Starting phenix.real_space_refine
on Thu Jan 16 19:21:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9c0c_45079/01_2025/9c0c_45079.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9c0c_45079/01_2025/9c0c_45079.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.41
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9c0c_45079/01_2025/9c0c_45079.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9c0c_45079/01_2025/9c0c_45079.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9c0c_45079/01_2025/9c0c_45079.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9c0c_45079/01_2025/9c0c_45079.cif"
  }
  resolution = 3.41
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.071
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: 4
    Type Number    sf(0)   Gaussians
     S     280      5.16       5
     C   33558      2.51       5
     N    9310      2.21       5
     O   10822      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.14s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 53970
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 3855
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 524, 3855
          Classifications: {'peptide': 524}
          Link IDs: {'PTRANS': 14, 'TRANS': 509}
    Chain: "N"
      Number of atoms: 3855
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 524, 3855
          Classifications: {'peptide': 524}
          Link IDs: {'PTRANS': 14, 'TRANS': 509}
    Chain: "B"
      Number of atoms: 3855
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 524, 3855
          Classifications: {'peptide': 524}
          Link IDs: {'PTRANS': 14, 'TRANS': 509}
    Chain: "H"
      Number of atoms: 3855
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 524, 3855
          Classifications: {'peptide': 524}
          Link IDs: {'PTRANS': 14, 'TRANS': 509}
    Chain: "C"
      Number of atoms: 3855
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 524, 3855
          Classifications: {'peptide': 524}
          Link IDs: {'PTRANS': 14, 'TRANS': 509}
    Chain: "I"
      Number of atoms: 3855
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 524, 3855
          Classifications: {'peptide': 524}
          Link IDs: {'PTRANS': 14, 'TRANS': 509}
    Chain: "D"
      Number of atoms: 3855
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 524, 3855
          Classifications: {'peptide': 524}
          Link IDs: {'PTRANS': 14, 'TRANS': 509}
    Chain: "J"
      Number of atoms: 3855
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 524, 3855
          Classifications: {'peptide': 524}
          Link IDs: {'PTRANS': 14, 'TRANS': 509}
    Chain: "E"
      Number of atoms: 3855
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 524, 3855
          Classifications: {'peptide': 524}
          Link IDs: {'PTRANS': 14, 'TRANS': 509}
    Chain: "K"
      Number of atoms: 3855
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 524, 3855
          Classifications: {'peptide': 524}
          Link IDs: {'PTRANS': 14, 'TRANS': 509}
    Chain: "F"
      Number of atoms: 3855
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 524, 3855
          Classifications: {'peptide': 524}
          Link IDs: {'PTRANS': 14, 'TRANS': 509}
    Chain: "L"
      Number of atoms: 3855
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 524, 3855
          Classifications: {'peptide': 524}
          Link IDs: {'PTRANS': 14, 'TRANS': 509}
    Chain: "G"
      Number of atoms: 3855
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 524, 3855
          Classifications: {'peptide': 524}
          Link IDs: {'PTRANS': 14, 'TRANS': 509}
    Chain: "M"
      Number of atoms: 3855
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 524, 3855
          Classifications: {'peptide': 524}
          Link IDs: {'PTRANS': 14, 'TRANS': 509}
  Time building chain proxies: 23.85, per 1000 atoms: 0.44
  Number of scatterers: 53970
  At special positions: 0
  Unit cell: (159.85, 161, 158.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S     280     16.00
     O   10822      8.00
     N    9310      7.00
     C   33558      6.00
    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: 11.20
  Conformation dependent library (CDL) restraints added in 5.8 seconds
  

