL  398 is missing expected H atoms. Skipping.
Residue ILE  400 is missing expected H atoms. Skipping.
Residue LEU  405 is missing expected H atoms. Skipping.
Residue LEU  406 is missing expected H atoms. Skipping.
Residue LEU  407 is missing expected H atoms. Skipping.
Residue VAL  409 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue SER  417 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue THR  426 is missing expected H atoms. Skipping.
Residue LEU  429 is missing expected H atoms. Skipping.
Residue THR  435 is missing expected H atoms. Skipping.
Residue LYS  436 is missing expected H atoms. Skipping.
Residue SER  438 is missing expected H atoms. Skipping.
Residue THR  440 is missing expected H atoms. Skipping.
Residue LYS  445 is missing expected H atoms. Skipping.
Residue ILE  446 is missing expected H atoms. Skipping.
Residue MET  451 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue LEU  454 is missing expected H atoms. Skipping.
Residue SER  456 is missing expected H atoms. Skipping.
Residue VAL  457 is missing expected H atoms. Skipping.
Residue LYS  458 is missing expected H atoms. Skipping.
Residue ILE  460 is missing expected H atoms. Skipping.
Residue ILE  461 is missing expected H atoms. Skipping.
Residue THR  462 is missing expected H atoms. Skipping.
Residue SER  464 is missing expected H atoms. Skipping.
Residue VAL  465 is missing expected H atoms. Skipping.
Residue LYS  466 is missing expected H atoms. Skipping.
Residue ILE  470 is missing expected H atoms. Skipping.
Residue MET  474 is missing expected H atoms. Skipping.
Residue LEU  478 is missing expected H atoms. Skipping.
Residue THR  479 is missing expected H atoms. Skipping.
Residue VAL  481 is missing expected H atoms. Skipping.
Residue ILE  482 is missing expected H atoms. Skipping.
Residue LEU  483 is missing expected H atoms. Skipping.
Residue LEU  486 is missing expected H atoms. Skipping.
Residue LEU  488 is missing expected H atoms. Skipping.
Residue SER  489 is missing expected H atoms. Skipping.
Residue VAL  490 is missing expected H atoms. Skipping.
Residue SER  491 is missing expected H atoms. Skipping.
Residue LEU  494 is missing expected H atoms. Skipping.
Residue LEU  495 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  503 is missing expected H atoms. Skipping.
Residue THR  506 is missing expected H atoms. Skipping.
Residue VAL  507 is missing expected H atoms. Skipping.
Residue MET  509 is missing expected H atoms. Skipping.
Residue SER  510 is missing expected H atoms. Skipping.
Residue LEU  513 is missing expected H atoms. Skipping.
Residue ILE  514 is missing expected H atoms. Skipping.
Residue LEU  518 is missing expected H atoms. Skipping.
Residue THR  521 is missing expected H atoms. Skipping.
Residue VAL  522 is missing expected H atoms. Skipping.
Residue SER  523 is missing expected H atoms. Skipping.
Residue LEU  525 is missing expected H atoms. Skipping.
Residue THR  528 is missing expected H atoms. Skipping.
Residue SER  532 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  535 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  538 is missing expected H atoms. Skipping.
Residue ILE  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LEU  548 is missing expected H atoms. Skipping.
Residue LYS  549 is missing expected H atoms. Skipping.
Residue VAL  550 is missing expected H atoms. Skipping.
Residue SER  551 is missing expected H atoms. Skipping.
Residue SER  553 is missing expected H atoms. Skipping.
Residue THR  554 is missing expected H atoms. Skipping.
Residue VAL  556 is missing expected H atoms. Skipping.
Residue LEU  557 is missing expected H atoms. Skipping.
Residue LEU  561 is missing expected H atoms. Skipping.
Residue SER  563 is missing expected H atoms. Skipping.
Residue ILE  564 is missing expected H atoms. Skipping.
Residue LEU  565 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue LEU  571 is missing expected H atoms. Skipping.
Residue SER  576 is missing expected H atoms. Skipping.
Residue SER  577 is missing expected H atoms. Skipping.
Residue VAL  579 is missing expected H atoms. Skipping.
Residue LEU  580 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue VAL  583 is missing expected H atoms. Skipping.
Residue MET  584 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue LEU  587 is missing expected H atoms. Skipping.
Residue ILE  589 is missing expected H atoms. Skipping.
Residue VAL  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue VAL  593 is missing expected H atoms. Skipping.
Residue THR  598 is missing expected H atoms. Skipping.
Residue SER  600 is missing expected H atoms. Skipping.
Residue MET  601 is missing expected H atoms. Skipping.
Residue SER  603 is missing expected H atoms. Skipping.
Residue LYS  604 is missing expected H atoms. Skipping.
Residue ILE  605 is missing expected H atoms. Skipping.
Residue THR  609 is missing expected H atoms. Skipping.
Residue ILE  610 is missing expected H atoms. Skipping.
Residue ILE  612 is missing expected H atoms. Skipping.
Residue LEU  614 is missing expected H atoms. Skipping.
Residue LYS  615 is missing expected H atoms. Skipping.
Residue LEU  995 is missing expected H atoms. Skipping.
Residue LYS  996 is missing expected H atoms. Skipping.
Residue LEU  999 is missing expected H atoms. Skipping.
Residue TYR 1000 is missing expected H atoms. Skipping.
Residue ILE 1002 is missing expected H atoms. Skipping.
Residue LEU 1004 is missing expected H atoms. Skipping.
Residue TYR 1007 is missing expected H atoms. Skipping.
Residue LEU 1008 is missing expected H atoms. Skipping.
Residue THR 1009 is missing expected H atoms. Skipping.
Residue LEU 1012 is missing expected H atoms. Skipping.
Residue TYR 1021 is missing expected H atoms. Skipping.
Residue ILE 1022 is missing expected H atoms. Skipping.
Residue MET 1023 is missing expected H atoms. Skipping.
Residue SER 1025 is missing expected H atoms. Skipping.
Residue LEU 1028 is missing expected H atoms. Skipping.
Residue VAL 1035 is missing expected H atoms. Skipping.
Residue LEU 1036 is missing expected H atoms. Skipping.
Residue THR 1038 is missing expected H atoms. Skipping.
Residue ILE 1039 is missing expected H atoms. Skipping.
Residue VAL   72 is missing expected H atoms. Skipping.
Residue SER   73 is missing expected H atoms. Skipping.
Residue SER   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue THR   77 is missing expected H atoms. Skipping.
Residue VAL   72 is missing expected H atoms. Skipping.
Residue SER   73 is missing expected H atoms. Skipping.
Residue SER   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue THR   77 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  143 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue VAL  147 is missing expected H atoms. Skipping.
Residue MET  149 is missing expected H atoms. Skipping.
Residue ILE  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue VAL  162 is missing expected H atoms. Skipping.
Residue TYR  166 is missing expected H atoms. Skipping.
Residue ILE  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LEU  174 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  143 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue VAL  147 is missing expected H atoms. Skipping.
Residue MET  149 is missing expected H atoms. Skipping.
Residue ILE  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue VAL  162 is missing expected H atoms. Skipping.
Residue TYR  166 is missing expected H atoms. Skipping.
Residue ILE  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LEU  174 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue VAL  182 is missing expected H atoms. Skipping.
Residue LYS  183 is missing expected H atoms. Skipping.
Evaluate side-chains
  691 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 617
  time to evaluate  : 1.057 
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
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  661 LYS cc_start: 0.8844 (tmmt) cc_final: 0.8433 (tmmt)
REVERT: A  699 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6593 (mm-40)
REVERT: A  705 ASP cc_start: 0.7619 (t0) cc_final: 0.7305 (t0)
REVERT: A  742 TYR cc_start: 0.6538 (m-80) cc_final: 0.5593 (m-80)
REVERT: A  757 GLU cc_start: 0.7436 (pm20) cc_final: 0.7137 (pm20)
REVERT: A  797 GLU cc_start: 0.6820 (mm-30) cc_final: 0.6574 (mt-10)
REVERT: A  821 LEU cc_start: 0.6535 (OUTLIER) cc_final: 0.6243 (mm)
REVERT: A  822 GLU cc_start: 0.6741 (tt0) cc_final: 0.6188 (tt0)
REVERT: A  842 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7532 (mm-30)
REVERT: A  846 ARG cc_start: 0.8620 (ttm110) cc_final: 0.8377 (mtt-85)
REVERT: A  915 VAL cc_start: 0.7821 (t) cc_final: 0.7567 (p)
REVERT: A  924 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6745 (mm-30)
REVERT: B  168 GLU cc_start: 0.7530 (tp30) cc_final: 0.7121 (tp30)
REVERT: B  178 TYR cc_start: 0.8035 (t80) cc_final: 0.7632 (t80)
REVERT: B  188 GLN cc_start: 0.7996 (tp40) cc_final: 0.7369 (tp40)
REVERT: B  193 TYR cc_start: 0.8056 (m-80) cc_final: 0.7533 (m-80)
REVERT: C   88 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6542 (mm-30)
REVERT: C  161 LYS cc_start: 0.6572 (mtmt) cc_final: 0.6263 (mmmt)
REVERT: C  168 GLU cc_start: 0.7959 (tp30) cc_final: 0.7326 (tp30)
REVERT: C  187 ASP cc_start: 0.8172 (m-30) cc_final: 0.7930 (t0)
REVERT: F   59 GLU cc_start: 0.7712 (tp30) cc_final: 0.7430 (tp30)
REVERT: F   77 VAL cc_start: 0.8846 (p) cc_final: 0.8252 (m)
REVERT: F   93 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7141 (mm-30)
REVERT: F  124 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8325 (tt)
REVERT: F  136 MET cc_start: 0.8504 (mtt) cc_final: 0.8294 (mtt)
REVERT: F  236 GLU cc_start: 0.7765 (tt0) cc_final: 0.7474 (mt-10)
REVERT: F  241 GLU cc_start: 0.6697 (pp20) cc_final: 0.6440 (pp20)
REVERT: G   38 THR cc_start: 0.8901 (t) cc_final: 0.8466 (m)
REVERT: G   87 SER cc_start: 0.7455 (m) cc_final: 0.6979 (p)
REVERT: G   96 TYR cc_start: 0.8483 (t80) cc_final: 0.7764 (t80)
REVERT: G   97 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7732 (tp30)
REVERT: G  104 LYS cc_start: 0.8628 (ttpt) cc_final: 0.8251 (mtpp)
REVERT: G  118 ILE cc_start: 0.7697 (mm) cc_final: 0.7379 (mt)
REVERT: G  174 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7778 (mp0)
REVERT: G  234 GLU cc_start: 0.7861 (tp30) cc_final: 0.7456 (tp30)
REVERT: O   51 GLN cc_start: 0.6939 (mp10) cc_final: 0.6700 (mp10)
REVERT: O   69 LYS cc_start: 0.8576 (pttt) cc_final: 0.8268 (pttt)
REVERT: O  118 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.6985 (tp40)
REVERT: O  155 PHE cc_start: 0.8290 (m-80) cc_final: 0.8078 (m-10)
REVERT: O  175 LYS cc_start: 0.8895 (ttmt) cc_final: 0.8657 (ttmm)
REVERT: P    6 ASP cc_start: 0.8422 (t0) cc_final: 0.8216 (t0)
REVERT: P    8 ARG cc_start: 0.8078 (ttm110) cc_final: 0.7834 (ttm-80)
REVERT: P   67 LYS cc_start: 0.8520 (mtmt) cc_final: 0.7487 (pptt)
REVERT: P  166 ASN cc_start: 0.8027 (t0) cc_final: 0.7798 (m-40)
REVERT: P  177 GLN cc_start: 0.8452 (tt0) cc_final: 0.8096 (tp40)
REVERT: P  178 ASP cc_start: 0.8007 (m-30) cc_final: 0.7699 (t0)
REVERT: P  181 GLU cc_start: 0.8045 (tp30) cc_final: 0.7406 (tp30)
REVERT: P  184 MET cc_start: 0.8562 (mmp) cc_final: 0.8279 (mmm)
REVERT: P  222 LYS cc_start: 0.8402 (mmmt) cc_final: 0.8070 (mmmt)
REVERT: P  231 LYS cc_start: 0.8420 (tttt) cc_final: 0.8039 (mtpp)
REVERT: P  234 GLU cc_start: 0.7587 (tp30) cc_final: 0.7158 (tp30)
REVERT: P  239 LYS cc_start: 0.6923 (OUTLIER) cc_final: 0.6722 (mtpp)
REVERT: Q   62 ILE cc_start: 0.8321 (pt) cc_final: 0.7941 (mt)
REVERT: Q   67 ASP cc_start: 0.8292 (m-30) cc_final: 0.8045 (m-30)
REVERT: Q   99 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7658 (mm-30)
REVERT: Q  197 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7912 (mt-10)
REVERT: Q  227 LYS cc_start: 0.8040 (tmmt) cc_final: 0.7651 (ttmt)
REVERT: Q  228 TYR cc_start: 0.8192 (m-80) cc_final: 0.7967 (m-80)
REVERT: R   62 SER cc_start: 0.8339 (OUTLIER) cc_final: 0.8087 (t)
REVERT: R   65 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7422 (mm-30)
REVERT: R   90 ASP cc_start: 0.7996 (t0) cc_final: 0.7400 (t0)
REVERT: R  117 SER cc_start: 0.8734 (t) cc_final: 0.8217 (p)
REVERT: R  119 LEU cc_start: 0.8517 (tp) cc_final: 0.8310 (tt)
REVERT: R  156 MET cc_start: 0.7745 (tmm) cc_final: 0.7386 (tmm)
REVERT: R  216 GLU cc_start: 0.7573 (pm20) cc_final: 0.7210 (pm20)
REVERT: S    8 ASN cc_start: 0.8192 (m-40) cc_final: 0.7852 (m-40)
REVERT: S   16 GLN cc_start: 0.8133 (mp10) cc_final: 0.7873 (mp10)
REVERT: S   29 VAL cc_start: 0.8476 (m) cc_final: 0.8267 (p)
REVERT: S  122 ARG cc_start: 0.7960 (mtp85) cc_final: 0.7692 (mtp-110)
  outliers start: 74
  outliers final: 56
  residues processed: 659
  average time/residue: 0.3618
  time to fit residues: 342.7379
Evaluate side-chains
  640 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 579
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain A residue  667 CYS
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  814 HIS
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  821 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain C residue  166 TYR
Chi-restraints excluded: chain C residue  177 GLN
Chi-restraints excluded: chain F residue   30 VAL
Chi-restraints excluded: chain F residue   55 SER
Chi-restraints excluded: chain F residue   56 LYS
Chi-restraints excluded: chain F residue  119 VAL
Chi-restraints excluded: chain F residue  123 THR
Chi-restraints excluded: chain F residue  124 LEU
Chi-restraints excluded: chain F residue  156 VAL
Chi-restraints excluded: chain F residue  206 ASP
Chi-restraints excluded: chain F residue  244 LYS
Chi-restraints excluded: chain G residue   17 SER
Chi-restraints excluded: chain G residue   47 CYS
Chi-restraints excluded: chain G residue  211 LYS
Chi-restraints excluded: chain G residue  220 VAL
Chi-restraints excluded: chain G residue  240 VAL
Chi-restraints excluded: chain O residue   28 VAL
Chi-restraints excluded: chain O residue   50 LYS
Chi-restraints excluded: chain O residue  118 GLN
Chi-restraints excluded: chain O residue  126 VAL
Chi-restraints excluded: chain O residue  221 THR
Chi-restraints excluded: chain O residue  224 GLU
Chi-restraints excluded: chain O residue  227 ASP
Chi-restraints excluded: chain P residue    9 THR
Chi-restraints excluded: chain P residue   11 ILE
Chi-restraints excluded: chain P residue   54 LYS
Chi-restraints excluded: chain P residue   74 CYS
Chi-restraints excluded: chain P residue  105 ILE
Chi-restraints excluded: chain P residue  117 ILE
Chi-restraints excluded: chain P residue  194 ILE
Chi-restraints excluded: chain P residue  239 LYS
Chi-restraints excluded: chain Q residue   58 THR
Chi-restraints excluded: chain Q residue  103 THR
Chi-restraints excluded: chain Q residue  114 LEU
Chi-restraints excluded: chain Q residue  129 ILE
Chi-restraints excluded: chain Q residue  137 ASP
Chi-restraints excluded: chain Q residue  147 THR
Chi-restraints excluded: chain Q residue  191 VAL
Chi-restraints excluded: chain Q residue  196 LEU
Chi-restraints excluded: chain Q residue  206 ILE
Chi-restraints excluded: chain R residue   35 SER
Chi-restraints excluded: chain R residue   36 THR
Chi-restraints excluded: chain R residue   47 CYS
Chi-restraints excluded: chain R residue   62 SER
Chi-restraints excluded: chain R residue  113 THR
Chi-restraints excluded: chain R residue  165 CYS
Chi-restraints excluded: chain R residue  238 ILE
Chi-restraints excluded: chain S residue   38 LEU
Chi-restraints excluded: chain S residue   45 VAL
Chi-restraints excluded: chain S residue   53 GLN
Chi-restraints excluded: chain S residue  144 ILE
Chi-restraints excluded: chain S residue  147 THR
Chi-restraints excluded: chain S residue  227 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 283
   random chunks:
   chunk 138 optimal weight:    0.9980
   chunk 194 optimal weight:    0.0970
   chunk 237 optimal weight:    0.9990
   chunk 41 optimal weight:    4.9990
   chunk 259 optimal weight:    1.9990
   chunk 250 optimal weight:    0.9980
   chunk 179 optimal weight:    0.5980
   chunk 271 optimal weight:    1.9990
   chunk 180 optimal weight:    0.5980
   chunk 83 optimal weight:    0.9980
   chunk 278 optimal weight:    0.8980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
A 910 ASN
R 182 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.148157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.117896 restraints weight = 85461.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 1.90
r_work: 0.3293 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3140
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
r_final: 0.3140
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.7433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  20809  Z= 0.134
  Angle     :  0.528   6.166  28272  Z= 0.282
  Chirality :  0.039   0.161   3307
  Planarity :  0.004   0.041   3731
  Dihedral  :  4.888  48.886   3076
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 23.78 %
    Favored  : 72.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.40 (0.16), residues: 2833
  helix:  2.04 (0.14), residues: 1548
  sheet: -0.68 (0.26), residues: 363
  loop : -0.22 (0.21), residues: 922