  14616 Ramachandran restraints generated.
    7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  13272

  Finding SS restraints...
    Secondary structure from input PDB file:
      290 helices and 96 sheets defined
      58.8% alpha, 14.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 6.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 29
      removed outlier: 4.110A  pdb=" N   VAL A  29 " --> pdb=" O   ASP A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 60
      removed outlier: 3.644A  pdb=" N   VAL A  56 " --> pdb=" O   ASP A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 86
      removed outlier: 3.790A  pdb=" N   LYS A  80 " --> pdb=" O   GLU A  76 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   ALA A  81 " --> pdb=" O   VAL A  77 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ASN A  82 " --> pdb=" O   ALA A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 108
    Processing helix  chain 'A' and resid 112 through 135
    Processing helix  chain 'A' and resid 140 through 152
    Processing helix  chain 'A' and resid 155 through 170
    Processing helix  chain 'A' and resid 201 through 205
    Processing helix  chain 'A' and resid 233 through 244
    Processing helix  chain 'A' and resid 258 through 266
    Processing helix  chain 'A' and resid 282 through 297
      removed outlier: 3.533A  pdb=" N   LYS A 286 " --> pdb=" O   GLY A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 312
    Processing helix  chain 'A' and resid 338 through 355
    Processing helix  chain 'A' and resid 358 through 375
      removed outlier: 4.287A  pdb=" N   GLY A 375 " --> pdb=" O   LYS A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 410
    Processing helix  chain 'A' and resid 416 through 426
      removed outlier: 3.925A  pdb=" N   ILE A 420 " --> pdb=" O   GLY A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 447
    Processing helix  chain 'A' and resid 448 through 458
    Processing helix  chain 'A' and resid 461 through 472
      removed outlier: 3.697A  pdb=" N   VAL A 465 " --> pdb=" O   GLU A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 492
    Processing helix  chain 'A' and resid 497 through 516
    Processing helix  chain 'N' and resid 9 through 29
      removed outlier: 4.202A  pdb=" N   VAL N  29 " --> pdb=" O   ASP N  25 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 52 through 60
      removed outlier: 3.584A  pdb=" N   VAL N  56 " --> pdb=" O   ASP N  52 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 64 through 86
      removed outlier: 3.822A  pdb=" N   LYS N  80 " --> pdb=" O   GLU N  76 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ALA N  81 " --> pdb=" O   VAL N  77 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ASN N  82 " --> pdb=" O   ALA N  78 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 88 through 108
    Processing helix  chain 'N' and resid 112 through 135
    Processing helix  chain 'N' and resid 140 through 152
    Processing helix  chain 'N' and resid 155 through 170
      removed outlier: 3.541A  pdb=" N   GLY N 159 " --> pdb=" O   ASP N 155 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 201 through 205
    Processing helix  chain 'N' and resid 233 through 244
    Processing helix  chain 'N' and resid 258 through 266
      removed outlier: 3.567A  pdb=" N   LEU N 262 " --> pdb=" O   ALA N 258 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 282 through 297
      removed outlier: 3.558A  pdb=" N   LYS N 286 " --> pdb=" O   GLY N 282 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 308 through 312
    Processing helix  chain 'N' and resid 338 through 355
    Processing helix  chain 'N' and resid 358 through 375
      removed outlier: 4.351A  pdb=" N   GLY N 375 " --> pdb=" O   LYS N 371 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 385 through 410
    Processing helix  chain 'N' and resid 416 through 426
      removed outlier: 3.878A  pdb=" N   ILE N 420 " --> pdb=" O   GLY N 416 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 433 through 447
      removed outlier: 3.575A  pdb=" N   ASN N 437 " --> pdb=" O   ASN N 433 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 448 through 458
    Processing helix  chain 'N' and resid 461 through 472
      removed outlier: 3.596A  pdb=" N   VAL N 465 " --> pdb=" O   GLU N 461 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 497 through 516
    Processing helix  chain 'B' and resid 9 through 29
      removed outlier: 4.154A  pdb=" N   VAL B  29 " --> pdb=" O   ASP B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 60
      removed outlier: 3.626A  pdb=" N   VAL B  56 " --> pdb=" O   ASP B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 64 through 86
      removed outlier: 3.835A  pdb=" N   LYS B  80 " --> pdb=" O   GLU B  76 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   ALA B  81 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ASN B  82 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 108
    Processing helix  chain 'B' and resid 112 through 135
    Processing helix  chain 'B' and resid 140 through 152
    Processing helix  chain 'B' and resid 155 through 170
    Processing helix  chain 'B' and resid 201 through 205
    Processing helix  chain 'B' and resid 233 through 244
    Processing helix  chain 'B' and resid 258 through 266
    Processing helix  chain 'B' and resid 282 through 297
      removed outlier: 3.530A  pdb=" N   LYS B 286 " --> pdb=" O   GLY B 282 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 312
    Processing helix  chain 'B' and resid 338 through 355
    Processing helix  chain 'B' and resid 358 through 375
      removed outlier: 4.275A  pdb=" N   GLY B 375 " --> pdb=" O   LYS B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 410
    Processing helix  chain 'B' and resid 416 through 426
      removed outlier: 3.878A  pdb=" N   ILE B 420 " --> pdb=" O   GLY B 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 447
    Processing helix  chain 'B' and resid 448 through 458
    Processing helix  chain 'B' and resid 461 through 472
      removed outlier: 3.699A  pdb=" N   VAL B 465 " --> pdb=" O   GLU B 461 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 488 through 492
    Processing helix  chain 'B' and resid 497 through 516
    Processing helix  chain 'H' and resid 9 through 29
      removed outlier: 4.102A  pdb=" N   VAL H  29 " --> pdb=" O   ASP H  25 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 52 through 60
      removed outlier: 3.612A  pdb=" N   VAL H  56 " --> pdb=" O   ASP H  52 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 64 through 86
      removed outlier: 3.878A  pdb=" N   LYS H  80 " --> pdb=" O   GLU H  76 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   ALA H  81 " --> pdb=" O   VAL H  77 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ASN H  82 " --> pdb=" O   ALA H  78 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 88 through 108
    Processing helix  chain 'H' and resid 112 through 135
    Processing helix  chain 'H' and resid 140 through 152
    Processing helix  chain 'H' and resid 155 through 170
      removed outlier: 3.535A  pdb=" N   GLY H 159 " --> pdb=" O   ASP H 155 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 201 through 205
    Processing helix  chain 'H' and resid 233 through 244
    Processing helix  chain 'H' and resid 258 through 266
    Processing helix  chain 'H' and resid 282 through 297
      removed outlier: 3.557A  pdb=" N   LYS H 286 " --> pdb=" O   GLY H 282 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 308 through 312
    Processing helix  chain 'H' and resid 338 through 355
    Processing helix  chain 'H' and resid 358 through 375
      removed outlier: 4.356A  pdb=" N   GLY H 375 " --> pdb=" O   LYS H 371 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 385 through 410
    Processing helix  chain 'H' and resid 416 through 426
      removed outlier: 3.846A  pdb=" N   ILE H 420 " --> pdb=" O   GLY H 416 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 433 through 447
      removed outlier: 3.623A  pdb=" N   ASN H 437 " --> pdb=" O   ASN H 433 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 448 through 458
    Processing helix  chain 'H' and resid 461 through 472
      removed outlier: 3.610A  pdb=" N   VAL H 465 " --> pdb=" O   GLU H 461 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 488 through 492
    Processing helix  chain 'H' and resid 497 through 516
    Processing helix  chain 'C' and resid 9 through 29
      removed outlier: 4.097A  pdb=" N   VAL C  29 " --> pdb=" O   ASP C  25 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 52 through 60
      removed outlier: 3.644A  pdb=" N   VAL C  56 " --> pdb=" O   ASP C  52 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 64 through 86
      removed outlier: 3.821A  pdb=" N   LYS C  80 " --> pdb=" O   GLU C  76 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   ALA C  81 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ASN C  82 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 88 through 108
    Processing helix  chain 'C' and resid 112 through 135
    Processing helix  chain 'C' and resid 140 through 152
    Processing helix  chain 'C' and resid 155 through 170
    Processing helix  chain 'C' and resid 201 through 205
    Processing helix  chain 'C' and resid 233 through 244
    Processing helix  chain 'C' and resid 258 through 266
      removed outlier: 3.573A  pdb=" N   LEU C 262 " --> pdb=" O   ALA C 258 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 282 through 297
      removed outlier: 3.519A  pdb=" N   LYS C 286 " --> pdb=" O   GLY C 282 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 308 through 312
    Processing helix  chain 'C' and resid 338 through 355
    Processing helix  chain 'C' and resid 358 through 375
      removed outlier: 4.258A  pdb=" N   GLY C 375 " --> pdb=" O   LYS C 371 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 385 through 410
    Processing helix  chain 'C' and resid 416 through 426
      removed outlier: 3.823A  pdb=" N   ILE C 420 " --> pdb=" O   GLY C 416 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 433 through 447
    Processing helix  chain 'C' and resid 448 through 458
    Processing helix  chain 'C' and resid 461 through 472
      removed outlier: 3.697A  pdb=" N   VAL C 465 " --> pdb=" O   GLU C 461 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 497 through 516
    Processing helix  chain 'I' and resid 9 through 29
      removed outlier: 4.177A  pdb=" N   VAL I  29 " --> pdb=" O   ASP I  25 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 52 through 60
      removed outlier: 3.616A  pdb=" N   VAL I  56 " --> pdb=" O   ASP I  52 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 64 through 86
      removed outlier: 3.900A  pdb=" N   LYS I  80 " --> pdb=" O   GLU I  76 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ALA I  81 " --> pdb=" O   VAL I  77 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ASN I  82 " --> pdb=" O   ALA I  78 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 88 through 108
    Processing helix  chain 'I' and resid 112 through 135
    Processing helix  chain 'I' and resid 140 through 152
    Processing helix  chain 'I' and resid 155 through 170
      removed outlier: 3.535A  pdb=" N   GLY I 159 " --> pdb=" O   ASP I 155 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 201 through 205
    Processing helix  chain 'I' and resid 229 through 232
      removed outlier: 3.658A  pdb=" N   GLU I 232 " --> pdb=" O   ASN I 229 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 229 through 232'
    Processing helix  chain 'I' and resid 233 through 244
    Processing helix  chain 'I' and resid 258 through 265
      removed outlier: 3.549A  pdb=" N   LEU I 262 " --> pdb=" O   ALA I 258 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 282 through 297
      removed outlier: 3.564A  pdb=" N   LYS I 286 " --> pdb=" O   GLY I 282 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 308 through 312
    Processing helix  chain 'I' and resid 338 through 355
    Processing helix  chain 'I' and resid 358 through 375
      removed outlier: 4.378A  pdb=" N   GLY I 375 " --> pdb=" O   LYS I 371 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 385 through 410
    Processing helix  chain 'I' and resid 416 through 426
      removed outlier: 3.837A  pdb=" N   ILE I 420 " --> pdb=" O   GLY I 416 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 433 through 447
      removed outlier: 3.614A  pdb=" N   ASN I 437 " --> pdb=" O   ASN I 433 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 448 through 458
    Processing helix  chain 'I' and resid 461 through 472
      removed outlier: 3.628A  pdb=" N   VAL I 465 " --> pdb=" O   GLU I 461 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 488 through 492
    Processing helix  chain 'I' and resid 497 through 516
    Processing helix  chain 'D' and resid 9 through 29
      removed outlier: 4.081A  pdb=" N   VAL D  29 " --> pdb=" O   ASP D  25 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 52 through 60
      removed outlier: 3.620A  pdb=" N   VAL D  56 " --> pdb=" O   ASP D  52 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 64 through 86
      removed outlier: 3.876A  pdb=" N   LYS D  80 " --> pdb=" O   GLU D  76 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   ALA D  81 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ASN D  82 " --> pdb=" O   ALA D  78 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 88 through 108
    Processing helix  chain 'D' and resid 112 through 135
    Processing helix  chain 'D' and resid 140 through 152
    Processing helix  chain 'D' and resid 155 through 170
    Processing helix  chain 'D' and resid 201 through 205
    Processing helix  chain 'D' and resid 233 through 244
    Processing helix  chain 'D' and resid 258 through 266
      removed outlier: 3.530A  pdb=" N   LEU D 262 " --> pdb=" O   ALA D 258 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 282 through 297
    Processing helix  chain 'D' and resid 308 through 312
    Processing helix  chain 'D' and resid 338 through 355
    Processing helix  chain 'D' and resid 358 through 375
      removed outlier: 4.204A  pdb=" N   GLY D 375 " --> pdb=" O   LYS D 371 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 385 through 410
    Processing helix  chain 'D' and resid 416 through 426
      removed outlier: 3.965A  pdb=" N   ILE D 420 " --> pdb=" O   GLY D 416 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 433 through 447
    Processing helix  chain 'D' and resid 448 through 458
    Processing helix  chain 'D' and resid 461 through 472
      removed outlier: 3.714A  pdb=" N   VAL D 465 " --> pdb=" O   GLU D 461 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 488 through 492
    Processing helix  chain 'D' and resid 497 through 516
    Processing helix  chain 'J' and resid 9 through 29
      removed outlier: 4.129A  pdb=" N   VAL J  29 " --> pdb=" O   ASP J  25 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 52 through 60
      removed outlier: 3.619A  pdb=" N   VAL J  56 " --> pdb=" O   ASP J  52 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 64 through 86
      removed outlier: 3.842A  pdb=" N   LYS J  80 " --> pdb=" O   GLU J  76 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ALA J  81 " --> pdb=" O   VAL J  77 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ASN J  82 " --> pdb=" O   ALA J  78 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 88 through 108
    Processing helix  chain 'J' and resid 112 through 135
    Processing helix  chain 'J' and resid 140 through 152
    Processing helix  chain 'J' and resid 155 through 170
      removed outlier: 3.541A  pdb=" N   GLY J 159 " --> pdb=" O   ASP J 155 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 201 through 205
    Processing helix  chain 'J' and resid 233 through 244
    Processing helix  chain 'J' and resid 258 through 266
      removed outlier: 3.537A  pdb=" N   LEU J 262 " --> pdb=" O   ALA J 258 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 282 through 297
      removed outlier: 3.567A  pdb=" N   LYS J 286 " --> pdb=" O   GLY J 282 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 308 through 312
    Processing helix  chain 'J' and resid 338 through 355
    Processing helix  chain 'J' and resid 358 through 375
      removed outlier: 4.277A  pdb=" N   GLY J 375 " --> pdb=" O   LYS J 371 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 385 through 410
    Processing helix  chain 'J' and resid 416 through 426
      removed outlier: 3.831A  pdb=" N   ILE J 420 " --> pdb=" O   GLY J 416 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 433 through 447
      removed outlier: 3.608A  pdb=" N   ASN J 437 " --> pdb=" O   ASN J 433 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 448 through 458
    Processing helix  chain 'J' and resid 461 through 472
      removed outlier: 3.613A  pdb=" N   VAL J 465 " --> pdb=" O   GLU J 461 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 497 through 516
    Processing helix  chain 'E' and resid 9 through 29
      removed outlier: 4.125A  pdb=" N   VAL E  29 " --> pdb=" O   ASP E  25 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 52 through 60
      removed outlier: 3.590A  pdb=" N   VAL E  56 " --> pdb=" O   ASP E  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 64 through 86
      removed outlier: 3.866A  pdb=" N   LYS E  80 " --> pdb=" O   GLU E  76 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   ALA E  81 " --> pdb=" O   VAL E  77 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ASN E  82 " --> pdb=" O   ALA E  78 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 88 through 108
    Processing helix  chain 'E' and resid 112 through 135
    Processing helix  chain 'E' and resid 140 through 152
    Processing helix  chain 'E' and resid 155 through 170
    Processing helix  chain 'E' and resid 201 through 205
    Processing helix  chain 'E' and resid 233 through 244
    Processing helix  chain 'E' and resid 258 through 265
      removed outlier: 3.620A  pdb=" N   LEU E 262 " --> pdb=" O   ALA E 258 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 282 through 297
      removed outlier: 3.533A  pdb=" N   LYS E 286 " --> pdb=" O   GLY E 282 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 308 through 312
    Processing helix  chain 'E' and resid 338 through 355
    Processing helix  chain 'E' and resid 358 through 375
      removed outlier: 4.263A  pdb=" N   GLY E 375 " --> pdb=" O   LYS E 371 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 385 through 410
    Processing helix  chain 'E' and resid 416 through 426
      removed outlier: 3.916A  pdb=" N   ILE E 420 " --> pdb=" O   GLY E 416 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 433 through 447
    Processing helix  chain 'E' and resid 448 through 458
    Processing helix  chain 'E' and resid 461 through 472
      removed outlier: 3.700A  pdb=" N   VAL E 465 " --> pdb=" O   GLU E 461 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 488 through 492
    Processing helix  chain 'E' and resid 497 through 516
    Processing helix  chain 'K' and resid 9 through 29
      removed outlier: 4.165A  pdb=" N   VAL K  29 " --> pdb=" O   ASP K  25 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 52 through 60
      removed outlier: 3.631A  pdb=" N   VAL K  56 " --> pdb=" O   ASP K  52 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 64 through 86
      removed outlier: 3.816A  pdb=" N   LYS K  80 " --> pdb=" O   GLU K  76 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   ALA K  81 " --> pdb=" O   VAL K  77 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ASN K  82 " --> pdb=" O   ALA K  78 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 88 through 108
    Processing helix  chain 'K' and resid 112 through 135
    Processing helix  chain 'K' and resid 140 through 152
    Processing helix  chain 'K' and resid 155 through 170
      removed outlier: 3.540A  pdb=" N   GLY K 159 " --> pdb=" O   ASP K 155 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 201 through 205
    Processing helix  chain 'K' and resid 233 through 244
    Processing helix  chain 'K' and resid 258 through 265
      removed outlier: 3.502A  pdb=" N   LEU K 262 " --> pdb=" O   ALA K 258 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 282 through 297
      removed outlier: 3.546A  pdb=" N   LYS K 286 " --> pdb=" O   GLY K 282 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 308 through 312
    Processing helix  chain 'K' and resid 338 through 355
    Processing helix  chain 'K' and resid 358 through 375
      removed outlier: 4.366A  pdb=" N   GLY K 375 " --> pdb=" O   LYS K 371 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 385 through 410
    Processing helix  chain 'K' and resid 416 through 426
      removed outlier: 3.854A  pdb=" N   ILE K 420 " --> pdb=" O   GLY K 416 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 433 through 447
      removed outlier: 3.552A  pdb=" N   ASN K 437 " --> pdb=" O   ASN K 433 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 448 through 458
    Processing helix  chain 'K' and resid 461 through 472
      removed outlier: 3.605A  pdb=" N   VAL K 465 " --> pdb=" O   GLU K 461 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 497 through 516
    Processing helix  chain 'F' and resid 9 through 29
      removed outlier: 4.100A  pdb=" N   VAL F  29 " --> pdb=" O   ASP F  25 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 52 through 60
      removed outlier: 3.638A  pdb=" N   VAL F  56 " --> pdb=" O   ASP F  52 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 64 through 86
      removed outlier: 3.742A  pdb=" N   LYS F  80 " --> pdb=" O   GLU F  76 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   ALA F  81 " --> pdb=" O   VAL F  77 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ASN F  82 " --> pdb=" O   ALA F  78 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 88 through 108
    Processing helix  chain 'F' and resid 112 through 135
    Processing helix  chain 'F' and resid 140 through 152
    Processing helix  chain 'F' and resid 155 through 170
    Processing helix  chain 'F' and resid 201 through 205
    Processing helix  chain 'F' and resid 233 through 244
    Processing helix  chain 'F' and resid 258 through 266
      removed outlier: 3.519A  pdb=" N   LEU F 262 " --> pdb=" O   ALA F 258 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 282 through 297
      removed outlier: 3.504A  pdb=" N   LYS F 286 " --> pdb=" O   GLY F 282 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 308 through 312
    Processing helix  chain 'F' and resid 338 through 355
      removed outlier: 3.503A  pdb=" N   ILE F 342 " --> pdb=" O   GLU F 338 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 358 through 375
      removed outlier: 4.230A  pdb=" N   GLY F 375 " --> pdb=" O   LYS F 371 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 385 through 410
    Processing helix  chain 'F' and resid 416 through 426
      removed outlier: 3.862A  pdb=" N   ILE F 420 " --> pdb=" O   GLY F 416 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 433 through 447
    Processing helix  chain 'F' and resid 448 through 458
    Processing helix  chain 'F' and resid 461 through 472
      removed outlier: 3.698A  pdb=" N   VAL F 465 " --> pdb=" O   GLU F 461 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 488 through 492
    Processing helix  chain 'F' and resid 497 through 516
    Processing helix  chain 'L' and resid 9 through 29
      removed outlier: 4.164A  pdb=" N   VAL L  29 " --> pdb=" O   ASP L  25 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 52 through 60
      removed outlier: 3.615A  pdb=" N   VAL L  56 " --> pdb=" O   ASP L  52 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 64 through 86
      removed outlier: 3.805A  pdb=" N   LYS L  80 " --> pdb=" O   GLU L  76 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ALA L  81 " --> pdb=" O   VAL L  77 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ASN L  82 " --> pdb=" O   ALA L  78 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 88 through 108
    Processing helix  chain 'L' and resid 112 through 135
    Processing helix  chain 'L' and resid 140 through 152
    Processing helix  chain 'L' and resid 155 through 170
      removed outlier: 3.541A  pdb=" N   GLY L 159 " --> pdb=" O   ASP L 155 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 201 through 205
    Processing helix  chain 'L' and resid 233 through 244
    Processing helix  chain 'L' and resid 258 through 265
      removed outlier: 3.523A  pdb=" N   LEU L 262 " --> pdb=" O   ALA L 258 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 282 through 297
      removed outlier: 3.531A  pdb=" N   LYS L 286 " --> pdb=" O   GLY L 282 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 308 through 312
    Processing helix  chain 'L' and resid 338 through 355
    Processing helix  chain 'L' and resid 358 through 375
      removed outlier: 4.261A  pdb=" N   GLY L 375 " --> pdb=" O   LYS L 371 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 385 through 410
    Processing helix  chain 'L' and resid 416 through 426
      removed outlier: 3.857A  pdb=" N   ILE L 420 " --> pdb=" O   GLY L 416 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 433 through 447
      removed outlier: 3.572A  pdb=" N   ASN L 437 " --> pdb=" O   ASN L 433 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 448 through 458
    Processing helix  chain 'L' and resid 461 through 472
      removed outlier: 3.609A  pdb=" N   VAL L 465 " --> pdb=" O   GLU L 461 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 488 through 492
    Processing helix  chain 'L' and resid 497 through 516
    Processing helix  chain 'G' and resid 9 through 29
      removed outlier: 4.123A  pdb=" N   VAL G  29 " --> pdb=" O   ASP G  25 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 52 through 60
      removed outlier: 3.609A  pdb=" N   VAL G  56 " --> pdb=" O   ASP G  52 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 64 through 86
      removed outlier: 3.791A  pdb=" N   LYS G  80 " --> pdb=" O   GLU G  76 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   ALA G  81 " --> pdb=" O   VAL G  77 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ASN G  82 " --> pdb=" O   ALA G  78 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 88 through 108
    Processing helix  chain 'G' and resid 112 through 135
    Processing helix  chain 'G' and resid 140 through 152
    Processing helix  chain 'G' and resid 155 through 170
    Processing helix  chain 'G' and resid 201 through 205
    Processing helix  chain 'G' and resid 233 through 244
    Processing helix  chain 'G' and resid 258 through 266
    Processing helix  chain 'G' and resid 282 through 297
      removed outlier: 3.540A  pdb=" N   LYS G 286 " --> pdb=" O   GLY G 282 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 308 through 312
    Processing helix  chain 'G' and resid 338 through 355
      removed outlier: 3.502A  pdb=" N   ILE G 342 " --> pdb=" O   GLU G 338 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 358 through 375
      removed outlier: 4.250A  pdb=" N   GLY G 375 " --> pdb=" O   LYS G 371 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 385 through 410
    Processing helix  chain 'G' and resid 416 through 426
      removed outlier: 3.885A  pdb=" N   ILE G 420 " --> pdb=" O   GLY G 416 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 433 through 447
    Processing helix  chain 'G' and resid 448 through 458
    Processing helix  chain 'G' and resid 461 through 472
      removed outlier: 3.692A  pdb=" N   VAL G 465 " --> pdb=" O   GLU G 461 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 488 through 492
    Processing helix  chain 'G' and resid 497 through 516
    Processing helix  chain 'M' and resid 9 through 29
      removed outlier: 4.141A  pdb=" N   VAL M  29 " --> pdb=" O   ASP M  25 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 52 through 60
      removed outlier: 3.642A  pdb=" N   VAL M  56 " --> pdb=" O   ASP M  52 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 64 through 86
      removed outlier: 3.842A  pdb=" N   LYS M  80 " --> pdb=" O   GLU M  76 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ALA M  81 " --> pdb=" O   VAL M  77 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ASN M  82 " --> pdb=" O   ALA M  78 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 88 through 108
    Processing helix  chain 'M' and resid 112 through 135
    Processing helix  chain 'M' and resid 140 through 152
    Processing helix  chain 'M' and resid 155 through 170
      removed outlier: 3.539A  pdb=" N   GLY M 159 " --> pdb=" O   ASP M 155 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 201 through 205
    Processing helix  chain 'M' and resid 233 through 244
    Processing helix  chain 'M' and resid 258 through 266
      removed outlier: 3.570A  pdb=" N   LEU M 262 " --> pdb=" O   ALA M 258 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 282 through 297
      removed outlier: 3.540A  pdb=" N   LYS M 286 " --> pdb=" O   GLY M 282 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 308 through 312
    Processing helix  chain 'M' and resid 338 through 355
    Processing helix  chain 'M' and resid 358 through 375
      removed outlier: 4.338A  pdb=" N   GLY M 375 " --> pdb=" O   LYS M 371 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 385 through 410
    Processing helix  chain 'M' and resid 416 through 426
      removed outlier: 3.840A  pdb=" N   ILE M 420 " --> pdb=" O   GLY M 416 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 433 through 447
      removed outlier: 3.506A  pdb=" N   ASN M 437 " --> pdb=" O   ASN M 433 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 448 through 458
    Processing helix  chain 'M' and resid 461 through 472
      removed outlier: 3.602A  pdb=" N   VAL M 465 " --> pdb=" O   GLU M 461 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 497 through 516
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8
      removed outlier: 6.097A  pdb=" N   ASN G  37 " --> pdb=" O   THR A 517 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   CYS A 519 " --> pdb=" O   ASN G  37 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50
      removed outlier: 6.955A  pdb=" N   ASN A  37 " --> pdb=" O   CYS B 519 " (cutoff:3.500A)
      removed outlier: 8.294A  pdb=" N   VAL B 521 " --> pdb=" O   ASN A  37 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   VAL A  39 " --> pdb=" O   VAL B 521 " (cutoff:3.500A)
      removed outlier: 8.466A  pdb=" N   ASP B 523 " --> pdb=" O   VAL A  39 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 179
    Processing sheet with id=AA4, first strand: chain 'A' and resid 193 through 195
    Processing sheet with id=AA5, first strand: chain 'A' and resid 273 through 277
      removed outlier: 6.165A  pdb=" N   PHE A 219 " --> pdb=" O   LEU A 248 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   ILE A 250 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   LEU A 221 " --> pdb=" O   ILE A 250 " (cutoff:3.500A)
      removed outlier: 8.720A  pdb=" N   ILE A 301 " --> pdb=" O   ILE A 220 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   LEU A 222 " --> pdb=" O   ILE A 301 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 273 through 277
      removed outlier: 6.165A  pdb=" N   PHE A 219 " --> pdb=" O   LEU A 248 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   ILE A 250 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   LEU A 221 " --> pdb=" O   ILE A 250 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 411 through 413
    Processing sheet with id=AA8, first strand: chain 'A' and resid 476 through 479
    Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 8
      removed outlier: 3.505A  pdb=" N   LYS N   7 " --> pdb=" O   MET N 520 " (cutoff:3.500A)
      removed outlier: 7.578A  pdb=" N   VAL H  39 " --> pdb=" O   GLU N 518 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   MET N 520 " --> pdb=" O   VAL H  39 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 48 through 50
      removed outlier: 6.725A  pdb=" N   ASN N  37 " --> pdb=" O   CYS M 519 " (cutoff:3.500A)
      removed outlier: 8.317A  pdb=" N   VAL M 521 " --> pdb=" O   ASN N  37 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   VAL N  39 " --> pdb=" O   VAL M 521 " (cutoff:3.500A)
      removed outlier: 8.454A  pdb=" N   ASP M 523 " --> pdb=" O   VAL N  39 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 174 through 179
      removed outlier: 3.558A  pdb=" N   VAL N 381 " --> pdb=" O   GLU N 178 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'N' and resid 193 through 195
    Processing sheet with id=AB4, first strand: chain 'N' and resid 273 through 277
      removed outlier: 6.029A  pdb=" N   PHE N 219 " --> pdb=" O   LEU N 248 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   ILE N 250 " --> pdb=" O   PHE N 219 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   LEU N 221 " --> pdb=" O   ILE N 250 " (cutoff:3.500A)
      removed outlier: 8.737A  pdb=" N   ILE N 301 " --> pdb=" O   ILE N 220 " (cutoff:3.500A)
      removed outlier: 7.120A  pdb=" N   LEU N 222 " --> pdb=" O   ILE N 301 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'N' and resid 273 through 277
      removed outlier: 6.029A  pdb=" N   PHE N 219 " --> pdb=" O   LEU N 248 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   ILE N 250 " --> pdb=" O   PHE N 219 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   LEU N 221 " --> pdb=" O   ILE N 250 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'N' and resid 411 through 413
    Processing sheet with id=AB7, first strand: chain 'N' and resid 476 through 479
    Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 50
      removed outlier: 6.843A  pdb=" N   ASN B  37 " --> pdb=" O   CYS C 519 " (cutoff:3.500A)
      removed outlier: 8.300A  pdb=" N   VAL C 521 " --> pdb=" O   ASN B  37 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   VAL B  39 " --> pdb=" O   VAL C 521 " (cutoff:3.500A)
      removed outlier: 8.455A  pdb=" N   ASP C 523 " --> pdb=" O   VAL B  39 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 174 through 179
    Processing sheet with id=AC1, first strand: chain 'B' and resid 193 through 195
    Processing sheet with id=AC2, first strand: chain 'B' and resid 273 through 277
      removed outlier: 6.155A  pdb=" N   PHE B 219 " --> pdb=" O   LEU B 248 " (cutoff:3.500A)
      removed outlier: 7.264A  pdb=" N   ILE B 250 " --> pdb=" O   PHE B 219 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   LEU B 221 " --> pdb=" O   ILE B 250 " (cutoff:3.500A)
      removed outlier: 8.575A  pdb=" N   ILE B 301 " --> pdb=" O   ILE B 220 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   LEU B 222 " --> pdb=" O   ILE B 301 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 273 through 277
      removed outlier: 6.155A  pdb=" N   PHE B 219 " --> pdb=" O   LEU B 248 " (cutoff:3.500A)
      removed outlier: 7.264A  pdb=" N   ILE B 250 " --> pdb=" O   PHE B 219 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   LEU B 221 " --> pdb=" O   ILE B 250 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 411 through 413
    Processing sheet with id=AC5, first strand: chain 'B' and resid 476 through 479
    Processing sheet with id=AC6, first strand: chain 'H' and resid 4 through 8
      removed outlier: 5.985A  pdb=" N   ASN I  37 " --> pdb=" O   THR H 517 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   CYS H 519 " --> pdb=" O   ASN I  37 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'H' and resid 174 through 179
    Processing sheet with id=AC8, first strand: chain 'H' and resid 193 through 195
    Processing sheet with id=AC9, first strand: chain 'H' and resid 273 through 277
      removed outlier: 6.037A  pdb=" N   PHE H 219 " --> pdb=" O   LEU H 248 " (cutoff:3.500A)
      removed outlier: 7.219A  pdb=" N   ILE H 250 " --> pdb=" O   PHE H 219 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   LEU H 221 " --> pdb=" O   ILE H 250 " (cutoff:3.500A)
      removed outlier: 8.696A  pdb=" N   ILE H 301 " --> pdb=" O   ILE H 220 " (cutoff:3.500A)
      removed outlier: 7.134A  pdb=" N   LEU H 222 " --> pdb=" O   ILE H 301 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'H' and resid 273 through 277
      removed outlier: 6.037A  pdb=" N   PHE H 219 " --> pdb=" O   LEU H 248 " (cutoff:3.500A)
      removed outlier: 7.219A  pdb=" N   ILE H 250 " --> pdb=" O   PHE H 219 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   LEU H 221 " --> pdb=" O   ILE H 250 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'H' and resid 411 through 413
    Processing sheet with id=AD3, first strand: chain 'H' and resid 476 through 479
    Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 50
      removed outlier: 7.088A  pdb=" N   ASN C  37 " --> pdb=" O   CYS E 519 " (cutoff:3.500A)
      removed outlier: 8.420A  pdb=" N   VAL E 521 " --> pdb=" O   ASN C  37 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   VAL C  39 " --> pdb=" O   VAL E 521 " (cutoff:3.500A)
      removed outlier: 8.453A  pdb=" N   ASP E 523 " --> pdb=" O   VAL C  39 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'C' and resid 174 through 179
    Processing sheet with id=AD6, first strand: chain 'C' and resid 193 through 195
    Processing sheet with id=AD7, first strand: chain 'C' and resid 273 through 277
      removed outlier: 6.060A  pdb=" N   PHE C 219 " --> pdb=" O   LEU C 248 " (cutoff:3.500A)
      removed outlier: 7.234A  pdb=" N   ILE C 250 " --> pdb=" O   PHE C 219 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   LEU C 221 " --> pdb=" O   ILE C 250 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'C' and resid 411 through 413
    Processing sheet with id=AD9, first strand: chain 'C' and resid 476 through 479
    Processing sheet with id=AE1, first strand: chain 'I' and resid 4 through 8
      removed outlier: 5.933A  pdb=" N   ASN K  37 " --> pdb=" O   THR I 517 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   CYS I 519 " --> pdb=" O   ASN K  37 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'I' and resid 174 through 179
    Processing sheet with id=AE3, first strand: chain 'I' and resid 193 through 195
    Processing sheet with id=AE4, first strand: chain 'I' and resid 273 through 277
      removed outlier: 3.513A  pdb=" N   ALA I 251 " --> pdb=" O   VAL I 276 " (cutoff:3.500A)
      removed outlier: 5.966A  pdb=" N   PHE I 219 " --> pdb=" O   LEU I 248 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   ILE I 250 " --> pdb=" O   PHE I 219 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   LEU I 221 " --> pdb=" O   ILE I 250 " (cutoff:3.500A)
      removed outlier: 8.733A  pdb=" N   ILE I 301 " --> pdb=" O   ILE I 220 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   LEU I 222 " --> pdb=" O   ILE I 301 " (cutoff:3.500A)
    Processing sheet with id=AE5, first strand: chain 'I' and resid 273 through 277
      removed outlier: 3.513A  pdb=" N   ALA I 251 " --> pdb=" O   VAL I 276 " (cutoff:3.500A)
      removed outlier: 5.966A  pdb=" N   PHE I 219 " --> pdb=" O   LEU I 248 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   ILE I 250 " --> pdb=" O   PHE I 219 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   LEU I 221 " --> pdb=" O   ILE I 250 " (cutoff:3.500A)
    Processing sheet with id=AE6, first strand: chain 'I' and resid 411 through 413
    Processing sheet with id=AE7, first strand: chain 'I' and resid 476 through 479
    Processing sheet with id=AE8, first strand: chain 'D' and resid 4 through 8
      removed outlier: 6.108A  pdb=" N   ASN E  37 " --> pdb=" O   THR D 517 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   CYS D 519 " --> pdb=" O   ASN E  37 " (cutoff:3.500A)
    Processing sheet with id=AE9, first strand: chain 'D' and resid 48 through 50
      removed outlier: 6.940A  pdb=" N   ASN D  37 " --> pdb=" O   CYS F 519 " (cutoff:3.500A)
      removed outlier: 8.390A  pdb=" N   VAL F 521 " --> pdb=" O   ASN D  37 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   VAL D  39 " --> pdb=" O   VAL F 521 " (cutoff:3.500A)
      removed outlier: 8.548A  pdb=" N   ASP F 523 " --> pdb=" O   VAL D  39 " (cutoff:3.500A)
    Processing sheet with id=AF1, first strand: chain 'D' and resid 174 through 179
    Processing sheet with id=AF2, first strand: chain 'D' and resid 193 through 195
    Processing sheet with id=AF3, first strand: chain 'D' and resid 273 through 277
      removed outlier: 6.068A  pdb=" N   PHE D 219 " --> pdb=" O   LEU D 248 " (cutoff:3.500A)
      removed outlier: 7.252A  pdb=" N   ILE D 250 " --> pdb=" O   PHE D 219 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   LEU D 221 " --> pdb=" O   ILE D 250 " (cutoff:3.500A)
      removed outlier: 8.618A  pdb=" N   ILE D 301 " --> pdb=" O   ILE D 220 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   LEU D 222 " --> pdb=" O   ILE D 301 " (cutoff:3.500A)
    Processing sheet with id=AF4, first strand: chain 'D' and resid 273 through 277
      removed outlier: 6.068A  pdb=" N   PHE D 219 " --> pdb=" O   LEU D 248 " (cutoff:3.500A)
      removed outlier: 7.252A  pdb=" N   ILE D 250 " --> pdb=" O   PHE D 219 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   LEU D 221 " --> pdb=" O   ILE D 250 " (cutoff:3.500A)
    Processing sheet with id=AF5, first strand: chain 'D' and resid 411 through 413
    Processing sheet with id=AF6, first strand: chain 'D' and resid 476 through 479
    Processing sheet with id=AF7, first strand: chain 'J' and resid 4 through 8
      removed outlier: 6.017A  pdb=" N   ASN L  37 " --> pdb=" O   THR J 517 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   CYS J 519 " --> pdb=" O   ASN L  37 " (cutoff:3.500A)
    Processing sheet with id=AF8, first strand: chain 'J' and resid 48 through 50
      removed outlier: 6.804A  pdb=" N   ASN J  37 " --> pdb=" O   CYS K 519 " (cutoff:3.500A)
      removed outlier: 8.359A  pdb=" N   VAL K 521 " --> pdb=" O   ASN J  37 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   VAL J  39 " --> pdb=" O   VAL K 521 " (cutoff:3.500A)
      removed outlier: 8.459A  pdb=" N   ASP K 523 " --> pdb=" O   VAL J  39 " (cutoff:3.500A)
    Processing sheet with id=AF9, first strand: chain 'J' and resid 174 through 179
      removed outlier: 3.563A  pdb=" N   VAL J 381 " --> pdb=" O   GLU J 178 " (cutoff:3.500A)
    Processing sheet with id=AG1, first strand: chain 'J' and resid 193 through 195
    Processing sheet with id=AG2, first strand: chain 'J' and resid 273 through 277
      removed outlier: 6.023A  pdb=" N   PHE J 219 " --> pdb=" O   LEU J 248 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   ILE J 250 " --> pdb=" O   PHE J 219 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   LEU J 221 " --> pdb=" O   ILE J 250 " (cutoff:3.500A)
      removed outlier: 8.733A  pdb=" N   ILE J 301 " --> pdb=" O   ILE J 220 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   LEU J 222 " --> pdb=" O   ILE J 301 " (cutoff:3.500A)
    Processing sheet with id=AG3, first strand: chain 'J' and resid 273 through 277
      removed outlier: 6.023A  pdb=" N   PHE J 219 " --> pdb=" O   LEU J 248 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   ILE J 250 " --> pdb=" O   PHE J 219 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   LEU J 221 " --> pdb=" O   ILE J 250 " (cutoff:3.500A)
    Processing sheet with id=AG4, first strand: chain 'J' and resid 411 through 413
    Processing sheet with id=AG5, first strand: chain 'J' and resid 476 through 479
    Processing sheet with id=AG6, first strand: chain 'E' and resid 174 through 179
    Processing sheet with id=AG7, first strand: chain 'E' and resid 193 through 195
    Processing sheet with id=AG8, first strand: chain 'E' and resid 273 through 277
      removed outlier: 6.180A  pdb=" N   PHE E 219 " --> pdb=" O   LEU E 248 " (cutoff:3.500A)
      removed outlier: 7.295A  pdb=" N   ILE E 250 " --> pdb=" O   PHE E 219 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   LEU E 221 " --> pdb=" O   ILE E 250 " (cutoff:3.500A)
      removed outlier: 8.590A  pdb=" N   ILE E 301 " --> pdb=" O   ILE E 220 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   LEU E 222 " --> pdb=" O   ILE E 301 " (cutoff:3.500A)
    Processing sheet with id=AG9, first strand: chain 'E' and resid 273 through 277
      removed outlier: 6.180A  pdb=" N   PHE E 219 " --> pdb=" O   LEU E 248 " (cutoff:3.500A)
      removed outlier: 7.295A  pdb=" N   ILE E 250 " --> pdb=" O   PHE E 219 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   LEU E 221 " --> pdb=" O   ILE E 250 " (cutoff:3.500A)
    Processing sheet with id=AH1, first strand: chain 'E' and resid 411 through 413
    Processing sheet with id=AH2, first strand: chain 'E' and resid 476 through 479
    Processing sheet with id=AH3, first strand: chain 'K' and resid 174 through 179
    Processing sheet with id=AH4, first strand: chain 'K' and resid 193 through 195
    Processing sheet with id=AH5, first strand: chain 'K' and resid 273 through 277
      removed outlier: 6.034A  pdb=" N   PHE K 219 " --> pdb=" O   LEU K 248 " (cutoff:3.500A)
      removed outlier: 7.221A  pdb=" N   ILE K 250 " --> pdb=" O   PHE K 219 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   LEU K 221 " --> pdb=" O   ILE K 250 " (cutoff:3.500A)
      removed outlier: 8.846A  pdb=" N   ILE K 301 " --> pdb=" O   ILE K 220 " (cutoff:3.500A)
      removed outlier: 7.192A  pdb=" N   LEU K 222 " --> pdb=" O   ILE K 301 " (cutoff:3.500A)
    Processing sheet with id=AH6, first strand: chain 'K' and resid 273 through 277
      removed outlier: 6.034A  pdb=" N   PHE K 219 " --> pdb=" O   LEU K 248 " (cutoff:3.500A)
      removed outlier: 7.221A  pdb=" N   ILE K 250 " --> pdb=" O   PHE K 219 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   LEU K 221 " --> pdb=" O   ILE K 250 " (cutoff:3.500A)
    Processing sheet with id=AH7, first strand: chain 'K' and resid 411 through 413
    Processing sheet with id=AH8, first strand: chain 'K' and resid 476 through 479
    Processing sheet with id=AH9, first strand: chain 'F' and resid 48 through 50
      removed outlier: 6.992A  pdb=" N   ASN F  37 " --> pdb=" O   CYS G 519 " (cutoff:3.500A)
      removed outlier: 8.426A  pdb=" N   VAL G 521 " --> pdb=" O   ASN F  37 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   VAL F  39 " --> pdb=" O   VAL G 521 " (cutoff:3.500A)
      removed outlier: 8.611A  pdb=" N   ASP G 523 " --> pdb=" O   VAL F  39 " (cutoff:3.500A)
    Processing sheet with id=AI1, first strand: chain 'F' and resid 174 through 179
    Processing sheet with id=AI2, first strand: chain 'F' and resid 193 through 195
    Processing sheet with id=AI3, first strand: chain 'F' and resid 273 through 277
      removed outlier: 6.064A  pdb=" N   PHE F 219 " --> pdb=" O   LEU F 248 " (cutoff:3.500A)
      removed outlier: 7.237A  pdb=" N   ILE F 250 " --> pdb=" O   PHE F 219 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   LEU F 221 " --> pdb=" O   ILE F 250 " (cutoff:3.500A)
    Processing sheet with id=AI4, first strand: chain 'F' and resid 411 through 413
    Processing sheet with id=AI5, first strand: chain 'F' and resid 476 through 479
    Processing sheet with id=AI6, first strand: chain 'L' and resid 4 through 8
      removed outlier: 6.008A  pdb=" N   ASN M  37 " --> pdb=" O   THR L 517 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   CYS L 519 " --> pdb=" O   ASN M  37 " (cutoff:3.500A)
    Processing sheet with id=AI7, first strand: chain 'L' and resid 174 through 179
    Processing sheet with id=AI8, first strand: chain 'L' and resid 193 through 195
    Processing sheet with id=AI9, first strand: chain 'L' and resid 273 through 277
      removed outlier: 6.028A  pdb=" N   PHE L 219 " --> pdb=" O   LEU L 248 " (cutoff:3.500A)
      removed outlier: 7.219A  pdb=" N   ILE L 250 " --> pdb=" O   PHE L 219 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   LEU L 221 " --> pdb=" O   ILE L 250 " (cutoff:3.500A)
      removed outlier: 8.739A  pdb=" N   ILE L 301 " --> pdb=" O   ILE L 220 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   LEU L 222 " --> pdb=" O   ILE L 301 " (cutoff:3.500A)
    Processing sheet with id=AJ1, first strand: chain 'L' and resid 273 through 277
      removed outlier: 6.028A  pdb=" N   PHE L 219 " --> pdb=" O   LEU L 248 " (cutoff:3.500A)
      removed outlier: 7.219A  pdb=" N   ILE L 250 " --> pdb=" O   PHE L 219 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   LEU L 221 " --> pdb=" O   ILE L 250 " (cutoff:3.500A)
    Processing sheet with id=AJ2, first strand: chain 'L' and resid 411 through 413
    Processing sheet with id=AJ3, first strand: chain 'L' and resid 476 through 479
    Processing sheet with id=AJ4, first strand: chain 'G' and resid 174 through 179
    Processing sheet with id=AJ5, first strand: chain 'G' and resid 193 through 195
    Processing sheet with id=AJ6, first strand: chain 'G' and resid 273 through 277
      removed outlier: 3.516A  pdb=" N   ALA G 251 " --> pdb=" O   VAL G 276 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   PHE G 219 " --> pdb=" O   LEU G 248 " (cutoff:3.500A)
      removed outlier: 7.263A  pdb=" N   ILE G 250 " --> pdb=" O   PHE G 219 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   LEU G 221 " --> pdb=" O   ILE G 250 " (cutoff:3.500A)
      removed outlier: 8.555A  pdb=" N   ILE G 301 " --> pdb=" O   ILE G 220 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   LEU G 222 " --> pdb=" O   ILE G 301 " (cutoff:3.500A)
    Processing sheet with id=AJ7, first strand: chain 'G' and resid 273 through 277
      removed outlier: 3.516A  pdb=" N   ALA G 251 " --> pdb=" O   VAL G 276 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   PHE G 219 " --> pdb=" O   LEU G 248 " (cutoff:3.500A)
      removed outlier: 7.263A  pdb=" N   ILE G 250 " --> pdb=" O   PHE G 219 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   LEU G 221 " --> pdb=" O   ILE G 250 " (cutoff:3.500A)
    Processing sheet with id=AJ8, first strand: chain 'G' and resid 411 through 413
    Processing sheet with id=AJ9, first strand: chain 'G' and resid 476 through 479
    Processing sheet with id=AK1, first strand: chain 'M' and resid 174 through 179
    Processing sheet with id=AK2, first strand: chain 'M' and resid 193 through 195
    Processing sheet with id=AK3, first strand: chain 'M' and resid 273 through 277
      removed outlier: 6.025A  pdb=" N   PHE M 219 " --> pdb=" O   LEU M 248 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   ILE M 250 " --> pdb=" O   PHE M 219 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   LEU M 221 " --> pdb=" O   ILE M 250 " (cutoff:3.500A)
      removed outlier: 8.747A  pdb=" N   ILE M 301 " --> pdb=" O   ILE M 220 " (cutoff:3.500A)
      removed outlier: 7.121A  pdb=" N   LEU M 222 " --> pdb=" O   ILE M 301 " (cutoff:3.500A)
    Processing sheet with id=AK4, first strand: chain 'M' and resid 273 through 277
      removed outlier: 6.025A  pdb=" N   PHE M 219 " --> pdb=" O   LEU M 248 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   ILE M 250 " --> pdb=" O   PHE M 219 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   LEU M 221 " --> pdb=" O   ILE M 250 " (cutoff:3.500A)
    Processing sheet with id=AK5, first strand: chain 'M' and resid 411 through 413
    Processing sheet with id=AK6, first strand: chain 'M' and resid 476 through 479