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG Q  38 
 TYR   0.010   0.001   TYR G 107 
 PHE   0.013   0.001   PHE P 130 
 TRP   0.007   0.001   TRP A 843 
 HIS   0.005   0.001   HIS B 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (20809)
  covalent geometry    : angle       0.52805 (28272)
  hydrogen bonds       : bond        0.03688 ( 1327)
  hydrogen bonds       : angle       3.97962 ( 3822)

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

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

  5666 Ramachandran restraints generated.
    2833 Oldfield, 0 Emsley, 2833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5666 Ramachandran restraints generated.
    2833 Oldfield, 0 Emsley, 2833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL   17 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue VAL   26 is missing expected H atoms. Skipping.
Residue THR   28 is missing expected H atoms. Skipping.
Residue LEU   29 is missing expected H atoms. Skipping.
Residue THR   30 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue LEU   33 is missing expected H atoms. Skipping.
Residue SER   34 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue VAL   39 is missing expected H atoms. Skipping.
Residue ILE   47 is missing expected H atoms. Skipping.
Residue LYS   48 is missing expected H atoms. Skipping.
Residue VAL   49 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue VAL   52 is missing expected H atoms. Skipping.
Residue THR   53 is missing expected H atoms. Skipping.
Residue VAL   58 is missing expected H atoms. Skipping.
Residue LEU   60 is missing expected H atoms. Skipping.
Residue LEU   63 is missing expected H atoms. Skipping.
Residue THR   64 is missing expected H atoms. Skipping.
Residue VAL   65 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ILE   73 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue SER   78 is missing expected H atoms. Skipping.
Residue VAL   79 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue LEU   81 is missing expected H atoms. Skipping.
Residue LYS   82 is missing expected H atoms. Skipping.
Residue TYR   84 is missing expected H atoms. Skipping.
Residue VAL   85 is missing expected H atoms. Skipping.
Residue THR   87 is missing expected H atoms. Skipping.
Residue SER   93 is missing expected H atoms. Skipping.
Residue LYS   95 is missing expected H atoms. Skipping.
Residue THR  101 is missing expected H atoms. Skipping.
Residue THR  102 is missing expected H atoms. Skipping.
Residue LYS  106 is missing expected H atoms. Skipping.
Residue ILE  107 is missing expected H atoms. Skipping.
Residue VAL  108 is missing expected H atoms. Skipping.
Residue ILE  109 is missing expected H atoms. Skipping.
Residue LEU  112 is missing expected H atoms. Skipping.
Residue LEU  113 is missing expected H atoms. Skipping.
Residue LEU  117 is missing expected H atoms. Skipping.
Residue SER  120 is missing expected H atoms. Skipping.
Residue ILE  121 is missing expected H atoms. Skipping.
Residue SER  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue VAL  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue SER  127 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue TYR  130 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue SER  133 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  147 is missing expected H atoms. Skipping.
Residue LEU  150 is missing expected H atoms. Skipping.
Residue LEU  151 is missing expected H atoms. Skipping.
Residue MET  152 is missing expected H atoms. Skipping.
Residue MET  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue VAL  156 is missing expected H atoms. Skipping.
Residue SER  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue VAL  163 is missing expected H atoms. Skipping.
Residue MET  167 is missing expected H atoms. Skipping.
Residue VAL  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue THR  174 is missing expected H atoms. Skipping.
Residue VAL  177 is missing expected H atoms. Skipping.
Residue THR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue MET  182 is missing expected H atoms. Skipping.
Residue LEU  184 is missing expected H atoms. Skipping.
Residue VAL  185 is missing expected H atoms. Skipping.
Residue VAL  188 is missing expected H atoms. Skipping.
Residue ILE  189 is missing expected H atoms. Skipping.
Residue LEU  190 is missing expected H atoms. Skipping.
Residue MET  193 is missing expected H atoms. Skipping.
Residue TYR  194 is missing expected H atoms. Skipping.
Residue LYS  195 is missing expected H atoms. Skipping.
Residue ILE  196 is missing expected H atoms. Skipping.
Residue THR  198 is missing expected H atoms. Skipping.
Residue MET  199 is missing expected H atoms. Skipping.
Residue VAL  202 is missing expected H atoms. Skipping.
Residue TYR  203 is missing expected H atoms. Skipping.
Residue ILE  205 is missing expected H atoms. Skipping.
Residue THR  207 is missing expected H atoms. Skipping.
Residue SER  209 is missing expected H atoms. Skipping.
Residue VAL  212 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue THR  216 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue MET  221 is missing expected H atoms. Skipping.
Residue ILE  222 is missing expected H atoms. Skipping.
Residue MET  225 is missing expected H atoms. Skipping.
Residue LEU  228 is missing expected H atoms. Skipping.
Residue LYS  230 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue VAL  235 is missing expected H atoms. Skipping.
Residue LEU  236 is missing expected H atoms. Skipping.
Residue ILE  237 is missing expected H atoms. Skipping.
Residue VAL  240 is missing expected H atoms. Skipping.
Residue VAL  241 is missing expected H atoms. Skipping.
Residue THR  245 is missing expected H atoms. Skipping.
Residue VAL  249 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue ILE  254 is missing expected H atoms. Skipping.
Residue THR  259 is missing expected H atoms. Skipping.
Residue SER  260 is missing expected H atoms. Skipping.
Residue SER  262 is missing expected H atoms. Skipping.
Residue LYS  265 is missing expected H atoms. Skipping.
Residue MET  266 is missing expected H atoms. Skipping.
Residue VAL  268 is missing expected H atoms. Skipping.
Residue LEU  269 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue VAL  272 is missing expected H atoms. Skipping.
Residue THR  273 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue VAL  276 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue MET  283 is missing expected H atoms. Skipping.
Residue VAL  284 is missing expected H atoms. Skipping.
Residue SER  285 is missing expected H atoms. Skipping.
Residue SER  286 is missing expected H atoms. Skipping.
Residue MET  287 is missing expected H atoms. Skipping.
Residue ILE  290 is missing expected H atoms. Skipping.
Residue LEU  291 is missing expected H atoms. Skipping.
Residue ILE  293 is missing expected H atoms. Skipping.
Residue VAL  294 is missing expected H atoms. Skipping.
Residue THR  297 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue THR  299 is missing expected H atoms. Skipping.
Residue SER  301 is missing expected H atoms. Skipping.
Residue TYR  305 is missing expected H atoms. Skipping.
Residue VAL  306 is missing expected H atoms. Skipping.
Residue THR  308 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue VAL  333 is missing expected H atoms. Skipping.
Residue SER  335 is missing expected H atoms. Skipping.
Residue ILE  336 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  344 is missing expected H atoms. Skipping.
Residue SER  347 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LYS  350 is missing expected H atoms. Skipping.
Residue SER  351 is missing expected H atoms. Skipping.
Residue THR  352 is missing expected H atoms. Skipping.
Residue VAL  353 is missing expected H atoms. Skipping.
Residue LYS  354 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LEU  357 is missing expected H atoms. Skipping.
Residue LEU  360 is missing expected H atoms. Skipping.
Residue ILE  361 is missing expected H atoms. Skipping.
Residue TYR  362 is missing expected H atoms. Skipping.
Residue TYR  363 is missing expected H atoms. Skipping.
Residue ILE  364 is missing expected H atoms. Skipping.
Residue ILE  365 is missing expected H atoms. Skipping.
Residue LEU  366 is missing expected H atoms. Skipping.
Residue TYR  367 is missing expected H atoms. Skipping.
Residue MET  368 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue THR  371 is missing expected H atoms. Skipping.
Residue ILE  375 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue VAL  377 is missing expected H atoms. Skipping.
Residue THR  379 is missing expected H atoms. Skipping.
Residue VAL  386 is missing expected H atoms. Skipping.
Residue THR  393 is missing expected H atoms. Skipping.
Residue SER  395 is missing expected H atoms. Skipping.
Residue TYR  396 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue VAL  398 is missing expected H atoms. Skipping.
Residue ILE  400 is missing expected H atoms. Skipping.
Residue LEU  405 is missing expected H atoms. Skipping.
Residue LEU  406 is missing expected H atoms. Skipping.
Residue LEU  407 is missing expected H atoms. Skipping.
Residue VAL  409 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue SER  417 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue THR  426 is missing expected H atoms. Skipping.
Residue LEU  429 is missing expected H atoms. Skipping.
Residue THR  435 is missing expected H atoms. Skipping.
Residue LYS  436 is missing expected H atoms. Skipping.
Residue SER  438 is missing expected H atoms. Skipping.
Residue THR  440 is missing expected H atoms. Skipping.
Residue LYS  445 is missing expected H atoms. Skipping.
Residue ILE  446 is missing expected H atoms. Skipping.
Residue MET  451 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue LEU  454 is missing expected H atoms. Skipping.
Residue SER  456 is missing expected H atoms. Skipping.
Residue VAL  457 is missing expected H atoms. Skipping.
Residue LYS  458 is missing expected H atoms. Skipping.
Residue ILE  460 is missing expected H atoms. Skipping.
Residue ILE  461 is missing expected H atoms. Skipping.
Residue THR  462 is missing expected H atoms. Skipping.
Residue SER  464 is missing expected H atoms. Skipping.
Residue VAL  465 is missing expected H atoms. Skipping.
Residue LYS  466 is missing expected H atoms. Skipping.
Residue ILE  470 is missing expected H atoms. Skipping.
Residue MET  474 is missing expected H atoms. Skipping.
Residue LEU  478 is missing expected H atoms. Skipping.
Residue THR  479 is missing expected H atoms. Skipping.
Residue VAL  481 is missing expected H atoms. Skipping.
Residue ILE  482 is missing expected H atoms. Skipping.
Residue LEU  483 is missing expected H atoms. Skipping.
Residue LEU  486 is missing expected H atoms. Skipping.
Residue LEU  488 is missing expected H atoms. Skipping.
Residue SER  489 is missing expected H atoms. Skipping.
Residue VAL  490 is missing expected H atoms. Skipping.
Residue SER  491 is missing expected H atoms. Skipping.
Residue LEU  494 is missing expected H atoms. Skipping.
Residue LEU  495 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  503 is missing expected H atoms. Skipping.
Residue THR  506 is missing expected H atoms. Skipping.
Residue VAL  507 is missing expected H atoms. Skipping.
Residue MET  509 is missing expected H atoms. Skipping.
Residue SER  510 is missing expected H atoms. Skipping.
Residue LEU  513 is missing expected H atoms. Skipping.
Residue ILE  514 is missing expected H atoms. Skipping.
Residue LEU  518 is missing expected H atoms. Skipping.
Residue THR  521 is missing expected H atoms. Skipping.
Residue VAL  522 is missing expected H atoms. Skipping.
Residue SER  523 is missing expected H atoms. Skipping.
Residue LEU  525 is missing expected H atoms. Skipping.
Residue THR  528 is missing expected H atoms. Skipping.
Residue SER  532 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  535 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  538 is missing expected H atoms. Skipping.
Residue ILE  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LEU  548 is missing expected H atoms. Skipping.
Residue LYS  549 is missing expected H atoms. Skipping.
Residue VAL  550 is missing expected H atoms. Skipping.
Residue SER  551 is missing expected H atoms. Skipping.
Residue SER  553 is missing expected H atoms. Skipping.
Residue THR  554 is missing expected H atoms. Skipping.
Residue VAL  556 is missing expected H atoms. Skipping.
Residue LEU  557 is missing expected H atoms. Skipping.
Residue LEU  561 is missing expected H atoms. Skipping.
Residue SER  563 is missing expected H atoms. Skipping.
Residue ILE  564 is missing expected H atoms. Skipping.
Residue LEU  565 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue LEU  571 is missing expected H atoms. Skipping.
Residue SER  576 is missing expected H atoms. Skipping.
Residue SER  577 is missing expected H atoms. Skipping.
Residue VAL  579 is missing expected H atoms. Skipping.
Residue LEU  580 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue VAL  583 is missing expected H atoms. Skipping.
Residue MET  584 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue LEU  587 is missing expected H atoms. Skipping.
Residue ILE  589 is missing expected H atoms. Skipping.
Residue VAL  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue VAL  593 is missing expected H atoms. Skipping.
Residue THR  598 is missing expected H atoms. Skipping.
Residue SER  600 is missing expected H atoms. Skipping.
Residue MET  601 is missing expected H atoms. Skipping.
Residue SER  603 is missing expected H atoms. Skipping.
Residue LYS  604 is missing expected H atoms. Skipping.
Residue ILE  605 is missing expected H atoms. Skipping.
Residue THR  609 is missing expected H atoms. Skipping.
Residue ILE  610 is missing expected H atoms. Skipping.
Residue ILE  612 is missing expected H atoms. Skipping.
Residue LEU  614 is missing expected H atoms. Skipping.
Residue LYS  615 is missing expected H atoms. Skipping.
Residue LEU  995 is missing expected H atoms. Skipping.
Residue LYS  996 is missing expected H atoms. Skipping.
Residue LEU  999 is missing expected H atoms. Skipping.
Residue TYR 1000 is missing expected H atoms. Skipping.
Residue ILE 1002 is missing expected H atoms. Skipping.
Residue LEU 1004 is missing expected H atoms. Skipping.
Residue TYR 1007 is missing expected H atoms. Skipping.
Residue LEU 1008 is missing expected H atoms. Skipping.
Residue THR 1009 is missing expected H atoms. Skipping.
Residue LEU 1012 is missing expected H atoms. Skipping.
Residue TYR 1021 is missing expected H atoms. Skipping.
Residue ILE 1022 is missing expected H atoms. Skipping.
Residue MET 1023 is missing expected H atoms. Skipping.
Residue SER 1025 is missing expected H atoms. Skipping.
Residue LEU 1028 is missing expected H atoms. Skipping.
Residue VAL 1035 is missing expected H atoms. Skipping.
Residue LEU 1036 is missing expected H atoms. Skipping.
Residue THR 1038 is missing expected H atoms. Skipping.
Residue ILE 1039 is missing expected H atoms. Skipping.
Residue VAL   72 is missing expected H atoms. Skipping.
Residue SER   73 is missing expected H atoms. Skipping.
Residue SER   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue THR   77 is missing expected H atoms. Skipping.
Residue VAL   72 is missing expected H atoms. Skipping.
Residue SER   73 is missing expected H atoms. Skipping.
Residue SER   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue THR   77 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  143 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue VAL  147 is missing expected H atoms. Skipping.
Residue MET  149 is missing expected H atoms. Skipping.
Residue ILE  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue VAL  162 is missing expected H atoms. Skipping.
Residue TYR  166 is missing expected H atoms. Skipping.
Residue ILE  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LEU  174 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  143 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue VAL  147 is missing expected H atoms. Skipping.
Residue MET  149 is missing expected H atoms. Skipping.
Residue ILE  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue VAL  162 is missing expected H atoms. Skipping.
Residue TYR  166 is missing expected H atoms. Skipping.
Residue ILE  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LEU  174 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue VAL  182 is missing expected H atoms. Skipping.
Residue LYS  183 is missing expected H atoms. Skipping.
Evaluate side-chains
  634 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 572
  time to evaluate  : 1.062 
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
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  661 LYS cc_start: 0.8843 (tmmt) cc_final: 0.8416 (tmmt)
REVERT: A  677 VAL cc_start: 0.9281 (t) cc_final: 0.9025 (p)
REVERT: A  699 GLN cc_start: 0.7371 (mm-40) cc_final: 0.6721 (mm-40)
REVERT: A  705 ASP cc_start: 0.7616 (t0) cc_final: 0.7318 (t0)
REVERT: A  742 TYR cc_start: 0.6496 (m-80) cc_final: 0.5689 (m-80)
REVERT: A  757 GLU cc_start: 0.7553 (pm20) cc_final: 0.7238 (pm20)
REVERT: A  797 GLU cc_start: 0.6793 (mm-30) cc_final: 0.6566 (mt-10)
REVERT: A  821 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.6322 (mm)
REVERT: A  825 CYS cc_start: 0.7031 (p) cc_final: 0.6662 (p)
REVERT: A  842 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7503 (mm-30)
REVERT: A  846 ARG cc_start: 0.8570 (ttm110) cc_final: 0.8313 (mpt-90)
REVERT: B  149 MET cc_start: 0.5699 (mtp) cc_final: 0.5180 (mtp)
REVERT: B  168 GLU cc_start: 0.7536 (tp30) cc_final: 0.7162 (tp30)
REVERT: B  178 TYR cc_start: 0.7980 (t80) cc_final: 0.7588 (t80)
REVERT: C   88 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6337 (mm-30)
REVERT: C   95 ARG cc_start: 0.5984 (mtt180) cc_final: 0.5718 (mtt180)
REVERT: C  161 LYS cc_start: 0.6607 (mtmt) cc_final: 0.6284 (mmmt)
REVERT: C  168 GLU cc_start: 0.7830 (tp30) cc_final: 0.7182 (tp30)
REVERT: C  187 ASP cc_start: 0.8281 (m-30) cc_final: 0.8017 (t0)
REVERT: F   42 LYS cc_start: 0.8456 (tttp) cc_final: 0.8084 (tttp)
REVERT: F   59 GLU cc_start: 0.7718 (tp30) cc_final: 0.7425 (tp30)
REVERT: F   77 VAL cc_start: 0.8847 (p) cc_final: 0.8301 (m)
REVERT: F   93 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7048 (mm-30)
REVERT: F  124 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8351 (tt)
REVERT: F  232 ARG cc_start: 0.8047 (tpp80) cc_final: 0.7691 (ttp80)
REVERT: F  236 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7565 (mt-10)
REVERT: F  241 GLU cc_start: 0.6556 (pp20) cc_final: 0.6351 (pp20)
REVERT: G   38 THR cc_start: 0.8872 (t) cc_final: 0.8474 (m)
REVERT: G   96 TYR cc_start: 0.8450 (t80) cc_final: 0.7827 (t80)
REVERT: G   97 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7731 (mm-30)
REVERT: G  174 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7763 (mp0)
REVERT: G  234 GLU cc_start: 0.7889 (tp30) cc_final: 0.7431 (tp30)
REVERT: O   69 LYS cc_start: 0.8499 (pttt) cc_final: 0.8247 (pttt)
REVERT: O  101 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8370 (mm110)
REVERT: O  118 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7050 (tp40)
REVERT: O  149 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7769 (p0)
REVERT: O  155 PHE cc_start: 0.8262 (m-80) cc_final: 0.8032 (m-10)
REVERT: O  175 LYS cc_start: 0.8890 (ttmt) cc_final: 0.8686 (ttmm)
REVERT: O  198 PHE cc_start: 0.8511 (t80) cc_final: 0.8308 (t80)
REVERT: P    8 ARG cc_start: 0.7888 (ttm110) cc_final: 0.7424 (tpp80)
REVERT: P  121 TYR cc_start: 0.8462 (m-10) cc_final: 0.8133 (m-80)
REVERT: P  177 GLN cc_start: 0.8446 (tt0) cc_final: 0.8105 (tp40)
REVERT: P  178 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7635 (t0)
REVERT: P  181 GLU cc_start: 0.8222 (tp30) cc_final: 0.7820 (tp30)
REVERT: P  184 MET cc_start: 0.8530 (mmp) cc_final: 0.8106 (mmm)
REVERT: P  201 MET cc_start: 0.8248 (ttm) cc_final: 0.7973 (ttp)
REVERT: P  222 LYS cc_start: 0.8416 (mmmt) cc_final: 0.8149 (mmmt)
REVERT: P  231 LYS cc_start: 0.8335 (tttt) cc_final: 0.7919 (ttmm)
REVERT: Q   62 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7936 (mt)
REVERT: Q   67 ASP cc_start: 0.8270 (m-30) cc_final: 0.8053 (m-30)
REVERT: Q   96 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8318 (tt)
REVERT: Q   99 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7667 (mm-30)
REVERT: Q  197 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8080 (mt-10)
REVERT: Q  215 GLN cc_start: 0.7880 (tt0) cc_final: 0.7660 (tt0)
REVERT: R   62 SER cc_start: 0.8375 (p) cc_final: 0.8042 (t)
REVERT: R   65 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7389 (mm-30)
REVERT: R  117 SER cc_start: 0.8802 (t) cc_final: 0.8321 (p)
REVERT: R  119 LEU cc_start: 0.8443 (tp) cc_final: 0.8213 (tt)
REVERT: R  156 MET cc_start: 0.7694 (tmm) cc_final: 0.7339 (tmm)
REVERT: R  164 GLN cc_start: 0.8467 (tm-30) cc_final: 0.8085 (tm-30)
REVERT: S   16 GLN cc_start: 0.8219 (mp10) cc_final: 0.7784 (mp10)
REVERT: S   27 GLU cc_start: 0.8333 (tp30) cc_final: 0.8039 (tp30)
  outliers start: 62
  outliers final: 45
  residues processed: 601
  average time/residue: 0.3842
  time to fit residues: 331.6403
Evaluate side-chains
  614 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 561
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain A residue  667 CYS
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain A residue  771 ILE
Chi-restraints excluded: chain A residue  798 THR
Chi-restraints excluded: chain A residue  814 HIS
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  821 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain C residue  166 TYR
Chi-restraints excluded: chain C residue  177 GLN
Chi-restraints excluded: chain F residue   17 ASP
Chi-restraints excluded: chain F residue   30 VAL
Chi-restraints excluded: chain F residue   56 LYS
Chi-restraints excluded: chain F residue  119 VAL
Chi-restraints excluded: chain F residue  123 THR
Chi-restraints excluded: chain F residue  124 LEU
Chi-restraints excluded: chain F residue  156 VAL
Chi-restraints excluded: chain F residue  236 GLU
Chi-restraints excluded: chain F residue  244 LYS
Chi-restraints excluded: chain G residue  211 LYS
Chi-restraints excluded: chain G residue  240 VAL
Chi-restraints excluded: chain O residue   28 VAL
Chi-restraints excluded: chain O residue   50 LYS
Chi-restraints excluded: chain O residue  118 GLN
Chi-restraints excluded: chain O residue  126 VAL
Chi-restraints excluded: chain O residue  149 ASP
Chi-restraints excluded: chain O residue  214 GLU
Chi-restraints excluded: chain O residue  224 GLU
Chi-restraints excluded: chain P residue    9 THR
Chi-restraints excluded: chain P residue   11 ILE
Chi-restraints excluded: chain P residue  134 LEU
Chi-restraints excluded: chain P residue  178 ASP
Chi-restraints excluded: chain P residue  194 ILE
Chi-restraints excluded: chain Q residue   58 THR
Chi-restraints excluded: chain Q residue   62 ILE
Chi-restraints excluded: chain Q residue   96 LEU
Chi-restraints excluded: chain Q residue  114 LEU
Chi-restraints excluded: chain Q residue  129 ILE
Chi-restraints excluded: chain Q residue  147 THR
Chi-restraints excluded: chain Q residue  191 VAL
Chi-restraints excluded: chain Q residue  196 LEU
Chi-restraints excluded: chain Q residue  206 ILE
Chi-restraints excluded: chain R residue   35 SER
Chi-restraints excluded: chain R residue   47 CYS
Chi-restraints excluded: chain R residue  165 CYS
Chi-restraints excluded: chain R residue  183 GLU
Chi-restraints excluded: chain R residue  238 ILE
Chi-restraints excluded: chain S residue   38 LEU
Chi-restraints excluded: chain S residue   53 GLN
Chi-restraints excluded: chain S residue  144 ILE
Chi-restraints excluded: chain S residue  208 LYS
Chi-restraints excluded: chain S residue  227 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 283
   random chunks:
   chunk 194 optimal weight:    1.9990
   chunk 5 optimal weight:    8.9990
   chunk 153 optimal weight:    1.9990
   chunk 243 optimal weight:    2.9990
   chunk 142 optimal weight:    2.9990
   chunk 29 optimal weight:   10.0000
   chunk 247 optimal weight:    0.5980
   chunk 126 optimal weight:    0.9990
   chunk 207 optimal weight:    1.9990
   chunk 86 optimal weight:    4.9990
   chunk 76 optimal weight:    0.7980
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
A 910 ASN
** P 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  13 ASN
R  99 HIS
R 182 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.147337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.117187 restraints weight = 85006.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 1.88
r_work: 0.3245 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3117 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3102
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3102 r_free = 0.3102    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3103 r_free = 0.3103    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
r_final: 0.3103
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.7933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  20809  Z= 0.237
  Angle     :  0.566   5.532  28272  Z= 0.307
  Chirality :  0.040   0.152   3307
  Planarity :  0.004   0.044   3731
  Dihedral  :  4.921  53.706   3072
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 24.21 %
    Favored  : 72.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.28 (0.16), residues: 2833
  helix:  2.00 (0.14), residues: 1547
  sheet: -0.85 (0.26), residues: 366
  loop : -0.35 (0.21), residues: 920