    3660 hydrogen bonds defined for protein.
    10518 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: 28.07

  Time building geometry restraints manager: 13.11 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 18774
        1.34 -     1.46: 9400
        1.46 -     1.58: 25670
        1.58 -     1.70: 0
        1.70 -     1.82: 518
  Bond restraints: 54362
  Sorted by residual:
  bond pdb=" CB  VAL J 510 "
       pdb=" CG2 VAL J 510 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.58e+00
  bond pdb=" CB  VAL M 510 "
       pdb=" CG2 VAL M 510 "
    ideal  model  delta    sigma   weight residual
    1.521  1.480  0.041 3.30e-02 9.18e+02 1.58e+00
  bond pdb=" CB  GLU A  76 "
       pdb=" CG  GLU A  76 "
    ideal  model  delta    sigma   weight residual
    1.520  1.556 -0.036 3.00e-02 1.11e+03 1.48e+00
  bond pdb=" CB  VAL K 510 "
       pdb=" CG2 VAL K 510 "
    ideal  model  delta    sigma   weight residual
    1.521  1.481  0.040 3.30e-02 9.18e+02 1.46e+00
  bond pdb=" CB  VAL L 510 "
       pdb=" CG2 VAL L 510 "
    ideal  model  delta    sigma   weight residual
    1.521  1.481  0.040 3.30e-02 9.18e+02 1.44e+00
  ... (remaining 54357 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.85: 72907
        2.85 -     5.70: 441
        5.70 -     8.56: 30
        8.56 -    11.41: 10
       11.41 -    14.26: 14
  Bond angle restraints: 73402
  Sorted by residual:
  angle pdb=" CB  MET B 267 "
        pdb=" CG  MET B 267 "
        pdb=" SD  MET B 267 "
      ideal   model   delta    sigma   weight residual
     112.70  126.96  -14.26 3.00e+00 1.11e-01 2.26e+01
  angle pdb=" CB  MET K 267 "
        pdb=" CG  MET K 267 "
        pdb=" SD  MET K 267 "
      ideal   model   delta    sigma   weight residual
     112.70  126.39  -13.69 3.00e+00 1.11e-01 2.08e+01
  angle pdb=" CB  MET H 267 "
        pdb=" CG  MET H 267 "
        pdb=" SD  MET H 267 "
      ideal   model   delta    sigma   weight residual
     112.70  125.99  -13.29 3.00e+00 1.11e-01 1.96e+01
  angle pdb=" CB  MET I 267 "
        pdb=" CG  MET I 267 "
        pdb=" SD  MET I 267 "
      ideal   model   delta    sigma   weight residual
     112.70  125.95  -13.25 3.00e+00 1.11e-01 1.95e+01
  angle pdb=" CB  MET C 267 "
        pdb=" CG  MET C 267 "
        pdb=" SD  MET C 267 "
      ideal   model   delta    sigma   weight residual
     112.70  125.93  -13.23 3.00e+00 1.11e-01 1.94e+01
  ... (remaining 73397 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 30481
       18.00 -    35.99: 2512
       35.99 -    53.99: 588
       53.99 -    71.98: 122
       71.98 -    89.98: 65
  Dihedral angle restraints: 33768
    sinusoidal: 13076
      harmonic: 20692
  Sorted by residual:
  dihedral pdb=" CA  ARG M 231 "
           pdb=" C   ARG M 231 "
           pdb=" N   GLU M 232 "
           pdb=" CA  GLU M 232 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.56  -16.44     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CG  ARG H  58 "
           pdb=" CD  ARG H  58 "
           pdb=" NE  ARG H  58 "
           pdb=" CZ  ARG H  58 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.06   44.94     2      1.50e+01 4.44e-03 1.06e+01
  dihedral pdb=" CG  ARG L  58 "
           pdb=" CD  ARG L  58 "
           pdb=" NE  ARG L  58 "
           pdb=" CZ  ARG L  58 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.91  -44.91     2      1.50e+01 4.44e-03 1.06e+01
  ... (remaining 33765 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 5611
       0.029 -    0.058: 2069
       0.058 -    0.087: 745
       0.087 -    0.116: 445
       0.116 -    0.145: 62
  Chirality restraints: 8932
  Sorted by residual:
  chirality pdb=" CA  GLU A 232 "
            pdb=" N   GLU A 232 "
            pdb=" C   GLU A 232 "
            pdb=" CB  GLU A 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.29e-01
  chirality pdb=" CA  GLU D 232 "
            pdb=" N   GLU D 232 "
            pdb=" C   GLU D 232 "
            pdb=" CB  GLU D 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.94e-01
  chirality pdb=" CA  VAL F 271 "
            pdb=" N   VAL F 271 "
            pdb=" C   VAL F 271 "
            pdb=" CB  VAL F 271 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.70e-01
  ... (remaining 8929 not shown)

  Planarity restraints: 9618
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B 267 "   -0.010 2.00e-02 2.50e+03   2.01e-02 4.04e+00
        pdb=" C   MET B 267 "    0.035 2.00e-02 2.50e+03
        pdb=" O   MET B 267 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ARG B 268 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET C 267 "   -0.010 2.00e-02 2.50e+03   2.01e-02 4.04e+00
        pdb=" C   MET C 267 "    0.035 2.00e-02 2.50e+03
        pdb=" O   MET C 267 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ARG C 268 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU F  76 "    0.010 2.00e-02 2.50e+03   2.01e-02 4.03e+00
        pdb=" CD  GLU F  76 "   -0.035 2.00e-02 2.50e+03
        pdb=" OE1 GLU F  76 "    0.013 2.00e-02 2.50e+03
        pdb=" OE2 GLU F  76 "    0.012 2.00e-02 2.50e+03
  ... (remaining 9615 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 6317
        2.74 -     3.28: 54878
        3.28 -     3.82: 91620
        3.82 -     4.36: 98267
        4.36 -     4.90: 180686
  Nonbonded interactions: 431768
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG J 421 "
            pdb=" O   VAL J 469 "
     model   vdw
     2.206 3.120
  nonbonded pdb=" NH2 ARG M 421 "
            pdb=" O   VAL M 469 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" NH2 ARG H 421 "
            pdb=" O   VAL H 469 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" O   ILE A 270 "
            pdb=" ND2 ASN B 229 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" ND2 ASN A 229 "
            pdb=" O   ILE G 270 "
     model   vdw
     2.210 3.120
  ... (remaining 431763 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.720
  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:             0.080
  Extract box with map and model:          1.710
  Check model and map are aligned:         0.340
  Set scattering table:                    0.390
  Process input model:                     105.630
  Find NCS groups from input model:        1.620
  Set up NCS constraints:                  0.320
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  113.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
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   0.042  54362  Z= 0.219
  Angle     :  0.581  14.260  73402  Z= 0.294
  Chirality :  0.040   0.145   8932
  Planarity :  0.003   0.027   9618
  Dihedral  : 14.856  89.981  20496
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  9.64 %
    Favored  : 89.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.10), residues: 7308
  helix:  2.39 (0.08), residues: 4032
  sheet: -0.01 (0.14), residues: 1232
  loop : -0.43 (0.13), residues: 2044

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS L 401 
 PHE   0.024   0.001   PHE B  44 
 TYR   0.011   0.001   TYR J 478 
 ARG   0.005   0.000   ARG J  13 

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

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

  14616 Ramachandran restraints generated.
    7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  14616 Ramachandran restraints generated.
    7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  770 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 737
  time to evaluate  : 4.800 
Fit side-chains
   revert: symmetry clash
REVERT: A  321 LYS cc_start: 0.8099 (ttpt) cc_final: 0.7677 (mmtp)
REVERT: A  322 ARG cc_start: 0.7508 (ttp80) cc_final: 0.7201 (ttm110)
REVERT: A  461 GLU cc_start: 0.7671 (pm20) cc_final: 0.7379 (pm20)
REVERT: A  514 MET cc_start: 0.8393 (mtp) cc_final: 0.7936 (mtp)
REVERT: N   69 MET cc_start: 0.5509 (mtm) cc_final: 0.5233 (mtp)
REVERT: N  121 ASP cc_start: 0.7417 (m-30) cc_final: 0.7204 (m-30)
REVERT: N  267 MET cc_start: 0.6336 (tmm) cc_final: 0.5363 (mmp)
REVERT: N  321 LYS cc_start: 0.7892 (ttpt) cc_final: 0.7490 (mmtp)
REVERT: N  447 MET cc_start: 0.8065 (mtm) cc_final: 0.7828 (mtp)
REVERT: B  160 LYS cc_start: 0.7755 (mtpp) cc_final: 0.7545 (ttmm)
REVERT: B  193 MET cc_start: 0.6529 (tpt) cc_final: 0.6091 (tpt)
REVERT: B  233 MET cc_start: 0.5060 (pmm) cc_final: 0.4814 (ptt)
REVERT: B  321 LYS cc_start: 0.7978 (ttpt) cc_final: 0.7529 (mmtp)
REVERT: B  523 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7778 (m-30)
REVERT: H  121 ASP cc_start: 0.7221 (m-30) cc_final: 0.6887 (m-30)
REVERT: H  321 LYS cc_start: 0.7961 (ttpt) cc_final: 0.7640 (mmtp)
REVERT: H  514 MET cc_start: 0.8246 (mtp) cc_final: 0.7936 (mtp)
REVERT: C   61 GLU cc_start: 0.7535 (pp20) cc_final: 0.7059 (pt0)
REVERT: C  252 GLU cc_start: 0.7057 (tt0) cc_final: 0.6624 (tt0)
REVERT: C  277 LYS cc_start: 0.7956 (mttt) cc_final: 0.7670 (mmmm)
REVERT: C  288 MET cc_start: 0.5971 (ptp) cc_final: 0.5621 (mtp)
REVERT: C  321 LYS cc_start: 0.8396 (ttpt) cc_final: 0.7892 (mmtp)
REVERT: C  322 ARG cc_start: 0.7538 (ttp80) cc_final: 0.7299 (ttm110)
REVERT: C  493 ILE cc_start: 0.8121 (mt) cc_final: 0.7879 (tt)
REVERT: C  514 MET cc_start: 0.8550 (mtp) cc_final: 0.8179 (mtp)
REVERT: C  523 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7357 (m-30)
REVERT: I  121 ASP cc_start: 0.7011 (m-30) cc_final: 0.6754 (m-30)
REVERT: I  193 MET cc_start: 0.6747 (tpt) cc_final: 0.6541 (tpt)
REVERT: I  204 PHE cc_start: 0.7807 (m-80) cc_final: 0.7508 (m-80)
REVERT: I  267 MET cc_start: 0.6556 (tmm) cc_final: 0.5466 (mmp)
REVERT: I  321 LYS cc_start: 0.7674 (ttpt) cc_final: 0.7375 (mmtp)
REVERT: I  336 VAL cc_start: 0.8094 (p) cc_final: 0.7718 (m)
REVERT: I  351 GLN cc_start: 0.8382 (tp40) cc_final: 0.8177 (tp-100)
REVERT: I  514 MET cc_start: 0.8317 (mtm) cc_final: 0.8059 (mtp)
REVERT: D  321 LYS cc_start: 0.8092 (ttpt) cc_final: 0.7499 (mmmt)
REVERT: D  495 ASP cc_start: 0.7499 (m-30) cc_final: 0.7271 (m-30)
REVERT: J  204 PHE cc_start: 0.7669 (m-80) cc_final: 0.7259 (m-80)
REVERT: J  336 VAL cc_start: 0.7996 (p) cc_final: 0.7591 (m)
REVERT: J  351 GLN cc_start: 0.8374 (tp40) cc_final: 0.8124 (tp40)
REVERT: E   72 GLN cc_start: 0.7634 (mm110) cc_final: 0.7344 (mm110)
REVERT: E  102 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6807 (mp0)
REVERT: E  166 MET cc_start: 0.7059 (mtt) cc_final: 0.6806 (mtt)
REVERT: E  233 MET cc_start: 0.5877 (ppp) cc_final: 0.5528 (ptt)
REVERT: E  252 GLU cc_start: 0.7005 (tt0) cc_final: 0.6741 (tt0)
REVERT: E  321 LYS cc_start: 0.8274 (ttpt) cc_final: 0.7695 (mmpt)
REVERT: E  520 MET cc_start: 0.8259 (mtt) cc_final: 0.7838 (mtt)
REVERT: K  267 MET cc_start: 0.6289 (tmm) cc_final: 0.4982 (mmm)
REVERT: K  351 GLN cc_start: 0.8539 (tp40) cc_final: 0.8307 (tp40)
REVERT: K  514 MET cc_start: 0.8302 (mtm) cc_final: 0.7931 (mtp)
REVERT: F   61 GLU cc_start: 0.7272 (pt0) cc_final: 0.6642 (pt0)
REVERT: F  160 LYS cc_start: 0.7821 (mtpp) cc_final: 0.7563 (ttmm)
REVERT: F  233 MET cc_start: 0.5417 (pmm) cc_final: 0.5137 (ptt)
REVERT: F  321 LYS cc_start: 0.8109 (ttpt) cc_final: 0.7603 (mmtp)
REVERT: F  389 MET cc_start: 0.6298 (tmt) cc_final: 0.5841 (tmm)
REVERT: L   61 GLU cc_start: 0.7359 (tm-30) cc_final: 0.7112 (pt0)
REVERT: L   69 MET cc_start: 0.6809 (mtm) cc_final: 0.6537 (mtp)
REVERT: L  121 ASP cc_start: 0.7332 (m-30) cc_final: 0.7110 (m-30)
REVERT: L  255 GLU cc_start: 0.7116 (pm20) cc_final: 0.6908 (pm20)
REVERT: L  267 MET cc_start: 0.5973 (tmm) cc_final: 0.4831 (mmm)
REVERT: L  321 LYS cc_start: 0.7875 (ttpt) cc_final: 0.7644 (mmtp)
REVERT: L  351 GLN cc_start: 0.8375 (tp40) cc_final: 0.8119 (tp40)
REVERT: L  433 ASN cc_start: 0.6264 (p0) cc_final: 0.5910 (p0)
REVERT: G   61 GLU cc_start: 0.7409 (pp20) cc_final: 0.7063 (pt0)
REVERT: G  277 LYS cc_start: 0.8069 (mttt) cc_final: 0.7691 (mmmm)
REVERT: G  321 LYS cc_start: 0.7987 (ttpt) cc_final: 0.7578 (mmmt)
REVERT: G  322 ARG cc_start: 0.7604 (ttp80) cc_final: 0.7323 (mtp-110)
REVERT: G  461 GLU cc_start: 0.7787 (pm20) cc_final: 0.7513 (pm20)
REVERT: M  321 LYS cc_start: 0.7806 (ttpt) cc_final: 0.7543 (mmtp)
REVERT: M  351 GLN cc_start: 0.8396 (tp40) cc_final: 0.8151 (tp40)
REVERT: M  397 GLU cc_start: 0.7699 (tp30) cc_final: 0.7368 (tt0)
REVERT: M  433 ASN cc_start: 0.6184 (p0) cc_final: 0.5716 (p0)
REVERT: M  491 MET cc_start: 0.7226 (ptm) cc_final: 0.7009 (ptm)
  outliers start: 33
  outliers final: 21
  residues processed: 763
  average time/residue: 0.5011
  time to fit residues: 649.6205
Evaluate side-chains
  515 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 492
  time to evaluate  : 4.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  523 ASP
Chi-restraints excluded: chain N residue   11 ASP
Chi-restraints excluded: chain N residue  240 VAL
Chi-restraints excluded: chain B residue  523 ASP
Chi-restraints excluded: chain H residue   11 ASP
Chi-restraints excluded: chain H residue  240 VAL
Chi-restraints excluded: chain H residue  442 VAL
Chi-restraints excluded: chain C residue  517 THR
Chi-restraints excluded: chain C residue  523 ASP
Chi-restraints excluded: chain I residue   11 ASP
Chi-restraints excluded: chain I residue  240 VAL
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  261 THR
Chi-restraints excluded: chain D residue  523 ASP
Chi-restraints excluded: chain E residue  240 VAL
Chi-restraints excluded: chain K residue  240 VAL
Chi-restraints excluded: chain F residue  261 THR
Chi-restraints excluded: chain F residue  517 THR
Chi-restraints excluded: chain F residue  523 ASP
Chi-restraints excluded: chain G residue  447 MET
Chi-restraints excluded: chain G residue  523 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 728
   random chunks:
   chunk 614 optimal weight:    0.3980
   chunk 551 optimal weight:   20.0000
   chunk 306 optimal weight:    1.9990
   chunk 188 optimal weight:    2.9990
   chunk 372 optimal weight:    9.9990
   chunk 294 optimal weight:    9.9990
   chunk 570 optimal weight:    1.9990
   chunk 220 optimal weight:    3.9990
   chunk 346 optimal weight:    5.9990
   chunk 424 optimal weight:    1.9990
   chunk 661 optimal weight:    9.9990
   overall best weight:    1.8788

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
A 348 GLN
C 112 ASN
C 146 GLN
D 112 ASN
D 184 GLN
E 112 ASN
E 184 GLN
F 112 ASN
F 348 GLN
G 112 ASN
G 348 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.153095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.114207 restraints weight = 68602.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 1.74
r_work: 0.3211 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.1240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  54362  Z= 0.213
  Angle     :  0.527  11.519  73402  Z= 0.280
  Chirality :  0.042   0.201   8932
  Planarity :  0.003   0.054   9618
  Dihedral  :  3.998  28.800   7762
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 11.26 %
    Favored  : 86.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.10), residues: 7308
  helix:  2.28 (0.08), residues: 4088
  sheet:  0.29 (0.16), residues: 980
  loop : -0.52 (0.12), residues: 2240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.000   0.000   HIS H 401 
 PHE   0.009   0.001   PHE H  44 
 TYR   0.009   0.001   TYR B 478 
 ARG   0.008   0.000   ARG N 345 