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F 223 
 TYR   0.019   0.002   TYR O 120 
 PHE   0.015   0.002   PHE S 154 
 TRP   0.011   0.002   TRP P 139 
 HIS   0.006   0.001   HIS B 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 (20809)
  covalent geometry    : angle       0.56610 (28272)
  hydrogen bonds       : bond        0.04136 ( 1327)
  hydrogen bonds       : angle       4.06845 ( 3822)

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

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

  5666 Ramachandran restraints generated.
    2833 Oldfield, 0 Emsley, 2833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5666 Ramachandran restraints generated.
    2833 Oldfield, 0 Emsley, 2833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL   17 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue VAL   26 is missing expected H atoms. Skipping.
Residue THR   28 is missing expected H atoms. Skipping.
Residue LEU   29 is missing expected H atoms. Skipping.
Residue THR   30 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue LEU   33 is missing expected H atoms. Skipping.
Residue SER   34 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue VAL   39 is missing expected H atoms. Skipping.
Residue ILE   47 is missing expected H atoms. Skipping.
Residue LYS   48 is missing expected H atoms. Skipping.
Residue VAL   49 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue VAL   52 is missing expected H atoms. Skipping.
Residue THR   53 is missing expected H atoms. Skipping.
Residue VAL   58 is missing expected H atoms. Skipping.
Residue LEU   60 is missing expected H atoms. Skipping.
Residue LEU   63 is missing expected H atoms. Skipping.
Residue THR   64 is missing expected H atoms. Skipping.
Residue VAL   65 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ILE   73 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue SER   78 is missing expected H atoms. Skipping.
Residue VAL   79 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue LEU   81 is missing expected H atoms. Skipping.
Residue LYS   82 is missing expected H atoms. Skipping.
Residue TYR   84 is missing expected H atoms. Skipping.
Residue VAL   85 is missing expected H atoms. Skipping.
Residue THR   87 is missing expected H atoms. Skipping.
Residue SER   93 is missing expected H atoms. Skipping.
Residue LYS   95 is missing expected H atoms. Skipping.
Residue THR  101 is missing expected H atoms. Skipping.
Residue THR  102 is missing expected H atoms. Skipping.
Residue LYS  106 is missing expected H atoms. Skipping.
Residue ILE  107 is missing expected H atoms. Skipping.
Residue VAL  108 is missing expected H atoms. Skipping.
Residue ILE  109 is missing expected H atoms. Skipping.
Residue LEU  112 is missing expected H atoms. Skipping.
Residue LEU  113 is missing expected H atoms. Skipping.
Residue LEU  117 is missing expected H atoms. Skipping.
Residue SER  120 is missing expected H atoms. Skipping.
Residue ILE  121 is missing expected H atoms. Skipping.
Residue SER  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue VAL  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue SER  127 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue TYR  130 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue SER  133 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  147 is missing expected H atoms. Skipping.
Residue LEU  150 is missing expected H atoms. Skipping.
Residue LEU  151 is missing expected H atoms. Skipping.
Residue MET  152 is missing expected H atoms. Skipping.
Residue MET  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue VAL  156 is missing expected H atoms. Skipping.
Residue SER  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue VAL  163 is missing expected H atoms. Skipping.
Residue MET  167 is missing expected H atoms. Skipping.
Residue VAL  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue THR  174 is missing expected H atoms. Skipping.
Residue VAL  177 is missing expected H atoms. Skipping.
Residue THR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue MET  182 is missing expected H atoms. Skipping.
Residue LEU  184 is missing expected H atoms. Skipping.
Residue VAL  185 is missing expected H atoms. Skipping.
Residue VAL  188 is missing expected H atoms. Skipping.
Residue ILE  189 is missing expected H atoms. Skipping.
Residue LEU  190 is missing expected H atoms. Skipping.
Residue MET  193 is missing expected H atoms. Skipping.
Residue TYR  194 is missing expected H atoms. Skipping.
Residue LYS  195 is missing expected H atoms. Skipping.
Residue ILE  196 is missing expected H atoms. Skipping.
Residue THR  198 is missing expected H atoms. Skipping.
Residue MET  199 is missing expected H atoms. Skipping.
Residue VAL  202 is missing expected H atoms. Skipping.
Residue TYR  203 is missing expected H atoms. Skipping.
Residue ILE  205 is missing expected H atoms. Skipping.
Residue THR  207 is missing expected H atoms. Skipping.
Residue SER  209 is missing expected H atoms. Skipping.
Residue VAL  212 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue THR  216 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue MET  221 is missing expected H atoms. Skipping.
Residue ILE  222 is missing expected H atoms. Skipping.
Residue MET  225 is missing expected H atoms. Skipping.
Residue LEU  228 is missing expected H atoms. Skipping.
Residue LYS  230 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue VAL  235 is missing expected H atoms. Skipping.
Residue LEU  236 is missing expected H atoms. Skipping.
Residue ILE  237 is missing expected H atoms. Skipping.
Residue VAL  240 is missing expected H atoms. Skipping.
Residue VAL  241 is missing expected H atoms. Skipping.
Residue THR  245 is missing expected H atoms. Skipping.
Residue VAL  249 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue ILE  254 is missing expected H atoms. Skipping.
Residue THR  259 is missing expected H atoms. Skipping.
Residue SER  260 is missing expected H atoms. Skipping.
Residue SER  262 is missing expected H atoms. Skipping.
Residue LYS  265 is missing expected H atoms. Skipping.
Residue MET  266 is missing expected H atoms. Skipping.
Residue VAL  268 is missing expected H atoms. Skipping.
Residue LEU  269 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue VAL  272 is missing expected H atoms. Skipping.
Residue THR  273 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue VAL  276 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue MET  283 is missing expected H atoms. Skipping.
Residue VAL  284 is missing expected H atoms. Skipping.
Residue SER  285 is missing expected H atoms. Skipping.
Residue SER  286 is missing expected H atoms. Skipping.
Residue MET  287 is missing expected H atoms. Skipping.
Residue ILE  290 is missing expected H atoms. Skipping.
Residue LEU  291 is missing expected H atoms. Skipping.
Residue ILE  293 is missing expected H atoms. Skipping.
Residue VAL  294 is missing expected H atoms. Skipping.
Residue THR  297 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue THR  299 is missing expected H atoms. Skipping.
Residue SER  301 is missing expected H atoms. Skipping.
Residue TYR  305 is missing expected H atoms. Skipping.
Residue VAL  306 is missing expected H atoms. Skipping.
Residue THR  308 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue VAL  333 is missing expected H atoms. Skipping.
Residue SER  335 is missing expected H atoms. Skipping.
Residue ILE  336 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  344 is missing expected H atoms. Skipping.
Residue SER  347 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LYS  350 is missing expected H atoms. Skipping.
Residue SER  351 is missing expected H atoms. Skipping.
Residue THR  352 is missing expected H atoms. Skipping.
Residue VAL  353 is missing expected H atoms. Skipping.
Residue LYS  354 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LEU  357 is missing expected H atoms. Skipping.
Residue LEU  360 is missing expected H atoms. Skipping.
Residue ILE  361 is missing expected H atoms. Skipping.
Residue TYR  362 is missing expected H atoms. Skipping.
Residue TYR  363 is missing expected H atoms. Skipping.
Residue ILE  364 is missing expected H atoms. Skipping.
Residue ILE  365 is missing expected H atoms. Skipping.
Residue LEU  366 is missing expected H atoms. Skipping.
Residue TYR  367 is missing expected H atoms. Skipping.
Residue MET  368 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue THR  371 is missing expected H atoms. Skipping.
Residue ILE  375 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue VAL  377 is missing expected H atoms. Skipping.
Residue THR  379 is missing expected H atoms. Skipping.
Residue VAL  386 is missing expected H atoms. Skipping.
Residue THR  393 is missing expected H atoms. Skipping.
Residue SER  395 is missing expected H atoms. Skipping.
Residue TYR  396 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue VAL  398 is missing expected H atoms. Skipping.
Residue ILE  400 is missing expected H atoms. Skipping.
Residue LEU  405 is missing expected H atoms. Skipping.
Residue LEU  406 is missing expected H atoms. Skipping.
Residue LEU  407 is missing expected H atoms. Skipping.
Residue VAL  409 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue SER  417 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue THR  426 is missing expected H atoms. Skipping.
Residue LEU  429 is missing expected H atoms. Skipping.
Residue THR  435 is missing expected H atoms. Skipping.
Residue LYS  436 is missing expected H atoms. Skipping.
Residue SER  438 is missing expected H atoms. Skipping.
Residue THR  440 is missing expected H atoms. Skipping.
Residue LYS  445 is missing expected H atoms. Skipping.
Residue ILE  446 is missing expected H atoms. Skipping.
Residue MET  451 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue LEU  454 is missing expected H atoms. Skipping.
Residue SER  456 is missing expected H atoms. Skipping.
Residue VAL  457 is missing expected H atoms. Skipping.
Residue LYS  458 is missing expected H atoms. Skipping.
Residue ILE  460 is missing expected H atoms. Skipping.
Residue ILE  461 is missing expected H atoms. Skipping.
Residue THR  462 is missing expected H atoms. Skipping.
Residue SER  464 is missing expected H atoms. Skipping.
Residue VAL  465 is missing expected H atoms. Skipping.
Residue LYS  466 is missing expected H atoms. Skipping.
Residue ILE  470 is missing expected H atoms. Skipping.
Residue MET  474 is missing expected H atoms. Skipping.
Residue LEU  478 is missing expected H atoms. Skipping.
Residue THR  479 is missing expected H atoms. Skipping.
Residue VAL  481 is missing expected H atoms. Skipping.
Residue ILE  482 is missing expected H atoms. Skipping.
Residue LEU  483 is missing expected H atoms. Skipping.
Residue LEU  486 is missing expected H atoms. Skipping.
Residue LEU  488 is missing expected H atoms. Skipping.
Residue SER  489 is missing expected H atoms. Skipping.
Residue VAL  490 is missing expected H atoms. Skipping.
Residue SER  491 is missing expected H atoms. Skipping.
Residue LEU  494 is missing expected H atoms. Skipping.
Residue LEU  495 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  503 is missing expected H atoms. Skipping.
Residue THR  506 is missing expected H atoms. Skipping.
Residue VAL  507 is missing expected H atoms. Skipping.
Residue MET  509 is missing expected H atoms. Skipping.
Residue SER  510 is missing expected H atoms. Skipping.
Residue LEU  513 is missing expected H atoms. Skipping.
Residue ILE  514 is missing expected H atoms. Skipping.
Residue LEU  518 is missing expected H atoms. Skipping.
Residue THR  521 is missing expected H atoms. Skipping.
Residue VAL  522 is missing expected H atoms. Skipping.
Residue SER  523 is missing expected H atoms. Skipping.
Residue LEU  525 is missing expected H atoms. Skipping.
Residue THR  528 is missing expected H atoms. Skipping.
Residue SER  532 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  535 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  538 is missing expected H atoms. Skipping.
Residue ILE  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LEU  548 is missing expected H atoms. Skipping.
Residue LYS  549 is missing expected H atoms. Skipping.
Residue VAL  550 is missing expected H atoms. Skipping.
Residue SER  551 is missing expected H atoms. Skipping.
Residue SER  553 is missing expected H atoms. Skipping.
Residue THR  554 is missing expected H atoms. Skipping.
Residue VAL  556 is missing expected H atoms. Skipping.
Residue LEU  557 is missing expected H atoms. Skipping.
Residue LEU  561 is missing expected H atoms. Skipping.
Residue SER  563 is missing expected H atoms. Skipping.
Residue ILE  564 is missing expected H atoms. Skipping.
Residue LEU  565 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue LEU  571 is missing expected H atoms. Skipping.
Residue SER  576 is missing expected H atoms. Skipping.
Residue SER  577 is missing expected H atoms. Skipping.
Residue VAL  579 is missing expected H atoms. Skipping.
Residue LEU  580 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue VAL  583 is missing expected H atoms. Skipping.
Residue MET  584 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue LEU  587 is missing expected H atoms. Skipping.
Residue ILE  589 is missing expected H atoms. Skipping.
Residue VAL  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue VAL  593 is missing expected H atoms. Skipping.
Residue THR  598 is missing expected H atoms. Skipping.
Residue SER  600 is missing expected H atoms. Skipping.
Residue MET  601 is missing expected H atoms. Skipping.
Residue SER  603 is missing expected H atoms. Skipping.
Residue LYS  604 is missing expected H atoms. Skipping.
Residue ILE  605 is missing expected H atoms. Skipping.
Residue THR  609 is missing expected H atoms. Skipping.
Residue ILE  610 is missing expected H atoms. Skipping.
Residue ILE  612 is missing expected H atoms. Skipping.
Residue LEU  614 is missing expected H atoms. Skipping.
Residue LYS  615 is missing expected H atoms. Skipping.
Residue LEU  995 is missing expected H atoms. Skipping.
Residue LYS  996 is missing expected H atoms. Skipping.
Residue LEU  999 is missing expected H atoms. Skipping.
Residue TYR 1000 is missing expected H atoms. Skipping.
Residue ILE 1002 is missing expected H atoms. Skipping.
Residue LEU 1004 is missing expected H atoms. Skipping.
Residue TYR 1007 is missing expected H atoms. Skipping.
Residue LEU 1008 is missing expected H atoms. Skipping.
Residue THR 1009 is missing expected H atoms. Skipping.
Residue LEU 1012 is missing expected H atoms. Skipping.
Residue TYR 1021 is missing expected H atoms. Skipping.
Residue ILE 1022 is missing expected H atoms. Skipping.
Residue MET 1023 is missing expected H atoms. Skipping.
Residue SER 1025 is missing expected H atoms. Skipping.
Residue LEU 1028 is missing expected H atoms. Skipping.
Residue VAL 1035 is missing expected H atoms. Skipping.
Residue LEU 1036 is missing expected H atoms. Skipping.
Residue THR 1038 is missing expected H atoms. Skipping.
Residue ILE 1039 is missing expected H atoms. Skipping.
Residue VAL   72 is missing expected H atoms. Skipping.
Residue SER   73 is missing expected H atoms. Skipping.
Residue SER   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue THR   77 is missing expected H atoms. Skipping.
Residue VAL   72 is missing expected H atoms. Skipping.
Residue SER   73 is missing expected H atoms. Skipping.
Residue SER   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue THR   77 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  143 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue VAL  147 is missing expected H atoms. Skipping.
Residue MET  149 is missing expected H atoms. Skipping.
Residue ILE  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue VAL  162 is missing expected H atoms. Skipping.
Residue TYR  166 is missing expected H atoms. Skipping.
Residue ILE  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LEU  174 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  143 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue VAL  147 is missing expected H atoms. Skipping.
Residue MET  149 is missing expected H atoms. Skipping.
Residue ILE  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue VAL  162 is missing expected H atoms. Skipping.
Residue TYR  166 is missing expected H atoms. Skipping.
Residue ILE  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LEU  174 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue VAL  182 is missing expected H atoms. Skipping.
Residue LYS  183 is missing expected H atoms. Skipping.
Evaluate side-chains
  640 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 572
  time to evaluate  : 1.087 
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
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  699 GLN cc_start: 0.7542 (mm-40) cc_final: 0.6771 (mm110)
REVERT: A  705 ASP cc_start: 0.7830 (t0) cc_final: 0.7536 (t0)
REVERT: A  706 ASP cc_start: 0.7003 (t0) cc_final: 0.6746 (t0)
REVERT: A  742 TYR cc_start: 0.6872 (m-80) cc_final: 0.5800 (m-80)
REVERT: A  757 GLU cc_start: 0.7694 (pm20) cc_final: 0.7321 (pm20)
REVERT: A  797 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6715 (mt-10)
REVERT: A  821 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.6389 (mm)
REVERT: A  825 CYS cc_start: 0.7158 (p) cc_final: 0.6754 (p)
REVERT: A  842 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7471 (mm-30)
REVERT: A  846 ARG cc_start: 0.8575 (ttm110) cc_final: 0.8243 (mpt-90)
REVERT: A  917 ILE cc_start: 0.6720 (mp) cc_final: 0.6342 (pt)
REVERT: B  149 MET cc_start: 0.5643 (mtp) cc_final: 0.5360 (mtp)
REVERT: B  169 ILE cc_start: 0.7977 (tt) cc_final: 0.7650 (pt)
REVERT: B  178 TYR cc_start: 0.8185 (t80) cc_final: 0.7669 (t80)
REVERT: B  187 ASP cc_start: 0.7983 (t0) cc_final: 0.7753 (t0)
REVERT: C   88 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6612 (mm-30)
REVERT: C  146 GLN cc_start: 0.6289 (mp10) cc_final: 0.5761 (mp10)
REVERT: C  161 LYS cc_start: 0.6652 (mtmt) cc_final: 0.6310 (mmmt)
REVERT: C  168 GLU cc_start: 0.7814 (tp30) cc_final: 0.7145 (tp30)
REVERT: C  187 ASP cc_start: 0.8227 (m-30) cc_final: 0.7935 (t0)
REVERT: F   30 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8378 (t)
REVERT: F   42 LYS cc_start: 0.8423 (tttp) cc_final: 0.8019 (tttp)
REVERT: F   59 GLU cc_start: 0.7805 (tp30) cc_final: 0.7505 (tp30)
REVERT: F   77 VAL cc_start: 0.8853 (p) cc_final: 0.8320 (m)
REVERT: F   93 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7256 (mm-30)
REVERT: F  124 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8343 (tt)
REVERT: F  232 ARG cc_start: 0.8242 (tpp80) cc_final: 0.7914 (ttp80)
REVERT: F  236 GLU cc_start: 0.7874 (tt0) cc_final: 0.7657 (mt-10)
REVERT: G   24 GLN cc_start: 0.7103 (OUTLIER) cc_final: 0.6594 (mt0)
REVERT: G   38 THR cc_start: 0.9053 (t) cc_final: 0.8648 (m)
REVERT: G   96 TYR cc_start: 0.8514 (t80) cc_final: 0.7868 (t80)
REVERT: G   97 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7606 (mm-30)
REVERT: G  174 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7906 (mp0)
REVERT: G  234 GLU cc_start: 0.7859 (tp30) cc_final: 0.7371 (tp30)
REVERT: O  101 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8154 (mm-40)
REVERT: O  118 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7433 (tp40)
REVERT: O  155 PHE cc_start: 0.8359 (m-80) cc_final: 0.8142 (m-80)
REVERT: O  175 LYS cc_start: 0.8850 (ttmt) cc_final: 0.8569 (ttmm)
REVERT: O  196 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8099 (mm-30)
REVERT: P  177 GLN cc_start: 0.8427 (tt0) cc_final: 0.8051 (tp40)
REVERT: P  178 ASP cc_start: 0.8039 (m-30) cc_final: 0.7758 (m-30)
REVERT: P  181 GLU cc_start: 0.8166 (tp30) cc_final: 0.7768 (tp30)
REVERT: P  184 MET cc_start: 0.8564 (mmp) cc_final: 0.7958 (mmm)
REVERT: P  201 MET cc_start: 0.8320 (ttm) cc_final: 0.8063 (ttp)
REVERT: P  222 LYS cc_start: 0.8387 (mmmt) cc_final: 0.8073 (mmmt)
REVERT: P  231 LYS cc_start: 0.8357 (tttt) cc_final: 0.7910 (ttmm)
REVERT: P  235 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7199 (tm-30)
REVERT: Q   62 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7992 (mt)
REVERT: Q   67 ASP cc_start: 0.8320 (m-30) cc_final: 0.8073 (m-30)
REVERT: Q   96 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8384 (tt)
REVERT: Q  197 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8209 (mt-10)
REVERT: R   62 SER cc_start: 0.8583 (OUTLIER) cc_final: 0.8303 (t)
REVERT: R   65 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7538 (mm-30)
REVERT: R   90 ASP cc_start: 0.8097 (t0) cc_final: 0.7510 (t0)
REVERT: R  117 SER cc_start: 0.8839 (t) cc_final: 0.8452 (p)
REVERT: R  119 LEU cc_start: 0.8330 (tp) cc_final: 0.8130 (tt)
REVERT: R  156 MET cc_start: 0.7690 (tmm) cc_final: 0.7266 (tmm)
REVERT: R  164 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8112 (tm-30)
REVERT: R  207 GLU cc_start: 0.7848 (pt0) cc_final: 0.7474 (pp20)
REVERT: S   16 GLN cc_start: 0.8271 (mp10) cc_final: 0.7841 (mp10)
REVERT: S   27 GLU cc_start: 0.8380 (tp30) cc_final: 0.8100 (tp30)
  outliers start: 68
  outliers final: 46
  residues processed: 605
  average time/residue: 0.3729
  time to fit residues: 323.6156
Evaluate side-chains
  608 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 554
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain A residue  667 CYS
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain A residue  771 ILE
Chi-restraints excluded: chain A residue  798 THR
Chi-restraints excluded: chain A residue  814 HIS
Chi-restraints excluded: chain A residue  815 THR
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  821 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain C residue  166 TYR
Chi-restraints excluded: chain C residue  177 GLN
Chi-restraints excluded: chain F residue   30 VAL
Chi-restraints excluded: chain F residue  119 VAL
Chi-restraints excluded: chain F residue  120 HIS
Chi-restraints excluded: chain F residue  123 THR
Chi-restraints excluded: chain F residue  124 LEU
Chi-restraints excluded: chain F residue  156 VAL
Chi-restraints excluded: chain F residue  210 GLU
Chi-restraints excluded: chain F residue  244 LYS
Chi-restraints excluded: chain G residue   24 GLN
Chi-restraints excluded: chain G residue   59 LYS
Chi-restraints excluded: chain G residue  211 LYS
Chi-restraints excluded: chain G residue  240 VAL
Chi-restraints excluded: chain O residue   28 VAL
Chi-restraints excluded: chain O residue   50 LYS
Chi-restraints excluded: chain O residue  118 GLN
Chi-restraints excluded: chain O residue  119 GLU
Chi-restraints excluded: chain O residue  212 CYS
Chi-restraints excluded: chain O residue  214 GLU
Chi-restraints excluded: chain O residue  224 GLU
Chi-restraints excluded: chain P residue    9 THR
Chi-restraints excluded: chain P residue   11 ILE
Chi-restraints excluded: chain P residue   64 LYS
Chi-restraints excluded: chain P residue  194 ILE
Chi-restraints excluded: chain Q residue   58 THR
Chi-restraints excluded: chain Q residue   62 ILE
Chi-restraints excluded: chain Q residue   96 LEU
Chi-restraints excluded: chain Q residue  114 LEU
Chi-restraints excluded: chain Q residue  129 ILE
Chi-restraints excluded: chain Q residue  147 THR
Chi-restraints excluded: chain Q residue  196 LEU
Chi-restraints excluded: chain Q residue  206 ILE
Chi-restraints excluded: chain R residue   35 SER
Chi-restraints excluded: chain R residue   47 CYS
Chi-restraints excluded: chain R residue   62 SER
Chi-restraints excluded: chain R residue  122 GLN
Chi-restraints excluded: chain R residue  165 CYS
Chi-restraints excluded: chain S residue   38 LEU
Chi-restraints excluded: chain S residue   53 GLN
Chi-restraints excluded: chain S residue  144 ILE
Chi-restraints excluded: chain S residue  208 LYS
Chi-restraints excluded: chain S residue  227 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 283
   random chunks:
   chunk 132 optimal weight:    0.6980
   chunk 112 optimal weight:    8.9990
   chunk 19 optimal weight:    5.9990
   chunk 234 optimal weight:    0.1980
   chunk 141 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   chunk 27 optimal weight:    6.9990
   chunk 151 optimal weight:    0.9990
   chunk 102 optimal weight:    2.9990
   chunk 217 optimal weight:    0.6980
   chunk 104 optimal weight:    1.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 644 GLN
A 910 ASN
D  84 ASN
R 182 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.142786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.112424 restraints weight = 85266.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 1.82
r_work: 0.3277 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3123
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
r_final: 0.3123
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.8116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  20809  Z= 0.166
  Angle     :  0.535   6.088  28272  Z= 0.287
  Chirality :  0.039   0.151   3307
  Planarity :  0.004   0.054   3731
  Dihedral  :  4.814  55.730   3072
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 25.41 %
    Favored  : 71.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.16), residues: 2833
  helix:  2.14 (0.14), residues: 1548
  sheet: -0.63 (0.27), residues: 354
  loop : -0.24 (0.21), residues: 931

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG Q  38 
 TYR   0.014   0.001   TYR G 107 
 PHE   0.013   0.001   PHE R 226 
 TRP   0.009   0.001   TRP A 843 
 HIS   0.006   0.001   HIS B 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (20809)
  covalent geometry    : angle       0.53509 (28272)
  hydrogen bonds       : bond        0.03693 ( 1327)
  hydrogen bonds       : angle       3.93223 ( 3822)