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

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

  14616 Ramachandran restraints generated.
    7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  14616 Ramachandran restraints generated.
    7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  647 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 112
    poor density    : 535
  time to evaluate  : 4.918 
Fit side-chains
REVERT: A  267 MET cc_start: 0.5923 (mmm) cc_final: 0.4969 (mmm)
REVERT: A  307 MET cc_start: 0.8607 (mtm) cc_final: 0.8059 (ptp)
REVERT: N   69 MET cc_start: 0.7608 (mtm) cc_final: 0.7355 (mtp)
REVERT: N  111 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8421 (mtt)
REVERT: N  267 MET cc_start: 0.6565 (tmm) cc_final: 0.5757 (mmp)
REVERT: N  442 VAL cc_start: 0.9047 (OUTLIER) cc_final: 0.8798 (t)
REVERT: N  447 MET cc_start: 0.9081 (mtm) cc_final: 0.8844 (mtp)
REVERT: B  160 LYS cc_start: 0.8511 (mtpp) cc_final: 0.8291 (ttmm)
REVERT: B  193 MET cc_start: 0.8213 (tpt) cc_final: 0.8010 (tpt)
REVERT: B  233 MET cc_start: 0.5975 (pmm) cc_final: 0.5506 (ptt)
REVERT: B  267 MET cc_start: 0.6371 (tmm) cc_final: 0.4962 (mmm)
REVERT: B  367 GLU cc_start: 0.8453 (pp20) cc_final: 0.8160 (pp20)
REVERT: H  262 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6631 (tt)
REVERT: H  267 MET cc_start: 0.6273 (tmm) cc_final: 0.5284 (mmp)
REVERT: C   61 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7930 (pt0)
REVERT: C  267 MET cc_start: 0.6475 (tmm) cc_final: 0.5628 (mmp)
REVERT: C  288 MET cc_start: 0.7170 (ptp) cc_final: 0.6548 (mtp)
REVERT: C  321 LYS cc_start: 0.8757 (ttpt) cc_final: 0.8477 (mmtp)
REVERT: I  204 PHE cc_start: 0.8414 (m-80) cc_final: 0.8000 (m-80)
REVERT: I  233 MET cc_start: 0.5877 (pmm) cc_final: 0.5416 (ptt)
REVERT: I  267 MET cc_start: 0.7008 (tmm) cc_final: 0.5971 (mmp)
REVERT: D  193 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.8096 (tpt)
REVERT: D  242 LYS cc_start: 0.8095 (mmtt) cc_final: 0.7894 (mmtt)
REVERT: D  321 LYS cc_start: 0.8704 (ttpt) cc_final: 0.8447 (mmmt)
REVERT: J  204 PHE cc_start: 0.8325 (m-80) cc_final: 0.7762 (m-80)
REVERT: J  267 MET cc_start: 0.6267 (tmm) cc_final: 0.5007 (mmm)
REVERT: J  389 MET cc_start: 0.7990 (tmt) cc_final: 0.7673 (tmm)
REVERT: J  442 VAL cc_start: 0.9035 (OUTLIER) cc_final: 0.8787 (t)
REVERT: E  204 PHE cc_start: 0.8407 (m-80) cc_final: 0.8205 (m-80)
REVERT: E  233 MET cc_start: 0.6513 (ppp) cc_final: 0.6094 (ptt)
REVERT: E  252 GLU cc_start: 0.7412 (tt0) cc_final: 0.7193 (tt0)
REVERT: E  321 LYS cc_start: 0.8627 (ttpt) cc_final: 0.8417 (mmpt)
REVERT: K  267 MET cc_start: 0.6893 (tmm) cc_final: 0.5409 (mmp)
REVERT: F  160 LYS cc_start: 0.8603 (mtpp) cc_final: 0.8275 (ttmm)
REVERT: F  233 MET cc_start: 0.6258 (pmm) cc_final: 0.5959 (ptt)
REVERT: F  267 MET cc_start: 0.5952 (mmm) cc_final: 0.5145 (tmm)
REVERT: F  389 MET cc_start: 0.7738 (tmt) cc_final: 0.7348 (tmm)
REVERT: L   61 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8216 (tt0)
REVERT: L   69 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7966 (mtp)
REVERT: L  262 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6879 (tp)
REVERT: L  267 MET cc_start: 0.6596 (tmm) cc_final: 0.5206 (mmm)
REVERT: L  351 GLN cc_start: 0.8095 (tp40) cc_final: 0.7878 (tp40)
REVERT: G   61 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7773 (pt0)
REVERT: G  160 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8482 (ptmm)
REVERT: G  267 MET cc_start: 0.6093 (tmm) cc_final: 0.5177 (mmm)
REVERT: M   13 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7731 (mpt-90)
REVERT: M  267 MET cc_start: 0.6764 (tmm) cc_final: 0.5513 (mmm)
REVERT: M  351 GLN cc_start: 0.8118 (tp40) cc_final: 0.7915 (tp40)
  outliers start: 112
  outliers final: 57
  residues processed: 611
  average time/residue: 0.4939
  time to fit residues: 521.6042
Evaluate side-chains
  518 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 450
  time to evaluate  : 4.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  348 GLN
Chi-restraints excluded: chain A residue  351 GLN
Chi-restraints excluded: chain A residue  447 MET
Chi-restraints excluded: chain A residue  463 SER
Chi-restraints excluded: chain N residue   50 THR
Chi-restraints excluded: chain N residue  111 MET
Chi-restraints excluded: chain N residue  114 MET
Chi-restraints excluded: chain N residue  240 VAL
Chi-restraints excluded: chain N residue  442 VAL
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  261 THR
Chi-restraints excluded: chain H residue   61 GLU
Chi-restraints excluded: chain H residue  234 LEU
Chi-restraints excluded: chain H residue  240 VAL
Chi-restraints excluded: chain H residue  262 LEU
Chi-restraints excluded: chain H residue  442 VAL
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  300 VAL
Chi-restraints excluded: chain C residue  307 MET
Chi-restraints excluded: chain C residue  351 GLN
Chi-restraints excluded: chain I residue   61 GLU
Chi-restraints excluded: chain I residue  146 GLN
Chi-restraints excluded: chain I residue  228 SER
Chi-restraints excluded: chain I residue  234 LEU
Chi-restraints excluded: chain I residue  240 VAL
Chi-restraints excluded: chain I residue  514 MET
Chi-restraints excluded: chain D residue   48 THR
Chi-restraints excluded: chain D residue   50 THR
Chi-restraints excluded: chain D residue  193 MET
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  261 THR
Chi-restraints excluded: chain J residue  442 VAL
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue  213 VAL
Chi-restraints excluded: chain E residue  240 VAL
Chi-restraints excluded: chain K residue   62 LEU
Chi-restraints excluded: chain K residue  240 VAL
Chi-restraints excluded: chain K residue  273 VAL
Chi-restraints excluded: chain K residue  288 MET
Chi-restraints excluded: chain K residue  463 SER
Chi-restraints excluded: chain F residue   48 THR
Chi-restraints excluded: chain F residue   50 THR
Chi-restraints excluded: chain F residue  193 MET
Chi-restraints excluded: chain F residue  213 VAL
Chi-restraints excluded: chain F residue  261 THR
Chi-restraints excluded: chain F residue  348 GLN
Chi-restraints excluded: chain F residue  447 MET
Chi-restraints excluded: chain F residue  463 SER
Chi-restraints excluded: chain F residue  524 LEU
Chi-restraints excluded: chain L residue   50 THR
Chi-restraints excluded: chain L residue   69 MET
Chi-restraints excluded: chain L residue  146 GLN
Chi-restraints excluded: chain L residue  262 LEU
Chi-restraints excluded: chain G residue   48 THR
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue  160 LYS
Chi-restraints excluded: chain G residue  234 LEU
Chi-restraints excluded: chain G residue  300 VAL
Chi-restraints excluded: chain G residue  348 GLN
Chi-restraints excluded: chain M residue   13 ARG
Chi-restraints excluded: chain M residue   61 GLU
Chi-restraints excluded: chain M residue  259 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 728
   random chunks:
   chunk 558 optimal weight:    4.9990
   chunk 258 optimal weight:    0.8980
   chunk 337 optimal weight:   20.0000
   chunk 97 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 622 optimal weight:    4.9990
   chunk 153 optimal weight:    7.9990
   chunk 703 optimal weight:    0.8980
   chunk 33 optimal weight:   20.0000
   chunk 446 optimal weight:    2.9990
   chunk 453 optimal weight:   10.0000
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
B 351 GLN
H  37 ASN
C 467 ASN
G 351 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.152356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.114403 restraints weight = 68963.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 1.76
r_work: 0.3204 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3061 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.1606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  54362  Z= 0.206
  Angle     :  0.491   9.036  73402  Z= 0.262
  Chirality :  0.042   0.152   8932
  Planarity :  0.003   0.034   9618
  Dihedral  :  3.901  27.209   7737
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 12.61 %
    Favored  : 85.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.10), residues: 7308
  helix:  2.26 (0.08), residues: 4088
  sheet:  0.38 (0.16), residues: 980
  loop : -0.50 (0.12), residues: 2240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS H 401 
 PHE   0.009   0.001   PHE M 219 
 TYR   0.009   0.001   TYR K 476 
 ARG   0.005   0.000   ARG L 345 

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

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

  14616 Ramachandran restraints generated.
    7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  14616 Ramachandran restraints generated.
    7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  637 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 130
    poor density    : 507
  time to evaluate  : 4.898 
Fit side-chains
   revert: symmetry clash
REVERT: A  267 MET cc_start: 0.5948 (mmm) cc_final: 0.5032 (mmm)
REVERT: A  307 MET cc_start: 0.8645 (mtm) cc_final: 0.8150 (ptp)
REVERT: A  367 GLU cc_start: 0.8548 (pp20) cc_final: 0.8239 (pp20)
REVERT: A  514 MET cc_start: 0.9098 (mtm) cc_final: 0.8708 (mtp)
REVERT: N   16 MET cc_start: 0.8542 (mmm) cc_final: 0.8156 (mtt)
REVERT: N  111 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8422 (mtt)
REVERT: N  267 MET cc_start: 0.6480 (tmm) cc_final: 0.5794 (mmp)
REVERT: N  442 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8759 (t)
REVERT: B  160 LYS cc_start: 0.8512 (mtpp) cc_final: 0.8257 (ttmm)
REVERT: B  193 MET cc_start: 0.8196 (tpt) cc_final: 0.7945 (ttm)
REVERT: B  233 MET cc_start: 0.6227 (pmm) cc_final: 0.6005 (ptt)
REVERT: B  267 MET cc_start: 0.6194 (tmm) cc_final: 0.5567 (mmp)
REVERT: B  319 GLN cc_start: 0.7975 (mt0) cc_final: 0.7722 (mt0)
REVERT: B  367 GLU cc_start: 0.8472 (pp20) cc_final: 0.8162 (pp20)
REVERT: B  494 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8701 (pp)
REVERT: H  262 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6621 (tt)
REVERT: H  267 MET cc_start: 0.6718 (tmm) cc_final: 0.5146 (mmm)
REVERT: C   61 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7995 (pt0)
REVERT: C  267 MET cc_start: 0.6577 (tmm) cc_final: 0.5682 (mmp)
REVERT: C  288 MET cc_start: 0.7112 (ptp) cc_final: 0.6508 (mtp)
REVERT: C  367 GLU cc_start: 0.8568 (pp20) cc_final: 0.8230 (pp20)
REVERT: C  494 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8772 (pp)
REVERT: I  193 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8203 (ttm)
REVERT: I  204 PHE cc_start: 0.8437 (m-80) cc_final: 0.8038 (m-80)
REVERT: I  267 MET cc_start: 0.6685 (tmm) cc_final: 0.5870 (mmp)
REVERT: I  351 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8121 (pp30)
REVERT: D  242 LYS cc_start: 0.8096 (mmtt) cc_final: 0.7827 (mmmt)
REVERT: D  267 MET cc_start: 0.5543 (tmm) cc_final: 0.5206 (mmp)
REVERT: D  321 LYS cc_start: 0.8786 (ttpt) cc_final: 0.8528 (mmmt)
REVERT: D  367 GLU cc_start: 0.8580 (pp20) cc_final: 0.8327 (pp20)
REVERT: J  204 PHE cc_start: 0.8366 (m-80) cc_final: 0.7922 (m-80)
REVERT: J  267 MET cc_start: 0.6044 (tmm) cc_final: 0.4935 (mmm)
REVERT: J  442 VAL cc_start: 0.8995 (OUTLIER) cc_final: 0.8753 (t)
REVERT: E  111 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8147 (mtt)
REVERT: E  233 MET cc_start: 0.6358 (ppp) cc_final: 0.6016 (ptt)
REVERT: E  252 GLU cc_start: 0.7387 (tt0) cc_final: 0.7108 (tt0)
REVERT: E  267 MET cc_start: 0.6061 (tmm) cc_final: 0.5397 (mmp)
REVERT: E  447 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8889 (mtp)
REVERT: E  494 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8838 (pp)
REVERT: K  267 MET cc_start: 0.6809 (tmm) cc_final: 0.5469 (mmp)
REVERT: F  102 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7320 (mp0)
REVERT: F  160 LYS cc_start: 0.8609 (mtpp) cc_final: 0.8362 (ptmm)
REVERT: F  204 PHE cc_start: 0.8418 (m-80) cc_final: 0.8101 (m-80)
REVERT: F  367 GLU cc_start: 0.8436 (pp20) cc_final: 0.8144 (pp20)
REVERT: L   61 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8297 (tt0)
REVERT: L   69 MET cc_start: 0.8435 (mtm) cc_final: 0.8050 (mtp)
REVERT: L  267 MET cc_start: 0.6435 (tmm) cc_final: 0.5242 (mmm)
REVERT: L  288 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.6757 (mpp)
REVERT: L  351 GLN cc_start: 0.8125 (tp40) cc_final: 0.7908 (tp40)
REVERT: L  389 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7493 (tmm)
REVERT: G   61 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7926 (pt0)
REVERT: G  160 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8450 (ptmm)
REVERT: G  267 MET cc_start: 0.6205 (tmm) cc_final: 0.5349 (mmm)
REVERT: G  322 ARG cc_start: 0.8732 (mtp-110) cc_final: 0.8405 (ttm110)
REVERT: G  367 GLU cc_start: 0.8529 (pp20) cc_final: 0.8238 (pp20)
REVERT: G  491 MET cc_start: 0.9036 (mtt) cc_final: 0.8800 (mtt)
REVERT: G  494 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8833 (pp)
REVERT: M  267 MET cc_start: 0.6691 (tmm) cc_final: 0.5542 (mmm)
REVERT: M  351 GLN cc_start: 0.8161 (tp40) cc_final: 0.7925 (tp40)
  outliers start: 130
  outliers final: 72
  residues processed: 601
  average time/residue: 0.4758
  time to fit residues: 500.5399
Evaluate side-chains
  552 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 89
    poor density    : 463
  time to evaluate  : 6.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  463 SER
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain N residue   50 THR
Chi-restraints excluded: chain N residue  111 MET
Chi-restraints excluded: chain N residue  234 LEU
Chi-restraints excluded: chain N residue  240 VAL
Chi-restraints excluded: chain N residue  442 VAL
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  463 SER
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain H residue   61 GLU
Chi-restraints excluded: chain H residue  240 VAL
Chi-restraints excluded: chain H residue  262 LEU
Chi-restraints excluded: chain H residue  442 VAL
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  261 THR
Chi-restraints excluded: chain C residue  271 VAL
Chi-restraints excluded: chain C residue  494 LEU
Chi-restraints excluded: chain C residue  517 THR
Chi-restraints excluded: chain I residue   61 GLU
Chi-restraints excluded: chain I residue  124 VAL
Chi-restraints excluded: chain I residue  193 MET
Chi-restraints excluded: chain I residue  201 SER
Chi-restraints excluded: chain I residue  234 LEU
Chi-restraints excluded: chain I residue  351 GLN
Chi-restraints excluded: chain I residue  442 VAL
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue   48 THR
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  259 LEU
Chi-restraints excluded: chain D residue  261 THR
Chi-restraints excluded: chain D residue  351 GLN
Chi-restraints excluded: chain D residue  447 MET
Chi-restraints excluded: chain J residue  232 GLU
Chi-restraints excluded: chain J residue  273 VAL
Chi-restraints excluded: chain J residue  388 GLU
Chi-restraints excluded: chain J residue  442 VAL
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   50 THR
Chi-restraints excluded: chain E residue  111 MET
Chi-restraints excluded: chain E residue  213 VAL
Chi-restraints excluded: chain E residue  240 VAL
Chi-restraints excluded: chain E residue  288 MET
Chi-restraints excluded: chain E residue  300 VAL
Chi-restraints excluded: chain E residue  447 MET
Chi-restraints excluded: chain E residue  494 LEU
Chi-restraints excluded: chain K residue   43 SER
Chi-restraints excluded: chain K residue   62 LEU
Chi-restraints excluded: chain K residue  240 VAL
Chi-restraints excluded: chain K residue  273 VAL
Chi-restraints excluded: chain K residue  288 MET
Chi-restraints excluded: chain K residue  442 VAL
Chi-restraints excluded: chain K residue  463 SER
Chi-restraints excluded: chain F residue   48 THR
Chi-restraints excluded: chain F residue   50 THR
Chi-restraints excluded: chain F residue  193 MET
Chi-restraints excluded: chain F residue  213 VAL
Chi-restraints excluded: chain F residue  261 THR
Chi-restraints excluded: chain F residue  351 GLN
Chi-restraints excluded: chain F residue  463 SER
Chi-restraints excluded: chain F residue  517 THR
Chi-restraints excluded: chain F residue  524 LEU
Chi-restraints excluded: chain L residue  288 MET
Chi-restraints excluded: chain L residue  389 MET
Chi-restraints excluded: chain L residue  442 VAL
Chi-restraints excluded: chain G residue   48 THR
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue  160 LYS
Chi-restraints excluded: chain G residue  169 VAL
Chi-restraints excluded: chain G residue  234 LEU
Chi-restraints excluded: chain G residue  300 VAL
Chi-restraints excluded: chain G residue  307 MET
Chi-restraints excluded: chain G residue  494 LEU
Chi-restraints excluded: chain M residue   61 GLU
Chi-restraints excluded: chain M residue  259 LEU
Chi-restraints excluded: chain M residue  463 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 728
   random chunks:
   chunk 315 optimal weight:    2.9990
   chunk 389 optimal weight:    9.9990
   chunk 510 optimal weight:    0.9980
   chunk 398 optimal weight:   10.0000
   chunk 657 optimal weight:    0.7980
   chunk 331 optimal weight:   20.0000
   chunk 514 optimal weight:    0.9980
   chunk 34 optimal weight:    6.9990
   chunk 69 optimal weight:   10.0000
   chunk 554 optimal weight:    9.9990
   chunk 156 optimal weight:    8.9990
   overall best weight:    2.5584

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
C 112 ASN
C 467 ASN
I 319 GLN
D 112 ASN
E 112 ASN
K  37 ASN
F 112 ASN
M  37 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.150754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.112011 restraints weight = 68645.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 1.76
r_work: 0.3161 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.1894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  54362  Z= 0.250
  Angle     :  0.505   7.912  73402  Z= 0.268
  Chirality :  0.042   0.167   8932
  Planarity :  0.003   0.031   9618
  Dihedral  :  3.937  27.072   7736
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 12.89 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.10), residues: 7308
  helix:  2.21 (0.08), residues: 4088
  sheet:  0.63 (0.17), residues: 938
  loop : -0.46 (0.12), residues: 2282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS C 401 
 PHE   0.011   0.001   PHE J  66 
 TYR   0.010   0.001   TYR I 478 
 ARG   0.006   0.000   ARG C 322 

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

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

  14616 Ramachandran restraints generated.
    7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  14616 Ramachandran restraints generated.
    7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  692 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 181
    poor density    : 511
  time to evaluate  : 4.878 
Fit side-chains
   revert: symmetry clash
REVERT: A  267 MET cc_start: 0.6065 (mmm) cc_final: 0.5086 (mmm)
REVERT: A  367 GLU cc_start: 0.8525 (pp20) cc_final: 0.8231 (pp20)
REVERT: N   16 MET cc_start: 0.8605 (mmm) cc_final: 0.8329 (mtt)
REVERT: N  111 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8453 (mtt)
REVERT: N  201 SER cc_start: 0.8378 (t) cc_final: 0.8081 (m)
REVERT: N  267 MET cc_start: 0.6415 (tmm) cc_final: 0.5849 (mmp)
REVERT: N  442 VAL cc_start: 0.9005 (OUTLIER) cc_final: 0.8784 (t)
REVERT: N  494 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8868 (pp)
REVERT: B  160 LYS cc_start: 0.8527 (mtpp) cc_final: 0.8195 (ptmm)
REVERT: B  233 MET cc_start: 0.6457 (pmm) cc_final: 0.6215 (ptt)
REVERT: B  267 MET cc_start: 0.6143 (tmm) cc_final: 0.5560 (mmp)
REVERT: B  319 GLN cc_start: 0.8005 (mt0) cc_final: 0.7744 (mt0)
REVERT: B  367 GLU cc_start: 0.8484 (pp20) cc_final: 0.8151 (pp20)
REVERT: B  389 MET cc_start: 0.8311 (tmm) cc_final: 0.8055 (ttp)
REVERT: B  494 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8703 (pp)
REVERT: H  267 MET cc_start: 0.6670 (tmm) cc_final: 0.5377 (mmm)
REVERT: H  514 MET cc_start: 0.9065 (mtp) cc_final: 0.8789 (mtm)
REVERT: C   61 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8118 (pt0)
REVERT: C   69 MET cc_start: 0.8489 (mtp) cc_final: 0.8195 (ttm)
REVERT: C  102 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7408 (mp0)
REVERT: C  267 MET cc_start: 0.6556 (tmm) cc_final: 0.5788 (mmp)
REVERT: C  288 MET cc_start: 0.7050 (ptp) cc_final: 0.6631 (mtp)
REVERT: C  367 GLU cc_start: 0.8512 (pp20) cc_final: 0.8163 (pp20)
REVERT: C  514 MET cc_start: 0.9070 (mtp) cc_final: 0.8780 (mtm)
REVERT: I  193 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8201 (ttm)
REVERT: I  204 PHE cc_start: 0.8433 (m-80) cc_final: 0.8059 (m-80)
REVERT: I  267 MET cc_start: 0.6634 (tmm) cc_final: 0.5947 (mmp)
REVERT: I  351 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8152 (pp30)
REVERT: I  494 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8864 (pp)
REVERT: D  242 LYS cc_start: 0.8081 (mmtt) cc_final: 0.7814 (mmmt)
REVERT: D  267 MET cc_start: 0.6347 (tmm) cc_final: 0.5553 (mmm)
REVERT: D  321 LYS cc_start: 0.8807 (ttpt) cc_final: 0.8519 (mmmt)
REVERT: D  367 GLU cc_start: 0.8670 (pp20) cc_final: 0.8389 (pp20)
REVERT: J   16 MET cc_start: 0.8691 (mtp) cc_final: 0.8396 (mtm)
REVERT: J  204 PHE cc_start: 0.8334 (m-80) cc_final: 0.7972 (m-80)
REVERT: J  267 MET cc_start: 0.6017 (tmm) cc_final: 0.5028 (mmm)
REVERT: J  442 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8762 (t)
REVERT: J  494 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8819 (pp)
REVERT: E  111 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8210 (mtt)
REVERT: E  267 MET cc_start: 0.6482 (tmm) cc_final: 0.5757 (mmp)
REVERT: E  367 GLU cc_start: 0.8613 (pp20) cc_final: 0.8329 (pp20)
REVERT: E  447 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8885 (mtp)
REVERT: E  494 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8847 (pp)
REVERT: E  514 MET cc_start: 0.9207 (ttm) cc_final: 0.8813 (mtp)
REVERT: K  267 MET cc_start: 0.6682 (tmm) cc_final: 0.5391 (mmp)
REVERT: F  160 LYS cc_start: 0.8651 (mtpp) cc_final: 0.8364 (ptmm)
REVERT: F  367 GLU cc_start: 0.8418 (pp20) cc_final: 0.8098 (pp20)
REVERT: L   61 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8232 (tm-30)
REVERT: L   69 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8117 (mtp)
REVERT: L  262 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.6953 (tp)
REVERT: L  267 MET cc_start: 0.6339 (tmm) cc_final: 0.5332 (mmm)
REVERT: L  288 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.6783 (mpp)
REVERT: L  351 GLN cc_start: 0.8182 (tp40) cc_final: 0.7951 (tp40)
REVERT: G   61 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8020 (pt0)
REVERT: G  160 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8499 (ptmm)
REVERT: G  166 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8007 (mtt)
REVERT: G  267 MET cc_start: 0.6203 (tmm) cc_final: 0.5319 (mmp)
REVERT: G  367 GLU cc_start: 0.8608 (pp20) cc_final: 0.8274 (pp20)
REVERT: G  494 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8866 (pp)
REVERT: M   13 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7949 (mpt-90)
REVERT: M  267 MET cc_start: 0.6677 (tmm) cc_final: 0.5780 (mmt)
  outliers start: 181
  outliers final: 109
  residues processed: 647
  average time/residue: 0.4766
  time to fit residues: 542.2480
Evaluate side-chains
  591 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 130
    poor density    : 461
  time to evaluate  : 5.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  331 THR
Chi-restraints excluded: chain A residue  463 SER
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain N residue   50 THR
Chi-restraints excluded: chain N residue  111 MET
Chi-restraints excluded: chain N residue  114 MET
Chi-restraints excluded: chain N residue  200 LEU
Chi-restraints excluded: chain N residue  213 VAL
Chi-restraints excluded: chain N residue  234 LEU
Chi-restraints excluded: chain N residue  240 VAL
Chi-restraints excluded: chain N residue  442 VAL
Chi-restraints excluded: chain N residue  494 LEU
Chi-restraints excluded: chain N residue  517 THR
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  307 MET
Chi-restraints excluded: chain B residue  463 SER
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  517 THR
Chi-restraints excluded: chain H residue   61 GLU
Chi-restraints excluded: chain H residue  146 GLN
Chi-restraints excluded: chain H residue  187 LEU
Chi-restraints excluded: chain H residue  213 VAL
Chi-restraints excluded: chain H residue  228 SER
Chi-restraints excluded: chain H residue  240 VAL
Chi-restraints excluded: chain H residue  273 VAL
Chi-restraints excluded: chain H residue  442 VAL
Chi-restraints excluded: chain H residue  517 THR
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  187 LEU
Chi-restraints excluded: chain C residue  205 ILE
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  228 SER
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  261 THR
Chi-restraints excluded: chain C residue  300 VAL
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  517 THR
Chi-restraints excluded: chain I residue   61 GLU
Chi-restraints excluded: chain I residue  124 VAL
Chi-restraints excluded: chain I residue  193 MET
Chi-restraints excluded: chain I residue  201 SER
Chi-restraints excluded: chain I residue  213 VAL
Chi-restraints excluded: chain I residue  234 LEU
Chi-restraints excluded: chain I residue  240 VAL
Chi-restraints excluded: chain I residue  351 GLN
Chi-restraints excluded: chain I residue  442 VAL
Chi-restraints excluded: chain I residue  494 LEU
Chi-restraints excluded: chain D residue   48 THR
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  205 ILE
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  259 LEU
Chi-restraints excluded: chain D residue  261 THR
Chi-restraints excluded: chain D residue  351 GLN
Chi-restraints excluded: chain D residue  517 THR
Chi-restraints excluded: chain J residue  146 GLN
Chi-restraints excluded: chain J residue  232 GLU
Chi-restraints excluded: chain J residue  273 VAL
Chi-restraints excluded: chain J residue  388 GLU
Chi-restraints excluded: chain J residue  433 ASN
Chi-restraints excluded: chain J residue  442 VAL
Chi-restraints excluded: chain J residue  494 LEU
Chi-restraints excluded: chain E residue   11 ASP
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   50 THR
Chi-restraints excluded: chain E residue  111 MET
Chi-restraints excluded: chain E residue  177 VAL
Chi-restraints excluded: chain E residue  205 ILE
Chi-restraints excluded: chain E residue  213 VAL
Chi-restraints excluded: chain E residue  288 MET
Chi-restraints excluded: chain E residue  300 VAL
Chi-restraints excluded: chain E residue  447 MET
Chi-restraints excluded: chain E residue  494 LEU
Chi-restraints excluded: chain K residue   43 SER
Chi-restraints excluded: chain K residue   62 LEU
Chi-restraints excluded: chain K residue  146 GLN
Chi-restraints excluded: chain K residue  213 VAL
Chi-restraints excluded: chain K residue  240 VAL
Chi-restraints excluded: chain K residue  273 VAL
Chi-restraints excluded: chain K residue  288 MET
Chi-restraints excluded: chain K residue  307 MET
Chi-restraints excluded: chain K residue  463 SER
Chi-restraints excluded: chain K residue  517 THR
Chi-restraints excluded: chain F residue   48 THR
Chi-restraints excluded: chain F residue   50 THR
Chi-restraints excluded: chain F residue  124 VAL
Chi-restraints excluded: chain F residue  169 VAL
Chi-restraints excluded: chain F residue  193 MET
Chi-restraints excluded: chain F residue  205 ILE
Chi-restraints excluded: chain F residue  213 VAL
Chi-restraints excluded: chain F residue  255 GLU
Chi-restraints excluded: chain F residue  351 GLN
Chi-restraints excluded: chain F residue  463 SER
Chi-restraints excluded: chain F residue  517 THR
Chi-restraints excluded: chain F residue  524 LEU
Chi-restraints excluded: chain L residue   50 THR
Chi-restraints excluded: chain L residue   69 MET
Chi-restraints excluded: chain L residue  124 VAL
Chi-restraints excluded: chain L residue  213 VAL
Chi-restraints excluded: chain L residue  262 LEU
Chi-restraints excluded: chain L residue  288 MET
Chi-restraints excluded: chain L residue  517 THR
Chi-restraints excluded: chain G residue   11 ASP
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue  160 LYS
Chi-restraints excluded: chain G residue  166 MET
Chi-restraints excluded: chain G residue  234 LEU
Chi-restraints excluded: chain G residue  300 VAL
Chi-restraints excluded: chain G residue  307 MET
Chi-restraints excluded: chain G residue  494 LEU
Chi-restraints excluded: chain M residue   13 ARG
Chi-restraints excluded: chain M residue   61 GLU
Chi-restraints excluded: chain M residue  442 VAL
Chi-restraints excluded: chain M residue  463 SER
Chi-restraints excluded: chain M residue  489 ILE
Chi-restraints excluded: chain M residue  517 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 728
   random chunks:
   chunk 164 optimal weight:   10.0000
   chunk 62 optimal weight:    1.9990
   chunk 470 optimal weight:    0.7980
   chunk 455 optimal weight:    2.9990
   chunk 353 optimal weight:    4.9990
   chunk 334 optimal weight:    9.9990
   chunk 578 optimal weight:    6.9990
   chunk 673 optimal weight:    5.9990
   chunk 565 optimal weight:    1.9990
   chunk 558 optimal weight:    8.9990
   chunk 644 optimal weight:    1.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
C 319 GLN
E 348 GLN
L 319 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.150147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.108103 restraints weight = 68456.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 1.74
r_work: 0.3142 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2989 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.2028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  54362  Z= 0.202
  Angle     :  0.485  12.007  73402  Z= 0.256
  Chirality :  0.041   0.165   8932
  Planarity :  0.003   0.030   9618
  Dihedral  :  3.865  26.099   7733
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 14.14 %
    Favored  : 83.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.10), residues: 7308
  helix:  2.25 (0.08), residues: 4088
  sheet:  0.63 (0.17), residues: 938
  loop : -0.43 (0.12), residues: 2282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.000   0.000   HIS N 401 
 PHE   0.011   0.001   PHE G 204 
 TYR   0.010   0.001   TYR K 476 
 ARG   0.004   0.000   ARG L 345 