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

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

  5666 Ramachandran restraints generated.
    2833 Oldfield, 0 Emsley, 2833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5666 Ramachandran restraints generated.
    2833 Oldfield, 0 Emsley, 2833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL   17 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue VAL   26 is missing expected H atoms. Skipping.
Residue THR   28 is missing expected H atoms. Skipping.
Residue LEU   29 is missing expected H atoms. Skipping.
Residue THR   30 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue LEU   33 is missing expected H atoms. Skipping.
Residue SER   34 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue VAL   39 is missing expected H atoms. Skipping.
Residue ILE   47 is missing expected H atoms. Skipping.
Residue LYS   48 is missing expected H atoms. Skipping.
Residue VAL   49 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue VAL   52 is missing expected H atoms. Skipping.
Residue THR   53 is missing expected H atoms. Skipping.
Residue VAL   58 is missing expected H atoms. Skipping.
Residue LEU   60 is missing expected H atoms. Skipping.
Residue LEU   63 is missing expected H atoms. Skipping.
Residue THR   64 is missing expected H atoms. Skipping.
Residue VAL   65 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ILE   73 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue SER   78 is missing expected H atoms. Skipping.
Residue VAL   79 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue LEU   81 is missing expected H atoms. Skipping.
Residue LYS   82 is missing expected H atoms. Skipping.
Residue TYR   84 is missing expected H atoms. Skipping.
Residue VAL   85 is missing expected H atoms. Skipping.
Residue THR   87 is missing expected H atoms. Skipping.
Residue SER   93 is missing expected H atoms. Skipping.
Residue LYS   95 is missing expected H atoms. Skipping.
Residue THR  101 is missing expected H atoms. Skipping.
Residue THR  102 is missing expected H atoms. Skipping.
Residue LYS  106 is missing expected H atoms. Skipping.
Residue ILE  107 is missing expected H atoms. Skipping.
Residue VAL  108 is missing expected H atoms. Skipping.
Residue ILE  109 is missing expected H atoms. Skipping.
Residue LEU  112 is missing expected H atoms. Skipping.
Residue LEU  113 is missing expected H atoms. Skipping.
Residue LEU  117 is missing expected H atoms. Skipping.
Residue SER  120 is missing expected H atoms. Skipping.
Residue ILE  121 is missing expected H atoms. Skipping.
Residue SER  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue VAL  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue SER  127 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue TYR  130 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue SER  133 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  147 is missing expected H atoms. Skipping.
Residue LEU  150 is missing expected H atoms. Skipping.
Residue LEU  151 is missing expected H atoms. Skipping.
Residue MET  152 is missing expected H atoms. Skipping.
Residue MET  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue VAL  156 is missing expected H atoms. Skipping.
Residue SER  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue VAL  163 is missing expected H atoms. Skipping.
Residue MET  167 is missing expected H atoms. Skipping.
Residue VAL  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue THR  174 is missing expected H atoms. Skipping.
Residue VAL  177 is missing expected H atoms. Skipping.
Residue THR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue MET  182 is missing expected H atoms. Skipping.
Residue LEU  184 is missing expected H atoms. Skipping.
Residue VAL  185 is missing expected H atoms. Skipping.
Residue VAL  188 is missing expected H atoms. Skipping.
Residue ILE  189 is missing expected H atoms. Skipping.
Residue LEU  190 is missing expected H atoms. Skipping.
Residue MET  193 is missing expected H atoms. Skipping.
Residue TYR  194 is missing expected H atoms. Skipping.
Residue LYS  195 is missing expected H atoms. Skipping.
Residue ILE  196 is missing expected H atoms. Skipping.
Residue THR  198 is missing expected H atoms. Skipping.
Residue MET  199 is missing expected H atoms. Skipping.
Residue VAL  202 is missing expected H atoms. Skipping.
Residue TYR  203 is missing expected H atoms. Skipping.
Residue ILE  205 is missing expected H atoms. Skipping.
Residue THR  207 is missing expected H atoms. Skipping.
Residue SER  209 is missing expected H atoms. Skipping.
Residue VAL  212 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue THR  216 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue MET  221 is missing expected H atoms. Skipping.
Residue ILE  222 is missing expected H atoms. Skipping.
Residue MET  225 is missing expected H atoms. Skipping.
Residue LEU  228 is missing expected H atoms. Skipping.
Residue LYS  230 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue VAL  235 is missing expected H atoms. Skipping.
Residue LEU  236 is missing expected H atoms. Skipping.
Residue ILE  237 is missing expected H atoms. Skipping.
Residue VAL  240 is missing expected H atoms. Skipping.
Residue VAL  241 is missing expected H atoms. Skipping.
Residue THR  245 is missing expected H atoms. Skipping.
Residue VAL  249 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue ILE  254 is missing expected H atoms. Skipping.
Residue THR  259 is missing expected H atoms. Skipping.
Residue SER  260 is missing expected H atoms. Skipping.
Residue SER  262 is missing expected H atoms. Skipping.
Residue LYS  265 is missing expected H atoms. Skipping.
Residue MET  266 is missing expected H atoms. Skipping.
Residue VAL  268 is missing expected H atoms. Skipping.
Residue LEU  269 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue VAL  272 is missing expected H atoms. Skipping.
Residue THR  273 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue VAL  276 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue MET  283 is missing expected H atoms. Skipping.
Residue VAL  284 is missing expected H atoms. Skipping.
Residue SER  285 is missing expected H atoms. Skipping.
Residue SER  286 is missing expected H atoms. Skipping.
Residue MET  287 is missing expected H atoms. Skipping.
Residue ILE  290 is missing expected H atoms. Skipping.
Residue LEU  291 is missing expected H atoms. Skipping.
Residue ILE  293 is missing expected H atoms. Skipping.
Residue VAL  294 is missing expected H atoms. Skipping.
Residue THR  297 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue THR  299 is missing expected H atoms. Skipping.
Residue SER  301 is missing expected H atoms. Skipping.
Residue TYR  305 is missing expected H atoms. Skipping.
Residue VAL  306 is missing expected H atoms. Skipping.
Residue THR  308 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue VAL  333 is missing expected H atoms. Skipping.
Residue SER  335 is missing expected H atoms. Skipping.
Residue ILE  336 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  344 is missing expected H atoms. Skipping.
Residue SER  347 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LYS  350 is missing expected H atoms. Skipping.
Residue SER  351 is missing expected H atoms. Skipping.
Residue THR  352 is missing expected H atoms. Skipping.
Residue VAL  353 is missing expected H atoms. Skipping.
Residue LYS  354 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LEU  357 is missing expected H atoms. Skipping.
Residue LEU  360 is missing expected H atoms. Skipping.
Residue ILE  361 is missing expected H atoms. Skipping.
Residue TYR  362 is missing expected H atoms. Skipping.
Residue TYR  363 is missing expected H atoms. Skipping.
Residue ILE  364 is missing expected H atoms. Skipping.
Residue ILE  365 is missing expected H atoms. Skipping.
Residue LEU  366 is missing expected H atoms. Skipping.
Residue TYR  367 is missing expected H atoms. Skipping.
Residue MET  368 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue THR  371 is missing expected H atoms. Skipping.
Residue ILE  375 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue VAL  377 is missing expected H atoms. Skipping.
Residue THR  379 is missing expected H atoms. Skipping.
Residue VAL  386 is missing expected H atoms. Skipping.
Residue THR  393 is missing expected H atoms. Skipping.
Residue SER  395 is missing expected H atoms. Skipping.
Residue TYR  396 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue VAL  398 is missing expected H atoms. Skipping.
Residue ILE  400 is missing expected H atoms. Skipping.
Residue LEU  405 is missing expected H atoms. Skipping.
Residue LEU  406 is missing expected H atoms. Skipping.
Residue LEU  407 is missing expected H atoms. Skipping.
Residue VAL  409 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue SER  417 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue THR  426 is missing expected H atoms. Skipping.
Residue LEU  429 is missing expected H atoms. Skipping.
Residue THR  435 is missing expected H atoms. Skipping.
Residue LYS  436 is missing expected H atoms. Skipping.
Residue SER  438 is missing expected H atoms. Skipping.
Residue THR  440 is missing expected H atoms. Skipping.
Residue LYS  445 is missing expected H atoms. Skipping.
Residue ILE  446 is missing expected H atoms. Skipping.
Residue MET  451 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue LEU  454 is missing expected H atoms. Skipping.
Residue SER  456 is missing expected H atoms. Skipping.
Residue VAL  457 is missing expected H atoms. Skipping.
Residue LYS  458 is missing expected H atoms. Skipping.
Residue ILE  460 is missing expected H atoms. Skipping.
Residue ILE  461 is missing expected H atoms. Skipping.
Residue THR  462 is missing expected H atoms. Skipping.
Residue SER  464 is missing expected H atoms. Skipping.
Residue VAL  465 is missing expected H atoms. Skipping.
Residue LYS  466 is missing expected H atoms. Skipping.
Residue ILE  470 is missing expected H atoms. Skipping.
Residue MET  474 is missing expected H atoms. Skipping.
Residue LEU  478 is missing expected H atoms. Skipping.
Residue THR  479 is missing expected H atoms. Skipping.
Residue VAL  481 is missing expected H atoms. Skipping.
Residue ILE  482 is missing expected H atoms. Skipping.
Residue LEU  483 is missing expected H atoms. Skipping.
Residue LEU  486 is missing expected H atoms. Skipping.
Residue LEU  488 is missing expected H atoms. Skipping.
Residue SER  489 is missing expected H atoms. Skipping.
Residue VAL  490 is missing expected H atoms. Skipping.
Residue SER  491 is missing expected H atoms. Skipping.
Residue LEU  494 is missing expected H atoms. Skipping.
Residue LEU  495 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  503 is missing expected H atoms. Skipping.
Residue THR  506 is missing expected H atoms. Skipping.
Residue VAL  507 is missing expected H atoms. Skipping.
Residue MET  509 is missing expected H atoms. Skipping.
Residue SER  510 is missing expected H atoms. Skipping.
Residue LEU  513 is missing expected H atoms. Skipping.
Residue ILE  514 is missing expected H atoms. Skipping.
Residue LEU  518 is missing expected H atoms. Skipping.
Residue THR  521 is missing expected H atoms. Skipping.
Residue VAL  522 is missing expected H atoms. Skipping.
Residue SER  523 is missing expected H atoms. Skipping.
Residue LEU  525 is missing expected H atoms. Skipping.
Residue THR  528 is missing expected H atoms. Skipping.
Residue SER  532 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  535 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  538 is missing expected H atoms. Skipping.
Residue ILE  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LEU  548 is missing expected H atoms. Skipping.
Residue LYS  549 is missing expected H atoms. Skipping.
Residue VAL  550 is missing expected H atoms. Skipping.
Residue SER  551 is missing expected H atoms. Skipping.
Residue SER  553 is missing expected H atoms. Skipping.
Residue THR  554 is missing expected H atoms. Skipping.
Residue VAL  556 is missing expected H atoms. Skipping.
Residue LEU  557 is missing expected H atoms. Skipping.
Residue LEU  561 is missing expected H atoms. Skipping.
Residue SER  563 is missing expected H atoms. Skipping.
Residue ILE  564 is missing expected H atoms. Skipping.
Residue LEU  565 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue LEU  571 is missing expected H atoms. Skipping.
Residue SER  576 is missing expected H atoms. Skipping.
Residue SER  577 is missing expected H atoms. Skipping.
Residue VAL  579 is missing expected H atoms. Skipping.
Residue LEU  580 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue VAL  583 is missing expected H atoms. Skipping.
Residue MET  584 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue LEU  587 is missing expected H atoms. Skipping.
Residue ILE  589 is missing expected H atoms. Skipping.
Residue VAL  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue VAL  593 is missing expected H atoms. Skipping.
Residue THR  598 is missing expected H atoms. Skipping.
Residue SER  600 is missing expected H atoms. Skipping.
Residue MET  601 is missing expected H atoms. Skipping.
Residue SER  603 is missing expected H atoms. Skipping.
Residue LYS  604 is missing expected H atoms. Skipping.
Residue ILE  605 is missing expected H atoms. Skipping.
Residue THR  609 is missing expected H atoms. Skipping.
Residue ILE  610 is missing expected H atoms. Skipping.
Residue ILE  612 is missing expected H atoms. Skipping.
Residue LEU  614 is missing expected H atoms. Skipping.
Residue LYS  615 is missing expected H atoms. Skipping.
Residue LEU  995 is missing expected H atoms. Skipping.
Residue LYS  996 is missing expected H atoms. Skipping.
Residue LEU  999 is missing expected H atoms. Skipping.
Residue TYR 1000 is missing expected H atoms. Skipping.
Residue ILE 1002 is missing expected H atoms. Skipping.
Residue LEU 1004 is missing expected H atoms. Skipping.
Residue TYR 1007 is missing expected H atoms. Skipping.
Residue LEU 1008 is missing expected H atoms. Skipping.
Residue THR 1009 is missing expected H atoms. Skipping.
Residue LEU 1012 is missing expected H atoms. Skipping.
Residue TYR 1021 is missing expected H atoms. Skipping.
Residue ILE 1022 is missing expected H atoms. Skipping.
Residue MET 1023 is missing expected H atoms. Skipping.
Residue SER 1025 is missing expected H atoms. Skipping.
Residue LEU 1028 is missing expected H atoms. Skipping.
Residue VAL 1035 is missing expected H atoms. Skipping.
Residue LEU 1036 is missing expected H atoms. Skipping.
Residue THR 1038 is missing expected H atoms. Skipping.
Residue ILE 1039 is missing expected H atoms. Skipping.
Residue VAL   72 is missing expected H atoms. Skipping.
Residue SER   73 is missing expected H atoms. Skipping.
Residue SER   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue THR   77 is missing expected H atoms. Skipping.
Residue VAL   72 is missing expected H atoms. Skipping.
Residue SER   73 is missing expected H atoms. Skipping.
Residue SER   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue THR   77 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  143 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue VAL  147 is missing expected H atoms. Skipping.
Residue MET  149 is missing expected H atoms. Skipping.
Residue ILE  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue VAL  162 is missing expected H atoms. Skipping.
Residue TYR  166 is missing expected H atoms. Skipping.
Residue ILE  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LEU  174 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  143 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue VAL  147 is missing expected H atoms. Skipping.
Residue MET  149 is missing expected H atoms. Skipping.
Residue ILE  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue VAL  162 is missing expected H atoms. Skipping.
Residue TYR  166 is missing expected H atoms. Skipping.
Residue ILE  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LEU  174 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue VAL  182 is missing expected H atoms. Skipping.
Residue LYS  183 is missing expected H atoms. Skipping.
Evaluate side-chains
  614 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 557
  time to evaluate  : 1.026 
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: A  640 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7551 (mm110)
REVERT: A  644 GLN cc_start: 0.7887 (mt0) cc_final: 0.7677 (mt0)
REVERT: A  699 GLN cc_start: 0.6963 (mm-40) cc_final: 0.6584 (mm-40)
REVERT: A  705 ASP cc_start: 0.7820 (t0) cc_final: 0.7536 (t0)
REVERT: A  706 ASP cc_start: 0.7017 (t0) cc_final: 0.6714 (t0)
REVERT: A  757 GLU cc_start: 0.7689 (pm20) cc_final: 0.7328 (pm20)
REVERT: A  797 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6739 (mt-10)
REVERT: A  825 CYS cc_start: 0.7206 (p) cc_final: 0.6776 (p)
REVERT: A  843 TRP cc_start: 0.7095 (t60) cc_final: 0.6833 (t-100)
REVERT: A  846 ARG cc_start: 0.8546 (ttm110) cc_final: 0.8258 (mpt-90)
REVERT: B  149 MET cc_start: 0.5593 (mtp) cc_final: 0.5351 (mtp)
REVERT: B  169 ILE cc_start: 0.7985 (tt) cc_final: 0.7733 (pt)
REVERT: B  178 TYR cc_start: 0.8161 (t80) cc_final: 0.7679 (t80)
REVERT: C   88 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6810 (mm-30)
REVERT: C  146 GLN cc_start: 0.6292 (mp10) cc_final: 0.5768 (mp10)
REVERT: C  161 LYS cc_start: 0.6682 (mtmt) cc_final: 0.6328 (mmmt)
REVERT: C  168 GLU cc_start: 0.7847 (tp30) cc_final: 0.7091 (tp30)
REVERT: C  177 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7843 (mt0)
REVERT: C  187 ASP cc_start: 0.8211 (m-30) cc_final: 0.7971 (t0)
REVERT: C  196 GLN cc_start: 0.8522 (mm-40) cc_final: 0.8045 (mm-40)
REVERT: F   30 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8394 (t)
REVERT: F   42 LYS cc_start: 0.8460 (tttp) cc_final: 0.8044 (tttp)
REVERT: F   59 GLU cc_start: 0.7870 (tp30) cc_final: 0.7578 (tp30)
REVERT: F   77 VAL cc_start: 0.8821 (p) cc_final: 0.8311 (m)
REVERT: F  124 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8364 (tt)
REVERT: F  218 GLU cc_start: 0.7102 (tp30) cc_final: 0.6704 (tp30)
REVERT: F  232 ARG cc_start: 0.8212 (tpp80) cc_final: 0.7848 (ttp80)
REVERT: G   26 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7431 (mt-10)
REVERT: G   38 THR cc_start: 0.9059 (t) cc_final: 0.8682 (m)
REVERT: G   96 TYR cc_start: 0.8468 (t80) cc_final: 0.7827 (t80)
REVERT: G   97 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7838 (tp30)
REVERT: G  112 ASP cc_start: 0.7655 (t0) cc_final: 0.7344 (p0)
REVERT: G  174 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7908 (mp0)
REVERT: G  234 GLU cc_start: 0.7764 (tp30) cc_final: 0.7237 (tp30)
REVERT: O  101 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8351 (mm-40)
REVERT: O  118 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7587 (tp40)
REVERT: O  175 LYS cc_start: 0.8849 (ttmt) cc_final: 0.8314 (mtpp)
REVERT: P   15 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7776 (mt-10)
REVERT: P  143 TYR cc_start: 0.8430 (m-10) cc_final: 0.8168 (m-10)
REVERT: P  177 GLN cc_start: 0.8346 (tt0) cc_final: 0.8007 (tp40)
REVERT: P  178 ASP cc_start: 0.8072 (m-30) cc_final: 0.7618 (t0)
REVERT: P  180 LYS cc_start: 0.8564 (ttmm) cc_final: 0.8361 (ttmm)
REVERT: P  181 GLU cc_start: 0.8178 (tp30) cc_final: 0.7683 (tp30)
REVERT: P  184 MET cc_start: 0.8540 (mmp) cc_final: 0.7923 (mmt)
REVERT: P  201 MET cc_start: 0.8326 (ttm) cc_final: 0.8070 (ttp)
REVERT: P  222 LYS cc_start: 0.8378 (mmmt) cc_final: 0.8070 (mmmt)
REVERT: P  231 LYS cc_start: 0.8340 (tttt) cc_final: 0.7898 (ttmm)
REVERT: P  235 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7172 (tm-30)
REVERT: Q   62 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8101 (mt)
REVERT: Q   67 ASP cc_start: 0.8290 (m-30) cc_final: 0.8049 (m-30)
REVERT: Q   96 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8374 (tt)
REVERT: Q   99 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7532 (mm-30)
REVERT: Q  197 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8234 (mt-10)
REVERT: Q  227 LYS cc_start: 0.8180 (tmmt) cc_final: 0.7688 (tmmt)
REVERT: R   62 SER cc_start: 0.8592 (OUTLIER) cc_final: 0.8255 (t)
REVERT: R   65 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7478 (mm-30)
REVERT: R   90 ASP cc_start: 0.8039 (t0) cc_final: 0.7465 (t0)
REVERT: R   91 LYS cc_start: 0.8535 (tptt) cc_final: 0.8313 (tptt)
REVERT: R   95 GLU cc_start: 0.7716 (tp30) cc_final: 0.7375 (tp30)
REVERT: R  117 SER cc_start: 0.8835 (t) cc_final: 0.8447 (p)
REVERT: R  119 LEU cc_start: 0.8400 (tp) cc_final: 0.8193 (tt)
REVERT: R  156 MET cc_start: 0.7597 (tmm) cc_final: 0.7155 (tmm)
REVERT: R  164 GLN cc_start: 0.8404 (tm-30) cc_final: 0.7746 (tm-30)
REVERT: R  207 GLU cc_start: 0.7561 (pt0) cc_final: 0.7226 (pp20)
REVERT: S   27 GLU cc_start: 0.8388 (tp30) cc_final: 0.8128 (tp30)
REVERT: S  144 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7507 (mm)
REVERT: S  171 TYR cc_start: 0.8268 (t80) cc_final: 0.7595 (t80)
  outliers start: 57
  outliers final: 42
  residues processed: 583
  average time/residue: 0.3569
  time to fit residues: 298.0645
Evaluate side-chains
  603 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 553
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain A residue  667 CYS
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain A residue  771 ILE
Chi-restraints excluded: chain A residue  798 THR
Chi-restraints excluded: chain A residue  814 HIS
Chi-restraints excluded: chain A residue  815 THR
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain C residue  166 TYR
Chi-restraints excluded: chain C residue  177 GLN
Chi-restraints excluded: chain F residue   30 VAL
Chi-restraints excluded: chain F residue   94 GLU
Chi-restraints excluded: chain F residue  119 VAL
Chi-restraints excluded: chain F residue  123 THR
Chi-restraints excluded: chain F residue  124 LEU
Chi-restraints excluded: chain F residue  156 VAL
Chi-restraints excluded: chain F residue  202 ASP
Chi-restraints excluded: chain F residue  244 LYS
Chi-restraints excluded: chain G residue   59 LYS
Chi-restraints excluded: chain G residue  211 LYS
Chi-restraints excluded: chain G residue  240 VAL
Chi-restraints excluded: chain O residue   28 VAL
Chi-restraints excluded: chain O residue  118 GLN
Chi-restraints excluded: chain O residue  212 CYS
Chi-restraints excluded: chain O residue  224 GLU
Chi-restraints excluded: chain P residue    9 THR
Chi-restraints excluded: chain P residue   11 ILE
Chi-restraints excluded: chain P residue   74 CYS
Chi-restraints excluded: chain P residue  194 ILE
Chi-restraints excluded: chain Q residue   58 THR
Chi-restraints excluded: chain Q residue   62 ILE
Chi-restraints excluded: chain Q residue   96 LEU
Chi-restraints excluded: chain Q residue  114 LEU
Chi-restraints excluded: chain Q residue  129 ILE
Chi-restraints excluded: chain Q residue  147 THR
Chi-restraints excluded: chain Q residue  196 LEU
Chi-restraints excluded: chain R residue   35 SER
Chi-restraints excluded: chain R residue   47 CYS
Chi-restraints excluded: chain R residue   62 SER
Chi-restraints excluded: chain R residue  122 GLN
Chi-restraints excluded: chain R residue  165 CYS
Chi-restraints excluded: chain R residue  183 GLU
Chi-restraints excluded: chain S residue   38 LEU
Chi-restraints excluded: chain S residue   49 LEU
Chi-restraints excluded: chain S residue   53 GLN
Chi-restraints excluded: chain S residue  144 ILE
Chi-restraints excluded: chain S residue  208 LYS
Chi-restraints excluded: chain S residue  227 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 283
   random chunks:
   chunk 259 optimal weight:    1.9990
   chunk 153 optimal weight:    1.9990
   chunk 197 optimal weight:    0.9980
   chunk 150 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 185 optimal weight:    0.0980
   chunk 137 optimal weight:    2.9990
   chunk 169 optimal weight:    0.9980
   chunk 234 optimal weight:    0.7980
   chunk 202 optimal weight:    1.9990
   chunk 29 optimal weight:   10.0000
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 910 ASN
D  84 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.147381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.117385 restraints weight = 85343.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 1.90
r_work: 0.3267 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3156
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3156 r_free = 0.3156    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3156 r_free = 0.3156    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
r_final: 0.3156
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.8279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  20809  Z= 0.155
  Angle     :  0.533   6.583  28272  Z= 0.284
  Chirality :  0.039   0.174   3307
  Planarity :  0.004   0.062   3731
  Dihedral  :  4.749  55.851   3072
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 26.17 %
    Favored  : 71.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.57 (0.16), residues: 2833
  helix:  2.20 (0.14), residues: 1550
  sheet: -0.57 (0.27), residues: 348
  loop : -0.25 (0.21), residues: 935