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

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

  14616 Ramachandran restraints generated.
    7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  14616 Ramachandran restraints generated.
    7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  655 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 152
    poor density    : 503
  time to evaluate  : 4.912 
Fit side-chains
   revert: symmetry clash
REVERT: A  267 MET cc_start: 0.6120 (mmm) cc_final: 0.5147 (mmm)
REVERT: A  367 GLU cc_start: 0.8419 (pp20) cc_final: 0.8122 (pp20)
REVERT: A  514 MET cc_start: 0.9247 (mtm) cc_final: 0.8909 (mtp)
REVERT: N   16 MET cc_start: 0.8627 (mmm) cc_final: 0.8334 (mtt)
REVERT: N   69 MET cc_start: 0.7984 (mtm) cc_final: 0.7608 (mtp)
REVERT: N  111 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8461 (mtt)
REVERT: N  201 SER cc_start: 0.8365 (t) cc_final: 0.8070 (m)
REVERT: N  267 MET cc_start: 0.6330 (tmm) cc_final: 0.5930 (mmp)
REVERT: N  442 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8784 (t)
REVERT: N  494 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8855 (pp)
REVERT: B  160 LYS cc_start: 0.8558 (mtpp) cc_final: 0.8229 (ptmm)
REVERT: B  204 PHE cc_start: 0.8472 (m-80) cc_final: 0.8148 (m-80)
REVERT: B  267 MET cc_start: 0.6083 (tmm) cc_final: 0.5540 (mmp)
REVERT: B  367 GLU cc_start: 0.8465 (pp20) cc_final: 0.8124 (pp20)
REVERT: B  389 MET cc_start: 0.8255 (tmm) cc_final: 0.8042 (ttp)
REVERT: B  494 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8668 (pp)
REVERT: H  267 MET cc_start: 0.6340 (tmm) cc_final: 0.5311 (mmm)
REVERT: H  514 MET cc_start: 0.9087 (mtp) cc_final: 0.8836 (mtp)
REVERT: C   61 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8131 (pt0)
REVERT: C  267 MET cc_start: 0.6492 (tmm) cc_final: 0.5791 (mmp)
REVERT: C  288 MET cc_start: 0.7001 (ptp) cc_final: 0.6661 (mtp)
REVERT: C  322 ARG cc_start: 0.8926 (mtp-110) cc_final: 0.8690 (ttm110)
REVERT: C  367 GLU cc_start: 0.8487 (pp20) cc_final: 0.8109 (pp20)
REVERT: C  488 MET cc_start: 0.9039 (tpt) cc_final: 0.8651 (mmt)
REVERT: C  514 MET cc_start: 0.9104 (mtp) cc_final: 0.8881 (mtm)
REVERT: I  193 MET cc_start: 0.8463 (tpt) cc_final: 0.8230 (ttm)
REVERT: I  204 PHE cc_start: 0.8451 (m-80) cc_final: 0.8150 (m-80)
REVERT: I  267 MET cc_start: 0.6678 (tmm) cc_final: 0.5812 (mmp)
REVERT: I  351 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8146 (pp30)
REVERT: I  494 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8830 (pp)
REVERT: D  242 LYS cc_start: 0.8039 (mmtt) cc_final: 0.7777 (mmmt)
REVERT: D  267 MET cc_start: 0.6286 (tmm) cc_final: 0.5507 (mmm)
REVERT: D  321 LYS cc_start: 0.8821 (ttpt) cc_final: 0.8516 (mmmt)
REVERT: D  367 GLU cc_start: 0.8674 (pp20) cc_final: 0.8369 (pp20)
REVERT: J   16 MET cc_start: 0.8800 (mtp) cc_final: 0.8536 (mtm)
REVERT: J  204 PHE cc_start: 0.8325 (m-80) cc_final: 0.7978 (m-80)
REVERT: J  267 MET cc_start: 0.5962 (tmm) cc_final: 0.5042 (mmm)
REVERT: J  442 VAL cc_start: 0.8943 (OUTLIER) cc_final: 0.8725 (t)
REVERT: J  494 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8817 (pp)
REVERT: E  102 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7401 (mp0)
REVERT: E  111 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8310 (mtt)
REVERT: E  267 MET cc_start: 0.6500 (tmm) cc_final: 0.5822 (mmp)
REVERT: E  367 GLU cc_start: 0.8540 (pp20) cc_final: 0.8241 (pp20)
REVERT: E  447 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8912 (mtp)
REVERT: E  494 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8821 (pp)
REVERT: E  514 MET cc_start: 0.9132 (ttm) cc_final: 0.8919 (mtp)
REVERT: K  267 MET cc_start: 0.6683 (tmm) cc_final: 0.5483 (mmp)
REVERT: K  514 MET cc_start: 0.9241 (ttm) cc_final: 0.8859 (mtp)
REVERT: F  102 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7354 (mp0)
REVERT: F  160 LYS cc_start: 0.8655 (mtpp) cc_final: 0.8387 (ptmm)
REVERT: F  321 LYS cc_start: 0.8803 (mmtt) cc_final: 0.8402 (mmtp)
REVERT: F  367 GLU cc_start: 0.8382 (pp20) cc_final: 0.8097 (pp20)
REVERT: L   61 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8256 (tm-30)
REVERT: L   69 MET cc_start: 0.8483 (mtm) cc_final: 0.8057 (mtp)
REVERT: L  262 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7018 (tp)
REVERT: L  267 MET cc_start: 0.6174 (tmm) cc_final: 0.5243 (mmm)
REVERT: L  288 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.6810 (mpp)
REVERT: L  351 GLN cc_start: 0.8179 (tp40) cc_final: 0.7942 (tp40)
REVERT: L  461 GLU cc_start: 0.7906 (pm20) cc_final: 0.7528 (pm20)
REVERT: G   61 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8053 (pt0)
REVERT: G  160 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8464 (ptmm)
REVERT: G  204 PHE cc_start: 0.8487 (m-80) cc_final: 0.8218 (m-80)
REVERT: G  267 MET cc_start: 0.6258 (tmm) cc_final: 0.5412 (mmp)
REVERT: G  367 GLU cc_start: 0.8508 (pp20) cc_final: 0.8148 (pp20)
REVERT: G  494 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8889 (pp)
REVERT: M   13 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7979 (mpt-90)
REVERT: M  267 MET cc_start: 0.6541 (tmm) cc_final: 0.5749 (mmm)
  outliers start: 152
  outliers final: 108
  residues processed: 622
  average time/residue: 0.5013
  time to fit residues: 551.3913
Evaluate side-chains
  590 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 127
    poor density    : 463
  time to evaluate  : 4.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  463 SER
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain N residue   11 ASP
Chi-restraints excluded: chain N residue   50 THR
Chi-restraints excluded: chain N residue  111 MET
Chi-restraints excluded: chain N residue  442 VAL
Chi-restraints excluded: chain N residue  494 LEU
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  307 MET
Chi-restraints excluded: chain B residue  331 THR
Chi-restraints excluded: chain B residue  463 SER
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  517 THR
Chi-restraints excluded: chain H residue   61 GLU
Chi-restraints excluded: chain H residue  146 GLN
Chi-restraints excluded: chain H residue  213 VAL
Chi-restraints excluded: chain H residue  228 SER
Chi-restraints excluded: chain H residue  273 VAL
Chi-restraints excluded: chain H residue  442 VAL
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  228 SER
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  261 THR
Chi-restraints excluded: chain C residue  271 VAL
Chi-restraints excluded: chain C residue  300 VAL
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  331 THR
Chi-restraints excluded: chain C residue  517 THR
Chi-restraints excluded: chain I residue   61 GLU
Chi-restraints excluded: chain I residue  124 VAL
Chi-restraints excluded: chain I residue  201 SER
Chi-restraints excluded: chain I residue  213 VAL
Chi-restraints excluded: chain I residue  234 LEU
Chi-restraints excluded: chain I residue  240 VAL
Chi-restraints excluded: chain I residue  351 GLN
Chi-restraints excluded: chain I residue  442 VAL
Chi-restraints excluded: chain I residue  494 LEU
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue   48 THR
Chi-restraints excluded: chain D residue  124 VAL
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  259 LEU
Chi-restraints excluded: chain D residue  261 THR
Chi-restraints excluded: chain D residue  331 THR
Chi-restraints excluded: chain D residue  351 GLN
Chi-restraints excluded: chain D residue  517 THR
Chi-restraints excluded: chain J residue  213 VAL
Chi-restraints excluded: chain J residue  232 GLU
Chi-restraints excluded: chain J residue  273 VAL
Chi-restraints excluded: chain J residue  388 GLU
Chi-restraints excluded: chain J residue  433 ASN
Chi-restraints excluded: chain J residue  442 VAL
Chi-restraints excluded: chain J residue  494 LEU
Chi-restraints excluded: chain J residue  517 THR
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   50 THR
Chi-restraints excluded: chain E residue  111 MET
Chi-restraints excluded: chain E residue  213 VAL
Chi-restraints excluded: chain E residue  240 VAL
Chi-restraints excluded: chain E residue  288 MET
Chi-restraints excluded: chain E residue  300 VAL
Chi-restraints excluded: chain E residue  331 THR
Chi-restraints excluded: chain E residue  348 GLN
Chi-restraints excluded: chain E residue  447 MET
Chi-restraints excluded: chain E residue  494 LEU
Chi-restraints excluded: chain E residue  517 THR
Chi-restraints excluded: chain K residue   43 SER
Chi-restraints excluded: chain K residue   62 LEU
Chi-restraints excluded: chain K residue  213 VAL
Chi-restraints excluded: chain K residue  273 VAL
Chi-restraints excluded: chain K residue  288 MET
Chi-restraints excluded: chain K residue  307 MET
Chi-restraints excluded: chain K residue  463 SER
Chi-restraints excluded: chain F residue   48 THR
Chi-restraints excluded: chain F residue   50 THR
Chi-restraints excluded: chain F residue  102 GLU
Chi-restraints excluded: chain F residue  169 VAL
Chi-restraints excluded: chain F residue  193 MET
Chi-restraints excluded: chain F residue  213 VAL
Chi-restraints excluded: chain F residue  255 GLU
Chi-restraints excluded: chain F residue  331 THR
Chi-restraints excluded: chain F residue  351 GLN
Chi-restraints excluded: chain F residue  369 VAL
Chi-restraints excluded: chain F residue  463 SER
Chi-restraints excluded: chain F residue  517 THR
Chi-restraints excluded: chain F residue  524 LEU
Chi-restraints excluded: chain L residue   50 THR
Chi-restraints excluded: chain L residue  146 GLN
Chi-restraints excluded: chain L residue  213 VAL
Chi-restraints excluded: chain L residue  262 LEU
Chi-restraints excluded: chain L residue  288 MET
Chi-restraints excluded: chain L residue  517 THR
Chi-restraints excluded: chain G residue   11 ASP
Chi-restraints excluded: chain G residue   48 THR
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue  160 LYS
Chi-restraints excluded: chain G residue  169 VAL
Chi-restraints excluded: chain G residue  300 VAL
Chi-restraints excluded: chain G residue  307 MET
Chi-restraints excluded: chain G residue  494 LEU
Chi-restraints excluded: chain G residue  517 THR
Chi-restraints excluded: chain M residue   13 ARG
Chi-restraints excluded: chain M residue   61 GLU
Chi-restraints excluded: chain M residue  124 VAL
Chi-restraints excluded: chain M residue  146 GLN
Chi-restraints excluded: chain M residue  187 LEU
Chi-restraints excluded: chain M residue  259 LEU
Chi-restraints excluded: chain M residue  262 LEU
Chi-restraints excluded: chain M residue  442 VAL
Chi-restraints excluded: chain M residue  463 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 728
   random chunks:
   chunk 505 optimal weight:    0.8980
   chunk 379 optimal weight:    4.9990
   chunk 549 optimal weight:    7.9990
   chunk 23 optimal weight:   10.0000
   chunk 140 optimal weight:    5.9990
   chunk 690 optimal weight:    5.9990
   chunk 199 optimal weight:    0.7980
   chunk 679 optimal weight:    4.9990
   chunk 691 optimal weight:    5.9990
   chunk 421 optimal weight:    6.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
B 348 GLN
J 351 GLN
M 351 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.148829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.106590 restraints weight = 68515.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 1.74
r_work: 0.3112 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2958 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.2169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  54362  Z= 0.259
  Angle     :  0.506  10.738  73402  Z= 0.267
  Chirality :  0.042   0.176   8932
  Planarity :  0.003   0.035   9618
  Dihedral  :  3.882  19.159   7730
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 14.48 %
    Favored  : 82.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.76 (0.10), residues: 7308
  helix:  2.19 (0.08), residues: 4088
  sheet:  0.60 (0.17), residues: 938
  loop : -0.45 (0.12), residues: 2282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS C 401 
 PHE   0.008   0.001   PHE L   8 
 TYR   0.010   0.001   TYR I 478 
 ARG   0.005   0.000   ARG E 345 

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

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

  14616 Ramachandran restraints generated.
    7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  14616 Ramachandran restraints generated.
    7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  664 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 180
    poor density    : 484
  time to evaluate  : 4.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 MET cc_start: 0.6167 (mmm) cc_final: 0.5188 (mmm)
REVERT: A  367 GLU cc_start: 0.8407 (pp20) cc_final: 0.8110 (pp20)
REVERT: N  111 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8482 (mtt)
REVERT: N  201 SER cc_start: 0.8378 (t) cc_final: 0.8081 (m)
REVERT: N  267 MET cc_start: 0.6330 (tmm) cc_final: 0.5948 (mmp)
REVERT: N  442 VAL cc_start: 0.9048 (OUTLIER) cc_final: 0.8813 (t)
REVERT: N  494 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8850 (pp)
REVERT: N  514 MET cc_start: 0.9174 (ttm) cc_final: 0.8743 (mtp)
REVERT: N  520 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8523 (mmt)
REVERT: B  160 LYS cc_start: 0.8559 (mtpp) cc_final: 0.8216 (ptmm)
REVERT: B  204 PHE cc_start: 0.8493 (m-80) cc_final: 0.8173 (m-80)
REVERT: B  267 MET cc_start: 0.6544 (tmm) cc_final: 0.5404 (mmp)
REVERT: B  367 GLU cc_start: 0.8461 (pp20) cc_final: 0.8149 (pp20)
REVERT: B  389 MET cc_start: 0.8253 (tmm) cc_final: 0.8049 (ttp)
REVERT: B  494 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8661 (pp)
REVERT: H  267 MET cc_start: 0.6409 (tmm) cc_final: 0.5349 (mmp)
REVERT: H  514 MET cc_start: 0.9120 (mtp) cc_final: 0.8850 (mtm)
REVERT: C   61 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8102 (pt0)
REVERT: C   69 MET cc_start: 0.8486 (mtp) cc_final: 0.8071 (ttm)
REVERT: C  267 MET cc_start: 0.6425 (tmm) cc_final: 0.5775 (mmp)
REVERT: C  288 MET cc_start: 0.7011 (ptp) cc_final: 0.6776 (mtp)
REVERT: C  322 ARG cc_start: 0.8929 (mtp-110) cc_final: 0.8724 (ttm110)
REVERT: C  367 GLU cc_start: 0.8471 (pp20) cc_final: 0.8080 (pp20)
REVERT: C  494 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8747 (pp)
REVERT: C  514 MET cc_start: 0.9097 (mtp) cc_final: 0.8832 (mtm)
REVERT: I  193 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8273 (ttm)
REVERT: I  204 PHE cc_start: 0.8457 (m-80) cc_final: 0.8136 (m-80)
REVERT: I  267 MET cc_start: 0.6650 (tmm) cc_final: 0.5870 (mmp)
REVERT: I  351 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8152 (pp30)
REVERT: I  494 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8809 (pp)
REVERT: I  514 MET cc_start: 0.9197 (ttm) cc_final: 0.8827 (mtp)
REVERT: D  242 LYS cc_start: 0.8040 (mmtt) cc_final: 0.7780 (mmmt)
REVERT: D  267 MET cc_start: 0.6631 (tmm) cc_final: 0.5863 (mmm)
REVERT: D  321 LYS cc_start: 0.8823 (ttpt) cc_final: 0.8499 (mmmt)
REVERT: D  367 GLU cc_start: 0.8619 (pp20) cc_final: 0.8287 (pp20)
REVERT: J   16 MET cc_start: 0.8850 (mtp) cc_final: 0.8598 (mtm)
REVERT: J  204 PHE cc_start: 0.8350 (m-80) cc_final: 0.8014 (m-80)
REVERT: J  267 MET cc_start: 0.6001 (tmm) cc_final: 0.5109 (mmm)
REVERT: J  442 VAL cc_start: 0.8978 (OUTLIER) cc_final: 0.8759 (t)
REVERT: J  494 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8852 (pp)
REVERT: E  102 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7461 (mp0)
REVERT: E  111 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8354 (mtt)
REVERT: E  267 MET cc_start: 0.6799 (tmm) cc_final: 0.5817 (mmp)
REVERT: E  367 GLU cc_start: 0.8546 (pp20) cc_final: 0.8231 (pp20)
REVERT: E  389 MET cc_start: 0.7922 (tmm) cc_final: 0.7653 (tmt)
REVERT: E  447 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8920 (mtp)
REVERT: E  494 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8839 (pp)
REVERT: E  514 MET cc_start: 0.9178 (ttm) cc_final: 0.8949 (mtp)
REVERT: K  142 LYS cc_start: 0.8604 (tppt) cc_final: 0.8338 (ttpp)
REVERT: K  267 MET cc_start: 0.6660 (tmm) cc_final: 0.5508 (mmp)
REVERT: K  514 MET cc_start: 0.9237 (ttm) cc_final: 0.8946 (mtp)
REVERT: F  102 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7390 (mp0)
REVERT: F  111 MET cc_start: 0.8995 (mtp) cc_final: 0.8667 (mtt)
REVERT: F  160 LYS cc_start: 0.8674 (mtpp) cc_final: 0.8390 (ptmm)
REVERT: F  321 LYS cc_start: 0.8814 (mmtt) cc_final: 0.8408 (mmtp)
REVERT: F  367 GLU cc_start: 0.8382 (pp20) cc_final: 0.8062 (pp20)
REVERT: L   69 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8118 (mtp)
REVERT: L  262 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6947 (tp)
REVERT: L  267 MET cc_start: 0.6194 (tmm) cc_final: 0.5319 (mmm)
REVERT: L  288 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.6720 (mpp)
REVERT: L  351 GLN cc_start: 0.8221 (tp40) cc_final: 0.7978 (tp40)
REVERT: G   61 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8091 (pt0)
REVERT: G  160 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8496 (ptmm)
REVERT: G  166 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.7990 (mtt)
REVERT: G  204 PHE cc_start: 0.8545 (m-80) cc_final: 0.8242 (m-80)
REVERT: G  267 MET cc_start: 0.6266 (tmm) cc_final: 0.5479 (mmp)
REVERT: G  367 GLU cc_start: 0.8491 (pp20) cc_final: 0.8119 (pp20)
REVERT: G  494 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8891 (pp)
REVERT: M   13 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7959 (mpt-90)
REVERT: M  267 MET cc_start: 0.6483 (tmm) cc_final: 0.5678 (mmm)
  outliers start: 180
  outliers final: 134
  residues processed: 631
  average time/residue: 0.4580
  time to fit residues: 509.8252
Evaluate side-chains
  613 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 157
    poor density    : 456
  time to evaluate  : 4.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  331 THR
Chi-restraints excluded: chain A residue  463 SER
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain N residue   11 ASP
Chi-restraints excluded: chain N residue   50 THR
Chi-restraints excluded: chain N residue  111 MET
Chi-restraints excluded: chain N residue  213 VAL
Chi-restraints excluded: chain N residue  230 ILE
Chi-restraints excluded: chain N residue  234 LEU
Chi-restraints excluded: chain N residue  442 VAL
Chi-restraints excluded: chain N residue  494 LEU
Chi-restraints excluded: chain N residue  517 THR
Chi-restraints excluded: chain N residue  520 MET
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  261 THR
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  307 MET
Chi-restraints excluded: chain B residue  331 THR
Chi-restraints excluded: chain B residue  348 GLN
Chi-restraints excluded: chain B residue  463 SER
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  517 THR
Chi-restraints excluded: chain H residue   61 GLU
Chi-restraints excluded: chain H residue  146 GLN
Chi-restraints excluded: chain H residue  213 VAL
Chi-restraints excluded: chain H residue  240 VAL
Chi-restraints excluded: chain H residue  273 VAL
Chi-restraints excluded: chain H residue  300 VAL
Chi-restraints excluded: chain H residue  442 VAL
Chi-restraints excluded: chain H residue  517 THR
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  205 ILE
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  228 SER
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  261 THR
Chi-restraints excluded: chain C residue  271 VAL
Chi-restraints excluded: chain C residue  300 VAL
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  331 THR
Chi-restraints excluded: chain C residue  494 LEU
Chi-restraints excluded: chain C residue  517 THR
Chi-restraints excluded: chain I residue   61 GLU
Chi-restraints excluded: chain I residue  124 VAL
Chi-restraints excluded: chain I residue  146 GLN
Chi-restraints excluded: chain I residue  193 MET
Chi-restraints excluded: chain I residue  213 VAL
Chi-restraints excluded: chain I residue  234 LEU
Chi-restraints excluded: chain I residue  240 VAL
Chi-restraints excluded: chain I residue  351 GLN
Chi-restraints excluded: chain I residue  442 VAL
Chi-restraints excluded: chain I residue  494 LEU
Chi-restraints excluded: chain I residue  517 THR
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue   48 THR
Chi-restraints excluded: chain D residue   61 GLU
Chi-restraints excluded: chain D residue  124 VAL
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  205 ILE
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  259 LEU
Chi-restraints excluded: chain D residue  331 THR
Chi-restraints excluded: chain D residue  351 GLN
Chi-restraints excluded: chain D residue  517 THR
Chi-restraints excluded: chain J residue  146 GLN
Chi-restraints excluded: chain J residue  213 VAL
Chi-restraints excluded: chain J residue  232 GLU
Chi-restraints excluded: chain J residue  273 VAL
Chi-restraints excluded: chain J residue  314 LEU
Chi-restraints excluded: chain J residue  388 GLU
Chi-restraints excluded: chain J residue  433 ASN
Chi-restraints excluded: chain J residue  442 VAL
Chi-restraints excluded: chain J residue  494 LEU
Chi-restraints excluded: chain J residue  517 THR
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   50 THR
Chi-restraints excluded: chain E residue  111 MET
Chi-restraints excluded: chain E residue  177 VAL
Chi-restraints excluded: chain E residue  205 ILE
Chi-restraints excluded: chain E residue  213 VAL
Chi-restraints excluded: chain E residue  240 VAL
Chi-restraints excluded: chain E residue  271 VAL
Chi-restraints excluded: chain E residue  288 MET
Chi-restraints excluded: chain E residue  300 VAL
Chi-restraints excluded: chain E residue  331 THR
Chi-restraints excluded: chain E residue  447 MET
Chi-restraints excluded: chain E residue  494 LEU
Chi-restraints excluded: chain E residue  517 THR
Chi-restraints excluded: chain K residue   43 SER
Chi-restraints excluded: chain K residue   62 LEU
Chi-restraints excluded: chain K residue  146 GLN
Chi-restraints excluded: chain K residue  213 VAL
Chi-restraints excluded: chain K residue  273 VAL
Chi-restraints excluded: chain K residue  288 MET
Chi-restraints excluded: chain K residue  307 MET
Chi-restraints excluded: chain K residue  463 SER
Chi-restraints excluded: chain K residue  517 THR
Chi-restraints excluded: chain F residue   48 THR
Chi-restraints excluded: chain F residue   50 THR
Chi-restraints excluded: chain F residue  124 VAL
Chi-restraints excluded: chain F residue  169 VAL
Chi-restraints excluded: chain F residue  193 MET
Chi-restraints excluded: chain F residue  213 VAL
Chi-restraints excluded: chain F residue  255 GLU
Chi-restraints excluded: chain F residue  331 THR
Chi-restraints excluded: chain F residue  351 GLN
Chi-restraints excluded: chain F residue  369 VAL
Chi-restraints excluded: chain F residue  463 SER
Chi-restraints excluded: chain F residue  517 THR
Chi-restraints excluded: chain F residue  524 LEU
Chi-restraints excluded: chain L residue   50 THR
Chi-restraints excluded: chain L residue   69 MET
Chi-restraints excluded: chain L residue  124 VAL
Chi-restraints excluded: chain L residue  146 GLN
Chi-restraints excluded: chain L residue  213 VAL
Chi-restraints excluded: chain L residue  262 LEU
Chi-restraints excluded: chain L residue  288 MET
Chi-restraints excluded: chain L residue  517 THR
Chi-restraints excluded: chain G residue   11 ASP
Chi-restraints excluded: chain G residue   48 THR
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue  160 LYS
Chi-restraints excluded: chain G residue  166 MET
Chi-restraints excluded: chain G residue  169 VAL
Chi-restraints excluded: chain G residue  205 ILE
Chi-restraints excluded: chain G residue  300 VAL
Chi-restraints excluded: chain G residue  307 MET
Chi-restraints excluded: chain G residue  494 LEU
Chi-restraints excluded: chain G residue  517 THR
Chi-restraints excluded: chain M residue   11 ASP
Chi-restraints excluded: chain M residue   13 ARG
Chi-restraints excluded: chain M residue   61 GLU
Chi-restraints excluded: chain M residue  124 VAL
Chi-restraints excluded: chain M residue  146 GLN
Chi-restraints excluded: chain M residue  187 LEU
Chi-restraints excluded: chain M residue  205 ILE
Chi-restraints excluded: chain M residue  259 LEU
Chi-restraints excluded: chain M residue  262 LEU
Chi-restraints excluded: chain M residue  442 VAL
Chi-restraints excluded: chain M residue  463 SER
Chi-restraints excluded: chain M residue  489 ILE
Chi-restraints excluded: chain M residue  517 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 728
   random chunks:
   chunk 683 optimal weight:    0.7980
   chunk 420 optimal weight:    0.7980
   chunk 280 optimal weight:    0.4980
   chunk 214 optimal weight:    4.9990
   chunk 536 optimal weight:    4.9990
   chunk 223 optimal weight:    4.9990
   chunk 498 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 265 optimal weight:    4.9990
   chunk 241 optimal weight:   10.0000
   chunk 351 optimal weight:    1.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
B 351 GLN
C 467 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.150581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.109638 restraints weight = 68254.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 1.79
r_work: 0.3145 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.2207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  54362  Z= 0.172
  Angle     :  0.482  10.095  73402  Z= 0.254
  Chirality :  0.041   0.172   8932
  Planarity :  0.003   0.033   9618
  Dihedral  :  3.815  18.675   7729
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 15.33 %
    Favored  : 81.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.86 (0.10), residues: 7308
  helix:  2.27 (0.08), residues: 4088
  sheet:  0.63 (0.17), residues: 938
  loop : -0.41 (0.12), residues: 2282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.000   0.000   HIS N 401 
 PHE   0.008   0.001   PHE L 204 
 TYR   0.010   0.001   TYR J 476 
 ARG   0.006   0.000   ARG B 345 