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG S 174 
 TYR   0.013   0.001   TYR O 120 
 PHE   0.016   0.001   PHE B 181 
 TRP   0.009   0.001   TRP P 139 
 HIS   0.006   0.001   HIS B 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (20809)
  covalent geometry    : angle       0.53283 (28272)
  hydrogen bonds       : bond        0.03577 ( 1327)
  hydrogen bonds       : angle       3.88187 ( 3822)

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

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

  5666 Ramachandran restraints generated.
    2833 Oldfield, 0 Emsley, 2833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5666 Ramachandran restraints generated.
    2833 Oldfield, 0 Emsley, 2833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL   17 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue VAL   26 is missing expected H atoms. Skipping.
Residue THR   28 is missing expected H atoms. Skipping.
Residue LEU   29 is missing expected H atoms. Skipping.
Residue THR   30 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue LEU   33 is missing expected H atoms. Skipping.
Residue SER   34 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue VAL   39 is missing expected H atoms. Skipping.
Residue ILE   47 is missing expected H atoms. Skipping.
Residue LYS   48 is missing expected H atoms. Skipping.
Residue VAL   49 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue VAL   52 is missing expected H atoms. Skipping.
Residue THR   53 is missing expected H atoms. Skipping.
Residue VAL   58 is missing expected H atoms. Skipping.
Residue LEU   60 is missing expected H atoms. Skipping.
Residue LEU   63 is missing expected H atoms. Skipping.
Residue THR   64 is missing expected H atoms. Skipping.
Residue VAL   65 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ILE   73 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue SER   78 is missing expected H atoms. Skipping.
Residue VAL   79 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue LEU   81 is missing expected H atoms. Skipping.
Residue LYS   82 is missing expected H atoms. Skipping.
Residue TYR   84 is missing expected H atoms. Skipping.
Residue VAL   85 is missing expected H atoms. Skipping.
Residue THR   87 is missing expected H atoms. Skipping.
Residue SER   93 is missing expected H atoms. Skipping.
Residue LYS   95 is missing expected H atoms. Skipping.
Residue THR  101 is missing expected H atoms. Skipping.
Residue THR  102 is missing expected H atoms. Skipping.
Residue LYS  106 is missing expected H atoms. Skipping.
Residue ILE  107 is missing expected H atoms. Skipping.
Residue VAL  108 is missing expected H atoms. Skipping.
Residue ILE  109 is missing expected H atoms. Skipping.
Residue LEU  112 is missing expected H atoms. Skipping.
Residue LEU  113 is missing expected H atoms. Skipping.
Residue LEU  117 is missing expected H atoms. Skipping.
Residue SER  120 is missing expected H atoms. Skipping.
Residue ILE  121 is missing expected H atoms. Skipping.
Residue SER  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue VAL  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue SER  127 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue TYR  130 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue SER  133 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  147 is missing expected H atoms. Skipping.
Residue LEU  150 is missing expected H atoms. Skipping.
Residue LEU  151 is missing expected H atoms. Skipping.
Residue MET  152 is missing expected H atoms. Skipping.
Residue MET  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue VAL  156 is missing expected H atoms. Skipping.
Residue SER  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue VAL  163 is missing expected H atoms. Skipping.
Residue MET  167 is missing expected H atoms. Skipping.
Residue VAL  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue THR  174 is missing expected H atoms. Skipping.
Residue VAL  177 is missing expected H atoms. Skipping.
Residue THR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue MET  182 is missing expected H atoms. Skipping.
Residue LEU  184 is missing expected H atoms. Skipping.
Residue VAL  185 is missing expected H atoms. Skipping.
Residue VAL  188 is missing expected H atoms. Skipping.
Residue ILE  189 is missing expected H atoms. Skipping.
Residue LEU  190 is missing expected H atoms. Skipping.
Residue MET  193 is missing expected H atoms. Skipping.
Residue TYR  194 is missing expected H atoms. Skipping.
Residue LYS  195 is missing expected H atoms. Skipping.
Residue ILE  196 is missing expected H atoms. Skipping.
Residue THR  198 is missing expected H atoms. Skipping.
Residue MET  199 is missing expected H atoms. Skipping.
Residue VAL  202 is missing expected H atoms. Skipping.
Residue TYR  203 is missing expected H atoms. Skipping.
Residue ILE  205 is missing expected H atoms. Skipping.
Residue THR  207 is missing expected H atoms. Skipping.
Residue SER  209 is missing expected H atoms. Skipping.
Residue VAL  212 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue THR  216 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue MET  221 is missing expected H atoms. Skipping.
Residue ILE  222 is missing expected H atoms. Skipping.
Residue MET  225 is missing expected H atoms. Skipping.
Residue LEU  228 is missing expected H atoms. Skipping.
Residue LYS  230 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue VAL  235 is missing expected H atoms. Skipping.
Residue LEU  236 is missing expected H atoms. Skipping.
Residue ILE  237 is missing expected H atoms. Skipping.
Residue VAL  240 is missing expected H atoms. Skipping.
Residue VAL  241 is missing expected H atoms. Skipping.
Residue THR  245 is missing expected H atoms. Skipping.
Residue VAL  249 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue ILE  254 is missing expected H atoms. Skipping.
Residue THR  259 is missing expected H atoms. Skipping.
Residue SER  260 is missing expected H atoms. Skipping.
Residue SER  262 is missing expected H atoms. Skipping.
Residue LYS  265 is missing expected H atoms. Skipping.
Residue MET  266 is missing expected H atoms. Skipping.
Residue VAL  268 is missing expected H atoms. Skipping.
Residue LEU  269 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue VAL  272 is missing expected H atoms. Skipping.
Residue THR  273 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue VAL  276 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue MET  283 is missing expected H atoms. Skipping.
Residue VAL  284 is missing expected H atoms. Skipping.
Residue SER  285 is missing expected H atoms. Skipping.
Residue SER  286 is missing expected H atoms. Skipping.
Residue MET  287 is missing expected H atoms. Skipping.
Residue ILE  290 is missing expected H atoms. Skipping.
Residue LEU  291 is missing expected H atoms. Skipping.
Residue ILE  293 is missing expected H atoms. Skipping.
Residue VAL  294 is missing expected H atoms. Skipping.
Residue THR  297 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue THR  299 is missing expected H atoms. Skipping.
Residue SER  301 is missing expected H atoms. Skipping.
Residue TYR  305 is missing expected H atoms. Skipping.
Residue VAL  306 is missing expected H atoms. Skipping.
Residue THR  308 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue VAL  333 is missing expected H atoms. Skipping.
Residue SER  335 is missing expected H atoms. Skipping.
Residue ILE  336 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  344 is missing expected H atoms. Skipping.
Residue SER  347 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LYS  350 is missing expected H atoms. Skipping.
Residue SER  351 is missing expected H atoms. Skipping.
Residue THR  352 is missing expected H atoms. Skipping.
Residue VAL  353 is missing expected H atoms. Skipping.
Residue LYS  354 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LEU  357 is missing expected H atoms. Skipping.
Residue LEU  360 is missing expected H atoms. Skipping.
Residue ILE  361 is missing expected H atoms. Skipping.
Residue TYR  362 is missing expected H atoms. Skipping.
Residue TYR  363 is missing expected H atoms. Skipping.
Residue ILE  364 is missing expected H atoms. Skipping.
Residue ILE  365 is missing expected H atoms. Skipping.
Residue LEU  366 is missing expected H atoms. Skipping.
Residue TYR  367 is missing expected H atoms. Skipping.
Residue MET  368 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue THR  371 is missing expected H atoms. Skipping.
Residue ILE  375 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue VAL  377 is missing expected H atoms. Skipping.
Residue THR  379 is missing expected H atoms. Skipping.
Residue VAL  386 is missing expected H atoms. Skipping.
Residue THR  393 is missing expected H atoms. Skipping.
Residue SER  395 is missing expected H atoms. Skipping.
Residue TYR  396 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue VAL  398 is missing expected H atoms. Skipping.
Residue ILE  400 is missing expected H atoms. Skipping.
Residue LEU  405 is missing expected H atoms. Skipping.
Residue LEU  406 is missing expected H atoms. Skipping.
Residue LEU  407 is missing expected H atoms. Skipping.
Residue VAL  409 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue SER  417 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue THR  426 is missing expected H atoms. Skipping.
Residue LEU  429 is missing expected H atoms. Skipping.
Residue THR  435 is missing expected H atoms. Skipping.
Residue LYS  436 is missing expected H atoms. Skipping.
Residue SER  438 is missing expected H atoms. Skipping.
Residue THR  440 is missing expected H atoms. Skipping.
Residue LYS  445 is missing expected H atoms. Skipping.
Residue ILE  446 is missing expected H atoms. Skipping.
Residue MET  451 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue LEU  454 is missing expected H atoms. Skipping.
Residue SER  456 is missing expected H atoms. Skipping.
Residue VAL  457 is missing expected H atoms. Skipping.
Residue LYS  458 is missing expected H atoms. Skipping.
Residue ILE  460 is missing expected H atoms. Skipping.
Residue ILE  461 is missing expected H atoms. Skipping.
Residue THR  462 is missing expected H atoms. Skipping.
Residue SER  464 is missing expected H atoms. Skipping.
Residue VAL  465 is missing expected H atoms. Skipping.
Residue LYS  466 is missing expected H atoms. Skipping.
Residue ILE  470 is missing expected H atoms. Skipping.
Residue MET  474 is missing expected H atoms. Skipping.
Residue LEU  478 is missing expected H atoms. Skipping.
Residue THR  479 is missing expected H atoms. Skipping.
Residue VAL  481 is missing expected H atoms. Skipping.
Residue ILE  482 is missing expected H atoms. Skipping.
Residue LEU  483 is missing expected H atoms. Skipping.
Residue LEU  486 is missing expected H atoms. Skipping.
Residue LEU  488 is missing expected H atoms. Skipping.
Residue SER  489 is missing expected H atoms. Skipping.
Residue VAL  490 is missing expected H atoms. Skipping.
Residue SER  491 is missing expected H atoms. Skipping.
Residue LEU  494 is missing expected H atoms. Skipping.
Residue LEU  495 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  503 is missing expected H atoms. Skipping.
Residue THR  506 is missing expected H atoms. Skipping.
Residue VAL  507 is missing expected H atoms. Skipping.
Residue MET  509 is missing expected H atoms. Skipping.
Residue SER  510 is missing expected H atoms. Skipping.
Residue LEU  513 is missing expected H atoms. Skipping.
Residue ILE  514 is missing expected H atoms. Skipping.
Residue LEU  518 is missing expected H atoms. Skipping.
Residue THR  521 is missing expected H atoms. Skipping.
Residue VAL  522 is missing expected H atoms. Skipping.
Residue SER  523 is missing expected H atoms. Skipping.
Residue LEU  525 is missing expected H atoms. Skipping.
Residue THR  528 is missing expected H atoms. Skipping.
Residue SER  532 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  535 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  538 is missing expected H atoms. Skipping.
Residue ILE  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LEU  548 is missing expected H atoms. Skipping.
Residue LYS  549 is missing expected H atoms. Skipping.
Residue VAL  550 is missing expected H atoms. Skipping.
Residue SER  551 is missing expected H atoms. Skipping.
Residue SER  553 is missing expected H atoms. Skipping.
Residue THR  554 is missing expected H atoms. Skipping.
Residue VAL  556 is missing expected H atoms. Skipping.
Residue LEU  557 is missing expected H atoms. Skipping.
Residue LEU  561 is missing expected H atoms. Skipping.
Residue SER  563 is missing expected H atoms. Skipping.
Residue ILE  564 is missing expected H atoms. Skipping.
Residue LEU  565 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue LEU  571 is missing expected H atoms. Skipping.
Residue SER  576 is missing expected H atoms. Skipping.
Residue SER  577 is missing expected H atoms. Skipping.
Residue VAL  579 is missing expected H atoms. Skipping.
Residue LEU  580 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue VAL  583 is missing expected H atoms. Skipping.
Residue MET  584 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue LEU  587 is missing expected H atoms. Skipping.
Residue ILE  589 is missing expected H atoms. Skipping.
Residue VAL  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue VAL  593 is missing expected H atoms. Skipping.
Residue THR  598 is missing expected H atoms. Skipping.
Residue SER  600 is missing expected H atoms. Skipping.
Residue MET  601 is missing expected H atoms. Skipping.
Residue SER  603 is missing expected H atoms. Skipping.
Residue LYS  604 is missing expected H atoms. Skipping.
Residue ILE  605 is missing expected H atoms. Skipping.
Residue THR  609 is missing expected H atoms. Skipping.
Residue ILE  610 is missing expected H atoms. Skipping.
Residue ILE  612 is missing expected H atoms. Skipping.
Residue LEU  614 is missing expected H atoms. Skipping.
Residue LYS  615 is missing expected H atoms. Skipping.
Residue LEU  995 is missing expected H atoms. Skipping.
Residue LYS  996 is missing expected H atoms. Skipping.
Residue LEU  999 is missing expected H atoms. Skipping.
Residue TYR 1000 is missing expected H atoms. Skipping.
Residue ILE 1002 is missing expected H atoms. Skipping.
Residue LEU 1004 is missing expected H atoms. Skipping.
Residue TYR 1007 is missing expected H atoms. Skipping.
Residue LEU 1008 is missing expected H atoms. Skipping.
Residue THR 1009 is missing expected H atoms. Skipping.
Residue LEU 1012 is missing expected H atoms. Skipping.
Residue TYR 1021 is missing expected H atoms. Skipping.
Residue ILE 1022 is missing expected H atoms. Skipping.
Residue MET 1023 is missing expected H atoms. Skipping.
Residue SER 1025 is missing expected H atoms. Skipping.
Residue LEU 1028 is missing expected H atoms. Skipping.
Residue VAL 1035 is missing expected H atoms. Skipping.
Residue LEU 1036 is missing expected H atoms. Skipping.
Residue THR 1038 is missing expected H atoms. Skipping.
Residue ILE 1039 is missing expected H atoms. Skipping.
Residue VAL   72 is missing expected H atoms. Skipping.
Residue SER   73 is missing expected H atoms. Skipping.
Residue SER   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue THR   77 is missing expected H atoms. Skipping.
Residue VAL   72 is missing expected H atoms. Skipping.
Residue SER   73 is missing expected H atoms. Skipping.
Residue SER   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue THR   77 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  143 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue VAL  147 is missing expected H atoms. Skipping.
Residue MET  149 is missing expected H atoms. Skipping.
Residue ILE  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue VAL  162 is missing expected H atoms. Skipping.
Residue TYR  166 is missing expected H atoms. Skipping.
Residue ILE  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LEU  174 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  143 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue VAL  147 is missing expected H atoms. Skipping.
Residue MET  149 is missing expected H atoms. Skipping.
Residue ILE  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue VAL  162 is missing expected H atoms. Skipping.
Residue TYR  166 is missing expected H atoms. Skipping.
Residue ILE  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LEU  174 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue VAL  182 is missing expected H atoms. Skipping.
Residue LYS  183 is missing expected H atoms. Skipping.
Evaluate side-chains
  619 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 567
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: 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: A  661 LYS cc_start: 0.8883 (tmmt) cc_final: 0.8453 (tmmt)
REVERT: A  699 GLN cc_start: 0.7001 (mm-40) cc_final: 0.6623 (mm-40)
REVERT: A  705 ASP cc_start: 0.7841 (t0) cc_final: 0.7568 (t0)
REVERT: A  706 ASP cc_start: 0.7051 (t0) cc_final: 0.6725 (t0)
REVERT: A  757 GLU cc_start: 0.7730 (pm20) cc_final: 0.7344 (pm20)
REVERT: A  797 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6817 (mt-10)
REVERT: A  825 CYS cc_start: 0.7214 (p) cc_final: 0.6768 (p)
REVERT: B  149 MET cc_start: 0.5568 (mtp) cc_final: 0.5333 (mtp)
REVERT: B  169 ILE cc_start: 0.7985 (tt) cc_final: 0.7755 (pt)
REVERT: B  178 TYR cc_start: 0.8170 (t80) cc_final: 0.7683 (t80)
REVERT: B  187 ASP cc_start: 0.8035 (t0) cc_final: 0.7795 (t0)
REVERT: C   88 GLU cc_start: 0.7321 (mm-30) cc_final: 0.6820 (mm-30)
REVERT: C  146 GLN cc_start: 0.6310 (mp10) cc_final: 0.5810 (mp10)
REVERT: C  161 LYS cc_start: 0.6695 (mtmt) cc_final: 0.6339 (mmmt)
REVERT: C  168 GLU cc_start: 0.7833 (tp30) cc_final: 0.7084 (tp30)
REVERT: C  187 ASP cc_start: 0.8230 (m-30) cc_final: 0.8001 (t0)
REVERT: C  196 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8061 (mm-40)
REVERT: F   30 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8397 (t)
REVERT: F   42 LYS cc_start: 0.8425 (tttp) cc_final: 0.8044 (tttp)
REVERT: F   51 LYS cc_start: 0.8275 (ttmm) cc_final: 0.7883 (ttmm)
REVERT: F   59 GLU cc_start: 0.7893 (tp30) cc_final: 0.7625 (tp30)
REVERT: F   77 VAL cc_start: 0.8810 (p) cc_final: 0.8346 (m)
REVERT: F  124 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8355 (tp)
REVERT: F  218 GLU cc_start: 0.7218 (tp30) cc_final: 0.6913 (tp30)
REVERT: F  232 ARG cc_start: 0.8200 (tpp80) cc_final: 0.7854 (ttp80)
REVERT: G   24 GLN cc_start: 0.7092 (OUTLIER) cc_final: 0.6561 (mt0)
REVERT: G   26 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7455 (mt-10)
REVERT: G   38 THR cc_start: 0.9072 (t) cc_final: 0.8716 (m)
REVERT: G   96 TYR cc_start: 0.8497 (t80) cc_final: 0.7837 (t80)
REVERT: G   97 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7878 (tp30)
REVERT: G  112 ASP cc_start: 0.7645 (t0) cc_final: 0.7355 (p0)
REVERT: G  174 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7941 (mp0)
REVERT: G  234 GLU cc_start: 0.7762 (tp30) cc_final: 0.7232 (tp30)
REVERT: O  101 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8327 (mm-40)
REVERT: O  118 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7648 (tp40)
REVERT: O  155 PHE cc_start: 0.8292 (m-80) cc_final: 0.7807 (m-80)
REVERT: O  175 LYS cc_start: 0.8837 (ttmt) cc_final: 0.8330 (mtpp)
REVERT: O  196 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8085 (mm-30)
REVERT: P   15 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7826 (mt-10)
REVERT: P  143 TYR cc_start: 0.8414 (m-10) cc_final: 0.8147 (m-10)
REVERT: P  177 GLN cc_start: 0.8350 (tt0) cc_final: 0.7995 (tp40)
REVERT: P  178 ASP cc_start: 0.8090 (m-30) cc_final: 0.7653 (t70)
REVERT: P  181 GLU cc_start: 0.8162 (tp30) cc_final: 0.7673 (tp30)
REVERT: P  184 MET cc_start: 0.8482 (mmp) cc_final: 0.8020 (mmt)
REVERT: P  201 MET cc_start: 0.8254 (ttm) cc_final: 0.8024 (ttp)
REVERT: P  222 LYS cc_start: 0.8414 (mmmt) cc_final: 0.8078 (mmmt)
REVERT: P  231 LYS cc_start: 0.8370 (tttt) cc_final: 0.7910 (ttmm)
REVERT: P  235 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7200 (tm-30)
REVERT: Q   62 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8118 (mt)
REVERT: Q   67 ASP cc_start: 0.8290 (m-30) cc_final: 0.8041 (m-30)
REVERT: Q  153 TYR cc_start: 0.8649 (p90) cc_final: 0.8165 (p90)
REVERT: Q  227 LYS cc_start: 0.8235 (tmmt) cc_final: 0.7699 (tmmt)
REVERT: R   62 SER cc_start: 0.8567 (OUTLIER) cc_final: 0.8235 (t)
REVERT: R   65 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7578 (mm-30)
REVERT: R   90 ASP cc_start: 0.8103 (t0) cc_final: 0.7532 (t0)
REVERT: R  117 SER cc_start: 0.8836 (t) cc_final: 0.8474 (p)
REVERT: R  119 LEU cc_start: 0.8365 (tp) cc_final: 0.8159 (tt)
REVERT: R  156 MET cc_start: 0.7560 (tmm) cc_final: 0.7206 (ttp)
REVERT: R  164 GLN cc_start: 0.8409 (tm-30) cc_final: 0.7772 (tm-30)
REVERT: R  207 GLU cc_start: 0.7578 (pt0) cc_final: 0.7234 (pp20)
REVERT: S    8 ASN cc_start: 0.8163 (m-40) cc_final: 0.7872 (m-40)
REVERT: S  144 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7541 (mm)
REVERT: S  171 TYR cc_start: 0.8277 (t80) cc_final: 0.7650 (t80)
REVERT: S  178 GLU cc_start: 0.7526 (mp0) cc_final: 0.7277 (mp0)
  outliers start: 52
  outliers final: 40
  residues processed: 595
  average time/residue: 0.3590
  time to fit residues: 305.0124
Evaluate side-chains
  603 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 556
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain A residue  667 CYS
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain A residue  771 ILE
Chi-restraints excluded: chain A residue  798 THR
Chi-restraints excluded: chain A residue  814 HIS
Chi-restraints excluded: chain A residue  815 THR
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain C residue  166 TYR
Chi-restraints excluded: chain F residue   30 VAL
Chi-restraints excluded: chain F residue   94 GLU
Chi-restraints excluded: chain F residue  119 VAL
Chi-restraints excluded: chain F residue  123 THR
Chi-restraints excluded: chain F residue  124 LEU
Chi-restraints excluded: chain F residue  202 ASP
Chi-restraints excluded: chain F residue  244 LYS
Chi-restraints excluded: chain G residue   24 GLN
Chi-restraints excluded: chain G residue  211 LYS
Chi-restraints excluded: chain G residue  220 VAL
Chi-restraints excluded: chain O residue   28 VAL
Chi-restraints excluded: chain O residue   50 LYS
Chi-restraints excluded: chain O residue  118 GLN
Chi-restraints excluded: chain O residue  212 CYS
Chi-restraints excluded: chain O residue  224 GLU
Chi-restraints excluded: chain P residue    9 THR
Chi-restraints excluded: chain P residue   11 ILE
Chi-restraints excluded: chain P residue   74 CYS
Chi-restraints excluded: chain P residue  117 ILE
Chi-restraints excluded: chain P residue  194 ILE
Chi-restraints excluded: chain Q residue   62 ILE
Chi-restraints excluded: chain Q residue  114 LEU
Chi-restraints excluded: chain Q residue  129 ILE
Chi-restraints excluded: chain Q residue  147 THR
Chi-restraints excluded: chain Q residue  196 LEU
Chi-restraints excluded: chain R residue   35 SER
Chi-restraints excluded: chain R residue   47 CYS
Chi-restraints excluded: chain R residue   62 SER
Chi-restraints excluded: chain R residue  122 GLN
Chi-restraints excluded: chain R residue  165 CYS
Chi-restraints excluded: chain S residue   53 GLN
Chi-restraints excluded: chain S residue  144 ILE
Chi-restraints excluded: chain S residue  187 LEU
Chi-restraints excluded: chain S residue  208 LYS
Chi-restraints excluded: chain S residue  227 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 283
   random chunks:
   chunk 56 optimal weight:   10.0000
   chunk 191 optimal weight:    0.5980
   chunk 141 optimal weight:    0.9990
   chunk 113 optimal weight:   40.0000
   chunk 254 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 136 optimal weight:    0.0870
   chunk 122 optimal weight:    1.9990
   chunk 247 optimal weight:    1.9990
   chunk 245 optimal weight:    0.9980
   chunk 276 optimal weight:    1.9990
   overall best weight:    0.6960

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

Flipped N/Q/H residues before XYZ refinement:
A 910 ASN
D  84 ASN
S  16 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.146898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.116860 restraints weight = 84926.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 1.90
r_work: 0.3267 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3145 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3128
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
r_final: 0.3128
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.8408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  20809  Z= 0.142
  Angle     :  0.533   6.505  28272  Z= 0.282
  Chirality :  0.039   0.145   3307
  Planarity :  0.004   0.052   3731
  Dihedral  :  4.653  55.148   3071
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 26.33 %
    Favored  : 71.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.69 (0.17), residues: 2833
  helix:  2.30 (0.14), residues: 1550
  sheet: -0.50 (0.27), residues: 356
  loop : -0.19 (0.21), residues: 927

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F 223 
 TYR   0.018   0.001   TYR A 851 
 PHE   0.015   0.001   PHE S 154 
 TRP   0.008   0.001   TRP P 139 
 HIS   0.005   0.001   HIS B 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (20809)
  covalent geometry    : angle       0.53276 (28272)
  hydrogen bonds       : bond        0.03458 ( 1327)
  hydrogen bonds       : angle       3.82107 ( 3822)

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

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

  5666 Ramachandran restraints generated.
    2833 Oldfield, 0 Emsley, 2833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5666 Ramachandran restraints generated.
    2833 Oldfield, 0 Emsley, 2833 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL   17 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LEU   25 is missing expected H atoms. Skipping.
Residue VAL   26 is missing expected H atoms. Skipping.
Residue THR   28 is missing expected H atoms. Skipping.
Residue LEU   29 is missing expected H atoms. Skipping.
Residue THR   30 is missing expected H atoms. Skipping.
Residue ILE   32 is missing expected H atoms. Skipping.
Residue LEU   33 is missing expected H atoms. Skipping.
Residue SER   34 is missing expected H atoms. Skipping.
Residue VAL   36 is missing expected H atoms. Skipping.
Residue VAL   39 is missing expected H atoms. Skipping.
Residue ILE   47 is missing expected H atoms. Skipping.
Residue LYS   48 is missing expected H atoms. Skipping.
Residue VAL   49 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue VAL   52 is missing expected H atoms. Skipping.
Residue THR   53 is missing expected H atoms. Skipping.
Residue VAL   58 is missing expected H atoms. Skipping.
Residue LEU   60 is missing expected H atoms. Skipping.
Residue LEU   63 is missing expected H atoms. Skipping.
Residue THR   64 is missing expected H atoms. Skipping.
Residue VAL   65 is missing expected H atoms. Skipping.
Residue LEU   71 is missing expected H atoms. Skipping.
Residue ILE   73 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue SER   78 is missing expected H atoms. Skipping.
Residue VAL   79 is missing expected H atoms. Skipping.
Residue ILE   80 is missing expected H atoms. Skipping.
Residue LEU   81 is missing expected H atoms. Skipping.
Residue LYS   82 is missing expected H atoms. Skipping.
Residue TYR   84 is missing expected H atoms. Skipping.
Residue VAL   85 is missing expected H atoms. Skipping.
Residue THR   87 is missing expected H atoms. Skipping.
Residue SER   93 is missing expected H atoms. Skipping.
Residue LYS   95 is missing expected H atoms. Skipping.
Residue THR  101 is missing expected H atoms. Skipping.
Residue THR  102 is missing expected H atoms. Skipping.
Residue LYS  106 is missing expected H atoms. Skipping.
Residue ILE  107 is missing expected H atoms. Skipping.
Residue VAL  108 is missing expected H atoms. Skipping.
Residue ILE  109 is missing expected H atoms. Skipping.
Residue LEU  112 is missing expected H atoms. Skipping.
Residue LEU  113 is missing expected H atoms. Skipping.
Residue LEU  117 is missing expected H atoms. Skipping.
Residue SER  120 is missing expected H atoms. Skipping.
Residue ILE  121 is missing expected H atoms. Skipping.
Residue SER  122 is missing expected H atoms. Skipping.
Residue LYS  123 is missing expected H atoms. Skipping.
Residue VAL  124 is missing expected H atoms. Skipping.
Residue SER  126 is missing expected H atoms. Skipping.
Residue SER  127 is missing expected H atoms. Skipping.
Residue VAL  128 is missing expected H atoms. Skipping.
Residue TYR  130 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue SER  133 is missing expected H atoms. Skipping.
Residue ILE  135 is missing expected H atoms. Skipping.
Residue LEU  147 is missing expected H atoms. Skipping.
Residue LEU  150 is missing expected H atoms. Skipping.
Residue LEU  151 is missing expected H atoms. Skipping.
Residue MET  152 is missing expected H atoms. Skipping.
Residue MET  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue VAL  156 is missing expected H atoms. Skipping.
Residue SER  157 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue VAL  163 is missing expected H atoms. Skipping.
Residue MET  167 is missing expected H atoms. Skipping.
Residue VAL  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  171 is missing expected H atoms. Skipping.
Residue THR  174 is missing expected H atoms. Skipping.
Residue VAL  177 is missing expected H atoms. Skipping.
Residue THR  178 is missing expected H atoms. Skipping.
Residue THR  180 is missing expected H atoms. Skipping.
Residue MET  182 is missing expected H atoms. Skipping.
Residue LEU  184 is missing expected H atoms. Skipping.
Residue VAL  185 is missing expected H atoms. Skipping.
Residue VAL  188 is missing expected H atoms. Skipping.
Residue ILE  189 is missing expected H atoms. Skipping.
Residue LEU  190 is missing expected H atoms. Skipping.
Residue MET  193 is missing expected H atoms. Skipping.
Residue TYR  194 is missing expected H atoms. Skipping.
Residue LYS  195 is missing expected H atoms. Skipping.
Residue ILE  196 is missing expected H atoms. Skipping.
Residue THR  198 is missing expected H atoms. Skipping.
Residue MET  199 is missing expected H atoms. Skipping.
Residue VAL  202 is missing expected H atoms. Skipping.
Residue TYR  203 is missing expected H atoms. Skipping.
Residue ILE  205 is missing expected H atoms. Skipping.
Residue THR  207 is missing expected H atoms. Skipping.
Residue SER  209 is missing expected H atoms. Skipping.
Residue VAL  212 is missing expected H atoms. Skipping.
Residue ILE  214 is missing expected H atoms. Skipping.
Residue THR  216 is missing expected H atoms. Skipping.
Residue THR  217 is missing expected H atoms. Skipping.
Residue MET  221 is missing expected H atoms. Skipping.
Residue ILE  222 is missing expected H atoms. Skipping.
Residue MET  225 is missing expected H atoms. Skipping.
Residue LEU  228 is missing expected H atoms. Skipping.
Residue LYS  230 is missing expected H atoms. Skipping.
Residue LYS  234 is missing expected H atoms. Skipping.
Residue VAL  235 is missing expected H atoms. Skipping.
Residue LEU  236 is missing expected H atoms. Skipping.
Residue ILE  237 is missing expected H atoms. Skipping.
Residue VAL  240 is missing expected H atoms. Skipping.
Residue VAL  241 is missing expected H atoms. Skipping.
Residue THR  245 is missing expected H atoms. Skipping.
Residue VAL  249 is missing expected H atoms. Skipping.
Residue LEU  252 is missing expected H atoms. Skipping.
Residue ILE  254 is missing expected H atoms. Skipping.
Residue THR  259 is missing expected H atoms. Skipping.
Residue SER  260 is missing expected H atoms. Skipping.
Residue SER  262 is missing expected H atoms. Skipping.
Residue LYS  265 is missing expected H atoms. Skipping.
Residue MET  266 is missing expected H atoms. Skipping.
Residue VAL  268 is missing expected H atoms. Skipping.
Residue LEU  269 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue VAL  272 is missing expected H atoms. Skipping.
Residue THR  273 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue VAL  276 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  281 is missing expected H atoms. Skipping.
Residue MET  283 is missing expected H atoms. Skipping.
Residue VAL  284 is missing expected H atoms. Skipping.
Residue SER  285 is missing expected H atoms. Skipping.
Residue SER  286 is missing expected H atoms. Skipping.
Residue MET  287 is missing expected H atoms. Skipping.
Residue ILE  290 is missing expected H atoms. Skipping.
Residue LEU  291 is missing expected H atoms. Skipping.
Residue ILE  293 is missing expected H atoms. Skipping.
Residue VAL  294 is missing expected H atoms. Skipping.
Residue THR  297 is missing expected H atoms. Skipping.
Residue LEU  298 is missing expected H atoms. Skipping.
Residue THR  299 is missing expected H atoms. Skipping.
Residue SER  301 is missing expected H atoms. Skipping.
Residue TYR  305 is missing expected H atoms. Skipping.
Residue VAL  306 is missing expected H atoms. Skipping.
Residue THR  308 is missing expected H atoms. Skipping.
Residue LEU  332 is missing expected H atoms. Skipping.
Residue VAL  333 is missing expected H atoms. Skipping.
Residue SER  335 is missing expected H atoms. Skipping.
Residue ILE  336 is missing expected H atoms. Skipping.
Residue VAL  340 is missing expected H atoms. Skipping.
Residue LEU  343 is missing expected H atoms. Skipping.
Residue LEU  344 is missing expected H atoms. Skipping.
Residue SER  347 is missing expected H atoms. Skipping.
Residue LYS  348 is missing expected H atoms. Skipping.
Residue LYS  350 is missing expected H atoms. Skipping.
Residue SER  351 is missing expected H atoms. Skipping.
Residue THR  352 is missing expected H atoms. Skipping.
Residue VAL  353 is missing expected H atoms. Skipping.
Residue LYS  354 is missing expected H atoms. Skipping.
Residue LYS  355 is missing expected H atoms. Skipping.
Residue LEU  357 is missing expected H atoms. Skipping.
Residue LEU  360 is missing expected H atoms. Skipping.
Residue ILE  361 is missing expected H atoms. Skipping.
Residue TYR  362 is missing expected H atoms. Skipping.
Residue TYR  363 is missing expected H atoms. Skipping.
Residue ILE  364 is missing expected H atoms. Skipping.
Residue ILE  365 is missing expected H atoms. Skipping.
Residue LEU  366 is missing expected H atoms. Skipping.
Residue TYR  367 is missing expected H atoms. Skipping.
Residue MET  368 is missing expected H atoms. Skipping.
Residue ILE  370 is missing expected H atoms. Skipping.
Residue THR  371 is missing expected H atoms. Skipping.
Residue ILE  375 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue VAL  377 is missing expected H atoms. Skipping.
Residue THR  379 is missing expected H atoms. Skipping.
Residue VAL  386 is missing expected H atoms. Skipping.
Residue THR  393 is missing expected H atoms. Skipping.
Residue SER  395 is missing expected H atoms. Skipping.
Residue TYR  396 is missing expected H atoms. Skipping.
Residue THR  397 is missing expected H atoms. Skipping.
Residue VAL  398 is missing expected H atoms. Skipping.
Residue ILE  400 is missing expected H atoms. Skipping.
Residue LEU  405 is missing expected H atoms. Skipping.
Residue LEU  406 is missing expected H atoms. Skipping.
Residue LEU  407 is missing expected H atoms. Skipping.
Residue VAL  409 is missing expected H atoms. Skipping.
Residue THR  411 is missing expected H atoms. Skipping.
Residue SER  417 is missing expected H atoms. Skipping.
Residue LEU  421 is missing expected H atoms. Skipping.
Residue THR  426 is missing expected H atoms. Skipping.
Residue LEU  429 is missing expected H atoms. Skipping.
Residue THR  435 is missing expected H atoms. Skipping.
Residue LYS  436 is missing expected H atoms. Skipping.
Residue SER  438 is missing expected H atoms. Skipping.
Residue THR  440 is missing expected H atoms. Skipping.
Residue LYS  445 is missing expected H atoms. Skipping.
Residue ILE  446 is missing expected H atoms. Skipping.
Residue MET  451 is missing expected H atoms. Skipping.
Residue LEU  452 is missing expected H atoms. Skipping.
Residue LEU  454 is missing expected H atoms. Skipping.
Residue SER  456 is missing expected H atoms. Skipping.
Residue VAL  457 is missing expected H atoms. Skipping.
Residue LYS  458 is missing expected H atoms. Skipping.
Residue ILE  460 is missing expected H atoms. Skipping.
Residue ILE  461 is missing expected H atoms. Skipping.
Residue THR  462 is missing expected H atoms. Skipping.
Residue SER  464 is missing expected H atoms. Skipping.
Residue VAL  465 is missing expected H atoms. Skipping.
Residue LYS  466 is missing expected H atoms. Skipping.
Residue ILE  470 is missing expected H atoms. Skipping.
Residue MET  474 is missing expected H atoms. Skipping.
Residue LEU  478 is missing expected H atoms. Skipping.
Residue THR  479 is missing expected H atoms. Skipping.
Residue VAL  481 is missing expected H atoms. Skipping.
Residue ILE  482 is missing expected H atoms. Skipping.
Residue LEU  483 is missing expected H atoms. Skipping.
Residue LEU  486 is missing expected H atoms. Skipping.
Residue LEU  488 is missing expected H atoms. Skipping.
Residue SER  489 is missing expected H atoms. Skipping.
Residue VAL  490 is missing expected H atoms. Skipping.
Residue SER  491 is missing expected H atoms. Skipping.
Residue LEU  494 is missing expected H atoms. Skipping.
Residue LEU  495 is missing expected H atoms. Skipping.
Residue LEU  499 is missing expected H atoms. Skipping.
Residue SER  503 is missing expected H atoms. Skipping.
Residue THR  506 is missing expected H atoms. Skipping.
Residue VAL  507 is missing expected H atoms. Skipping.
Residue MET  509 is missing expected H atoms. Skipping.
Residue SER  510 is missing expected H atoms. Skipping.
Residue LEU  513 is missing expected H atoms. Skipping.
Residue ILE  514 is missing expected H atoms. Skipping.
Residue LEU  518 is missing expected H atoms. Skipping.
Residue THR  521 is missing expected H atoms. Skipping.
Residue VAL  522 is missing expected H atoms. Skipping.
Residue SER  523 is missing expected H atoms. Skipping.
Residue LEU  525 is missing expected H atoms. Skipping.
Residue THR  528 is missing expected H atoms. Skipping.
Residue SER  532 is missing expected H atoms. Skipping.
Residue VAL  533 is missing expected H atoms. Skipping.
Residue ILE  535 is missing expected H atoms. Skipping.
Residue SER  536 is missing expected H atoms. Skipping.
Residue VAL  538 is missing expected H atoms. Skipping.
Residue ILE  541 is missing expected H atoms. Skipping.
Residue TYR  544 is missing expected H atoms. Skipping.
Residue LEU  548 is missing expected H atoms. Skipping.
Residue LYS  549 is missing expected H atoms. Skipping.
Residue VAL  550 is missing expected H atoms. Skipping.
Residue SER  551 is missing expected H atoms. Skipping.
Residue SER  553 is missing expected H atoms. Skipping.
Residue THR  554 is missing expected H atoms. Skipping.
Residue VAL  556 is missing expected H atoms. Skipping.
Residue LEU  557 is missing expected H atoms. Skipping.
Residue LEU  561 is missing expected H atoms. Skipping.
Residue SER  563 is missing expected H atoms. Skipping.
Residue ILE  564 is missing expected H atoms. Skipping.
Residue LEU  565 is missing expected H atoms. Skipping.
Residue LEU  568 is missing expected H atoms. Skipping.
Residue ILE  569 is missing expected H atoms. Skipping.
Residue LEU  571 is missing expected H atoms. Skipping.
Residue SER  576 is missing expected H atoms. Skipping.
Residue SER  577 is missing expected H atoms. Skipping.
Residue VAL  579 is missing expected H atoms. Skipping.
Residue LEU  580 is missing expected H atoms. Skipping.
Residue LEU  582 is missing expected H atoms. Skipping.
Residue VAL  583 is missing expected H atoms. Skipping.
Residue MET  584 is missing expected H atoms. Skipping.
Residue THR  586 is missing expected H atoms. Skipping.
Residue LEU  587 is missing expected H atoms. Skipping.
Residue ILE  589 is missing expected H atoms. Skipping.
Residue VAL  590 is missing expected H atoms. Skipping.
Residue THR  592 is missing expected H atoms. Skipping.
Residue VAL  593 is missing expected H atoms. Skipping.
Residue THR  598 is missing expected H atoms. Skipping.
Residue SER  600 is missing expected H atoms. Skipping.
Residue MET  601 is missing expected H atoms. Skipping.
Residue SER  603 is missing expected H atoms. Skipping.
Residue LYS  604 is missing expected H atoms. Skipping.
Residue ILE  605 is missing expected H atoms. Skipping.
Residue THR  609 is missing expected H atoms. Skipping.
Residue ILE  610 is missing expected H atoms. Skipping.
Residue ILE  612 is missing expected H atoms. Skipping.
Residue LEU  614 is missing expected H atoms. Skipping.
Residue LYS  615 is missing expected H atoms. Skipping.
Residue LEU  995 is missing expected H atoms. Skipping.
Residue LYS  996 is missing expected H atoms. Skipping.
Residue LEU  999 is missing expected H atoms. Skipping.
Residue TYR 1000 is missing expected H atoms. Skipping.
Residue ILE 1002 is missing expected H atoms. Skipping.
Residue LEU 1004 is missing expected H atoms. Skipping.
Residue TYR 1007 is missing expected H atoms. Skipping.
Residue LEU 1008 is missing expected H atoms. Skipping.
Residue THR 1009 is missing expected H atoms. Skipping.
Residue LEU 1012 is missing expected H atoms. Skipping.
Residue TYR 1021 is missing expected H atoms. Skipping.
Residue ILE 1022 is missing expected H atoms. Skipping.
Residue MET 1023 is missing expected H atoms. Skipping.
Residue SER 1025 is missing expected H atoms. Skipping.
Residue LEU 1028 is missing expected H atoms. Skipping.
Residue VAL 1035 is missing expected H atoms. Skipping.
Residue LEU 1036 is missing expected H atoms. Skipping.
Residue THR 1038 is missing expected H atoms. Skipping.
Residue ILE 1039 is missing expected H atoms. Skipping.
Residue VAL   72 is missing expected H atoms. Skipping.
Residue SER   73 is missing expected H atoms. Skipping.
Residue SER   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue THR   77 is missing expected H atoms. Skipping.
Residue VAL   72 is missing expected H atoms. Skipping.
Residue SER   73 is missing expected H atoms. Skipping.
Residue SER   74 is missing expected H atoms. Skipping.
Residue LEU   76 is missing expected H atoms. Skipping.
Residue THR   77 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  143 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue VAL  147 is missing expected H atoms. Skipping.
Residue MET  149 is missing expected H atoms. Skipping.
Residue ILE  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue VAL  162 is missing expected H atoms. Skipping.
Residue TYR  166 is missing expected H atoms. Skipping.
Residue ILE  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LEU  174 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue LEU  141 is missing expected H atoms. Skipping.
Residue THR  143 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue VAL  147 is missing expected H atoms. Skipping.
Residue MET  149 is missing expected H atoms. Skipping.
Residue ILE  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LEU  155 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  161 is missing expected H atoms. Skipping.
Residue VAL  162 is missing expected H atoms. Skipping.
Residue TYR  166 is missing expected H atoms. Skipping.
Residue ILE  169 is missing expected H atoms. Skipping.
Residue LEU  170 is missing expected H atoms. Skipping.
Residue THR  172 is missing expected H atoms. Skipping.
Residue LYS  173 is missing expected H atoms. Skipping.
Residue LEU  174 is missing expected H atoms. Skipping.
Residue TYR  178 is missing expected H atoms. Skipping.
Residue VAL  182 is missing expected H atoms. Skipping.
Residue LYS  183 is missing expected H atoms. Skipping.
Evaluate side-chains
  606 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 558
  time to evaluate  : 1.001 
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: A  661 LYS cc_start: 0.8863 (tmmt) cc_final: 0.8444 (tmmt)
REVERT: A  677 VAL cc_start: 0.9325 (t) cc_final: 0.9112 (p)
REVERT: A  699 GLN cc_start: 0.7031 (mm-40) cc_final: 0.6578 (mm-40)
REVERT: A  705 ASP cc_start: 0.7837 (t0) cc_final: 0.7564 (t0)
REVERT: A  706 ASP cc_start: 0.6957 (t0) cc_final: 0.6636 (t0)
REVERT: A  756 SER cc_start: 0.8445 (p) cc_final: 0.8085 (t)
REVERT: A  757 GLU cc_start: 0.7651 (pm20) cc_final: 0.7142 (pm20)
REVERT: A  797 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6751 (mt-10)
REVERT: A  825 CYS cc_start: 0.7290 (p) cc_final: 0.6803 (p)
REVERT: A  843 TRP cc_start: 0.7208 (t60) cc_final: 0.6773 (t-100)
REVERT: C   88 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6814 (mm-30)
REVERT: C  146 GLN cc_start: 0.6314 (mp10) cc_final: 0.5857 (mp10)
REVERT: C  161 LYS cc_start: 0.6756 (mtmt) cc_final: 0.6388 (mmmt)
REVERT: C  168 GLU cc_start: 0.7621 (tp30) cc_final: 0.6879 (tp30)
REVERT: C  187 ASP cc_start: 0.8228 (m-30) cc_final: 0.8023 (t0)
REVERT: C  196 GLN cc_start: 0.8529 (mm-40) cc_final: 0.7985 (mm-40)
REVERT: F   30 VAL cc_start: 0.8595 (OUTLIER) cc_final: 0.8367 (t)
REVERT: F   42 LYS cc_start: 0.8401 (tttp) cc_final: 0.8019 (tttp)
REVERT: F   51 LYS cc_start: 0.8284 (ttmm) cc_final: 0.7965 (ttmm)
REVERT: F   59 GLU cc_start: 0.7894 (tp30) cc_final: 0.7665 (tp30)
REVERT: F   77 VAL cc_start: 0.8849 (p) cc_final: 0.8344 (m)
REVERT: F  124 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8341 (tp)
REVERT: F  218 GLU cc_start: 0.7161 (tp30) cc_final: 0.6933 (tp30)
REVERT: F  223 ARG cc_start: 0.7267 (mmm-85) cc_final: 0.7048 (mmm160)
REVERT: F  232 ARG cc_start: 0.8217 (tpp80) cc_final: 0.7895 (ttp80)
REVERT: G   24 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.6450 (mt0)
REVERT: G   26 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7512 (mt-10)
REVERT: G   38 THR cc_start: 0.9082 (t) cc_final: 0.8745 (m)
REVERT: G   96 TYR cc_start: 0.8505 (t80) cc_final: 0.7846 (t80)
REVERT: G   97 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7843 (tp30)
REVERT: G  112 ASP cc_start: 0.7615 (t0) cc_final: 0.7350 (p0)
REVERT: G  174 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7992 (mp0)
REVERT: G  234 GLU cc_start: 0.7716 (tp30) cc_final: 0.7509 (tp30)
REVERT: O  101 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8230 (mm110)
REVERT: O  118 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7694 (tp40)
REVERT: O  155 PHE cc_start: 0.8288 (m-80) cc_final: 0.7777 (m-80)
REVERT: O  175 LYS cc_start: 0.8831 (ttmt) cc_final: 0.8331 (mtpp)
REVERT: O  206 ASN cc_start: 0.8553 (p0) cc_final: 0.8319 (p0)
REVERT: P   15 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7839 (mt-10)
REVERT: P  143 TYR cc_start: 0.8408 (m-10) cc_final: 0.8165 (m-10)
REVERT: P  177 GLN cc_start: 0.8346 (tt0) cc_final: 0.7975 (tp40)
REVERT: P  178 ASP cc_start: 0.8121 (m-30) cc_final: 0.7671 (t70)
REVERT: P  181 GLU cc_start: 0.8155 (tp30) cc_final: 0.7680 (tp30)
REVERT: P  184 MET cc_start: 0.8472 (mmp) cc_final: 0.8051 (mmt)
REVERT: P  222 LYS cc_start: 0.8427 (mmmt) cc_final: 0.8160 (mmmt)
REVERT: P  231 LYS cc_start: 0.8339 (tttt) cc_final: 0.7855 (ttmm)
REVERT: P  235 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7196 (tm-30)
REVERT: Q   62 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8120 (mt)
REVERT: Q   67 ASP cc_start: 0.8249 (m-30) cc_final: 0.8024 (m-30)
REVERT: Q  227 LYS cc_start: 0.8208 (tmmt) cc_final: 0.7723 (tmmt)
REVERT: R   62 SER cc_start: 0.8578 (OUTLIER) cc_final: 0.8237 (t)
REVERT: R   65 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7596 (mm-30)
REVERT: R   90 ASP cc_start: 0.8093 (t0) cc_final: 0.7538 (t0)
REVERT: R  117 SER cc_start: 0.8836 (t) cc_final: 0.8477 (p)
REVERT: R  156 MET cc_start: 0.7537 (tmm) cc_final: 0.7239 (ttp)
REVERT: R  164 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7748 (tm-30)
REVERT: S  171 TYR cc_start: 0.8279 (t80) cc_final: 0.7667 (t80)
REVERT: S  178 GLU cc_start: 0.7539 (mp0) cc_final: 0.7233 (mp0)
  outliers start: 48
  outliers final: 41
  residues processed: 581
  average time/residue: 0.3683
  time to fit residues: 304.8407
Evaluate side-chains
  617 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 570
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain A residue  771 ILE
Chi-restraints excluded: chain A residue  798 THR
Chi-restraints excluded: chain A residue  814 HIS
Chi-restraints excluded: chain A residue  815 THR
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain C residue  166 TYR
Chi-restraints excluded: chain F residue   30 VAL
Chi-restraints excluded: chain F residue  119 VAL
Chi-restraints excluded: chain F residue  123 THR
Chi-restraints excluded: chain F residue  124 LEU
Chi-restraints excluded: chain F residue  202 ASP
Chi-restraints excluded: chain F residue  244 LYS
Chi-restraints excluded: chain G residue   24 GLN
Chi-restraints excluded: chain G residue  211 LYS
Chi-restraints excluded: chain G residue  220 VAL
Chi-restraints excluded: chain G residue  240 VAL
Chi-restraints excluded: chain O residue   28 VAL
Chi-restraints excluded: chain O residue   50 LYS
Chi-restraints excluded: chain O residue  118 GLN
Chi-restraints excluded: chain O residue  212 CYS
Chi-restraints excluded: chain O residue  224 GLU
Chi-restraints excluded: chain P residue    9 THR
Chi-restraints excluded: chain P residue   11 ILE
Chi-restraints excluded: chain P residue   74 CYS
Chi-restraints excluded: chain P residue  117 ILE
Chi-restraints excluded: chain P residue  194 ILE
Chi-restraints excluded: chain Q residue   62 ILE
Chi-restraints excluded: chain Q residue  114 LEU
Chi-restraints excluded: chain Q residue  129 ILE
Chi-restraints excluded: chain Q residue  147 THR
Chi-restraints excluded: chain Q residue  196 LEU
Chi-restraints excluded: chain R residue   35 SER
Chi-restraints excluded: chain R residue   47 CYS
Chi-restraints excluded: chain R residue   62 SER
Chi-restraints excluded: chain R residue  122 GLN
Chi-restraints excluded: chain R residue  165 CYS
Chi-restraints excluded: chain R residue  224 GLN
Chi-restraints excluded: chain S residue   38 LEU
Chi-restraints excluded: chain S residue   53 GLN
Chi-restraints excluded: chain S residue  144 ILE
Chi-restraints excluded: chain S residue  208 LYS
Chi-restraints excluded: chain S residue  227 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 283
   random chunks:
   chunk 42 optimal weight:    7.9990
   chunk 281 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 186 optimal weight:    0.8980
   chunk 2 optimal weight:    5.9990
   chunk 155 optimal weight:    0.9980
   chunk 39 optimal weight:    9.9990
   chunk 201 optimal weight:    0.9980
   chunk 22 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9990
   chunk 99 optimal weight:    4.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 910 ASN
R  99 HIS
S  16 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.146977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.117426 restraints weight = 85134.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 1.84
r_work: 0.3286 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3178
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3179 r_free = 0.3179    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       50 |
|-----------------------------------------------------------------------------|
r_final: 0.3179
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.8613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  20809  Z= 0.180
  Angle     :  0.550   8.286  28272  Z= 0.292
  Chirality :  0.039   0.156   3307
  Planarity :  0.004   0.057   3731
  Dihedral  :  4.697  55.228   3071
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 26.76 %
    Favored  : 70.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.60 (0.16), residues: 2833
  helix:  2.25 (0.14), residues: 1549
  sheet: -0.58 (0.27), residues: 351
  loop : -0.25 (0.21), residues: 933

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG Q  38 
 TYR   0.016   0.001   TYR O 120 
 PHE   0.014   0.002   PHE R 226 
 TRP   0.009   0.001   TRP P 139 
 HIS   0.008   0.001   HIS R  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (20809)
  covalent geometry    : angle       0.55017 (28272)
  hydrogen bonds       : bond        0.03648 ( 1327)
  hydrogen bonds       : angle       3.85829 ( 3822)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11471.27 seconds
wall clock time: 194 minutes 40.96 seconds (11680.96 seconds total)