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

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

  14616 Ramachandran restraints generated.
    7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  14616 Ramachandran restraints generated.
    7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  651 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 154
    poor density    : 497
  time to evaluate  : 4.820 
Fit side-chains
   revert: symmetry clash
REVERT: A  267 MET cc_start: 0.6163 (mmm) cc_final: 0.5192 (mmm)
REVERT: A  367 GLU cc_start: 0.8417 (pp20) cc_final: 0.8121 (pp20)
REVERT: N   69 MET cc_start: 0.7911 (mtm) cc_final: 0.7549 (mtp)
REVERT: N  111 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8423 (mtt)
REVERT: N  201 SER cc_start: 0.8331 (t) cc_final: 0.8011 (m)
REVERT: N  267 MET cc_start: 0.6218 (tmm) cc_final: 0.5971 (mmp)
REVERT: N  442 VAL cc_start: 0.8980 (OUTLIER) cc_final: 0.8767 (t)
REVERT: N  494 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8861 (pp)
REVERT: N  520 MET cc_start: 0.8774 (mmt) cc_final: 0.8546 (mmt)
REVERT: B  160 LYS cc_start: 0.8614 (mtpp) cc_final: 0.8257 (ptmm)
REVERT: B  204 PHE cc_start: 0.8456 (m-80) cc_final: 0.8092 (m-80)
REVERT: B  267 MET cc_start: 0.6527 (tmm) cc_final: 0.5406 (mmp)
REVERT: B  367 GLU cc_start: 0.8409 (pp20) cc_final: 0.8101 (pp20)
REVERT: B  494 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8659 (pp)
REVERT: H  267 MET cc_start: 0.6298 (tmm) cc_final: 0.5341 (mmp)
REVERT: C   61 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8076 (pt0)
REVERT: C   69 MET cc_start: 0.8358 (mtp) cc_final: 0.8015 (ttm)
REVERT: C  267 MET cc_start: 0.6422 (tmm) cc_final: 0.5745 (mmp)
REVERT: C  322 ARG cc_start: 0.8961 (mtp-110) cc_final: 0.8688 (ttm110)
REVERT: C  367 GLU cc_start: 0.8429 (pp20) cc_final: 0.8026 (pp20)
REVERT: C  514 MET cc_start: 0.9092 (mtp) cc_final: 0.8865 (mtm)
REVERT: I  193 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8231 (ttm)
REVERT: I  204 PHE cc_start: 0.8421 (m-80) cc_final: 0.8144 (m-80)
REVERT: I  267 MET cc_start: 0.6536 (tmm) cc_final: 0.5793 (mmp)
REVERT: I  351 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8157 (pp30)
REVERT: I  494 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8797 (pp)
REVERT: I  514 MET cc_start: 0.9201 (ttm) cc_final: 0.8907 (mtp)
REVERT: D  242 LYS cc_start: 0.8043 (mmtt) cc_final: 0.7778 (mmmt)
REVERT: D  267 MET cc_start: 0.6600 (tmm) cc_final: 0.5816 (mmm)
REVERT: D  321 LYS cc_start: 0.8820 (ttpt) cc_final: 0.8480 (mmmt)
REVERT: D  367 GLU cc_start: 0.8616 (pp20) cc_final: 0.8271 (pp20)
REVERT: J   16 MET cc_start: 0.8813 (mtp) cc_final: 0.8592 (mtm)
REVERT: J  204 PHE cc_start: 0.8305 (m-80) cc_final: 0.7980 (m-80)
REVERT: J  267 MET cc_start: 0.5697 (tmm) cc_final: 0.4914 (mmm)
REVERT: J  442 VAL cc_start: 0.8913 (OUTLIER) cc_final: 0.8706 (t)
REVERT: E  267 MET cc_start: 0.6737 (tmm) cc_final: 0.5859 (mmp)
REVERT: E  351 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7939 (tp-100)
REVERT: E  367 GLU cc_start: 0.8548 (pp20) cc_final: 0.8204 (pp20)
REVERT: E  389 MET cc_start: 0.7908 (tmm) cc_final: 0.7598 (tmt)
REVERT: E  447 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8919 (mtp)
REVERT: E  494 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8801 (pp)
REVERT: E  514 MET cc_start: 0.9145 (ttm) cc_final: 0.8732 (mtp)
REVERT: K  238 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6898 (mm-30)
REVERT: K  267 MET cc_start: 0.6531 (tmm) cc_final: 0.5425 (mmp)
REVERT: K  514 MET cc_start: 0.9165 (ttm) cc_final: 0.8913 (mtp)
REVERT: F  102 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7292 (mp0)
REVERT: F  111 MET cc_start: 0.8973 (mtp) cc_final: 0.8635 (mtt)
REVERT: F  160 LYS cc_start: 0.8662 (mtpp) cc_final: 0.8383 (ptmm)
REVERT: F  321 LYS cc_start: 0.8784 (mmtt) cc_final: 0.8377 (mmtp)
REVERT: F  367 GLU cc_start: 0.8360 (pp20) cc_final: 0.8054 (pp20)
REVERT: L   61 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8408 (tm-30)
REVERT: L   69 MET cc_start: 0.8469 (mtm) cc_final: 0.8035 (mtp)
REVERT: L  262 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7033 (tp)
REVERT: L  267 MET cc_start: 0.6129 (tmm) cc_final: 0.5373 (mmm)
REVERT: L  288 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.6727 (mpp)
REVERT: L  351 GLN cc_start: 0.8219 (tp40) cc_final: 0.7969 (tp40)
REVERT: G   61 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8071 (pt0)
REVERT: G  166 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.7914 (mtt)
REVERT: G  204 PHE cc_start: 0.8541 (m-80) cc_final: 0.8212 (m-80)
REVERT: G  267 MET cc_start: 0.6185 (tmm) cc_final: 0.5487 (mmp)
REVERT: G  367 GLU cc_start: 0.8470 (pp20) cc_final: 0.8095 (pp20)
REVERT: G  494 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8842 (pp)
REVERT: M  267 MET cc_start: 0.6367 (tmm) cc_final: 0.5690 (mmm)
  outliers start: 154
  outliers final: 118
  residues processed: 624
  average time/residue: 0.4663
  time to fit residues: 513.3552
Evaluate side-chains
  593 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 135
    poor density    : 458
  time to evaluate  : 4.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  463 SER
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain N residue   11 ASP
Chi-restraints excluded: chain N residue   50 THR
Chi-restraints excluded: chain N residue  111 MET
Chi-restraints excluded: chain N residue  213 VAL
Chi-restraints excluded: chain N residue  234 LEU
Chi-restraints excluded: chain N residue  240 VAL
Chi-restraints excluded: chain N residue  442 VAL
Chi-restraints excluded: chain N residue  494 LEU
Chi-restraints excluded: chain N residue  499 VAL
Chi-restraints excluded: chain N residue  517 THR
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  307 MET
Chi-restraints excluded: chain B residue  331 THR
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  517 THR
Chi-restraints excluded: chain H residue   61 GLU
Chi-restraints excluded: chain H residue  146 GLN
Chi-restraints excluded: chain H residue  213 VAL
Chi-restraints excluded: chain H residue  240 VAL
Chi-restraints excluded: chain H residue  300 VAL
Chi-restraints excluded: chain H residue  442 VAL
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue  174 VAL
Chi-restraints excluded: chain C residue  205 ILE
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  228 SER
Chi-restraints excluded: chain C residue  261 THR
Chi-restraints excluded: chain C residue  271 VAL
Chi-restraints excluded: chain C residue  300 VAL
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  331 THR
Chi-restraints excluded: chain C residue  517 THR
Chi-restraints excluded: chain I residue   61 GLU
Chi-restraints excluded: chain I residue  124 VAL
Chi-restraints excluded: chain I residue  146 GLN
Chi-restraints excluded: chain I residue  193 MET
Chi-restraints excluded: chain I residue  213 VAL
Chi-restraints excluded: chain I residue  234 LEU
Chi-restraints excluded: chain I residue  240 VAL
Chi-restraints excluded: chain I residue  351 GLN
Chi-restraints excluded: chain I residue  442 VAL
Chi-restraints excluded: chain I residue  494 LEU
Chi-restraints excluded: chain I residue  499 VAL
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue   48 THR
Chi-restraints excluded: chain D residue   61 GLU
Chi-restraints excluded: chain D residue  124 VAL
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  259 LEU
Chi-restraints excluded: chain D residue  331 THR
Chi-restraints excluded: chain D residue  351 GLN
Chi-restraints excluded: chain D residue  447 MET
Chi-restraints excluded: chain D residue  517 THR
Chi-restraints excluded: chain J residue   11 ASP
Chi-restraints excluded: chain J residue  146 GLN
Chi-restraints excluded: chain J residue  213 VAL
Chi-restraints excluded: chain J residue  232 GLU
Chi-restraints excluded: chain J residue  388 GLU
Chi-restraints excluded: chain J residue  433 ASN
Chi-restraints excluded: chain J residue  442 VAL
Chi-restraints excluded: chain J residue  517 THR
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   50 THR
Chi-restraints excluded: chain E residue  177 VAL
Chi-restraints excluded: chain E residue  205 ILE
Chi-restraints excluded: chain E residue  213 VAL
Chi-restraints excluded: chain E residue  240 VAL
Chi-restraints excluded: chain E residue  271 VAL
Chi-restraints excluded: chain E residue  288 MET
Chi-restraints excluded: chain E residue  300 VAL
Chi-restraints excluded: chain E residue  331 THR
Chi-restraints excluded: chain E residue  351 GLN
Chi-restraints excluded: chain E residue  447 MET
Chi-restraints excluded: chain E residue  494 LEU
Chi-restraints excluded: chain K residue   62 LEU
Chi-restraints excluded: chain K residue  146 GLN
Chi-restraints excluded: chain K residue  213 VAL
Chi-restraints excluded: chain K residue  240 VAL
Chi-restraints excluded: chain K residue  273 VAL
Chi-restraints excluded: chain K residue  288 MET
Chi-restraints excluded: chain K residue  307 MET
Chi-restraints excluded: chain K residue  463 SER
Chi-restraints excluded: chain F residue   48 THR
Chi-restraints excluded: chain F residue   50 THR
Chi-restraints excluded: chain F residue  169 VAL
Chi-restraints excluded: chain F residue  193 MET
Chi-restraints excluded: chain F residue  205 ILE
Chi-restraints excluded: chain F residue  213 VAL
Chi-restraints excluded: chain F residue  255 GLU
Chi-restraints excluded: chain F residue  270 ILE
Chi-restraints excluded: chain F residue  331 THR
Chi-restraints excluded: chain F residue  351 GLN
Chi-restraints excluded: chain F residue  369 VAL
Chi-restraints excluded: chain F residue  463 SER
Chi-restraints excluded: chain F residue  491 MET
Chi-restraints excluded: chain F residue  517 THR
Chi-restraints excluded: chain F residue  524 LEU
Chi-restraints excluded: chain L residue   50 THR
Chi-restraints excluded: chain L residue  146 GLN
Chi-restraints excluded: chain L residue  213 VAL
Chi-restraints excluded: chain L residue  262 LEU
Chi-restraints excluded: chain L residue  288 MET
Chi-restraints excluded: chain G residue   11 ASP
Chi-restraints excluded: chain G residue   48 THR
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue  160 LYS
Chi-restraints excluded: chain G residue  166 MET
Chi-restraints excluded: chain G residue  169 VAL
Chi-restraints excluded: chain G residue  205 ILE
Chi-restraints excluded: chain G residue  300 VAL
Chi-restraints excluded: chain G residue  307 MET
Chi-restraints excluded: chain G residue  331 THR
Chi-restraints excluded: chain G residue  494 LEU
Chi-restraints excluded: chain M residue   11 ASP
Chi-restraints excluded: chain M residue   61 GLU
Chi-restraints excluded: chain M residue  124 VAL
Chi-restraints excluded: chain M residue  146 GLN
Chi-restraints excluded: chain M residue  259 LEU
Chi-restraints excluded: chain M residue  262 LEU
Chi-restraints excluded: chain M residue  442 VAL
Chi-restraints excluded: chain M residue  463 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 728
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 554 optimal weight:    9.9990
   chunk 274 optimal weight:    6.9990
   chunk 172 optimal weight:    0.9990
   chunk 465 optimal weight:    4.9990
   chunk 412 optimal weight:    6.9990
   chunk 483 optimal weight:    0.0010
   chunk 594 optimal weight:   20.0000
   chunk 604 optimal weight:   10.0000
   chunk 579 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   overall best weight:    1.7792

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

Flipped N/Q/H residues before XYZ refinement:
J 351 GLN
K 351 GLN
G 351 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.150346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.108384 restraints weight = 68509.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 1.79
r_work: 0.3132 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.2287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  54362  Z= 0.193
  Angle     :  0.488   9.616  73402  Z= 0.256
  Chirality :  0.041   0.172   8932
  Planarity :  0.003   0.035   9618
  Dihedral  :  3.811  18.585   7729
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 15.22 %
    Favored  : 81.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.10), residues: 7308
  helix:  2.26 (0.08), residues: 4088
  sheet:  0.62 (0.17), residues: 938
  loop : -0.41 (0.12), residues: 2282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.000   0.000   HIS N 401 
 PHE   0.007   0.001   PHE L   8 
 TYR   0.010   0.001   TYR J 476 
 ARG   0.004   0.000   ARG I 345 

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

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

  14616 Ramachandran restraints generated.
    7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  14616 Ramachandran restraints generated.
    7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  648 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 164
    poor density    : 484
  time to evaluate  : 5.633 
Fit side-chains
REVERT: A  267 MET cc_start: 0.6053 (mmm) cc_final: 0.5121 (mmm)
REVERT: A  367 GLU cc_start: 0.8398 (pp20) cc_final: 0.8083 (pp20)
REVERT: N   69 MET cc_start: 0.7954 (mtm) cc_final: 0.7588 (mtp)
REVERT: N  111 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8443 (mtt)
REVERT: N  201 SER cc_start: 0.8324 (t) cc_final: 0.8013 (m)
REVERT: N  267 MET cc_start: 0.6682 (tmm) cc_final: 0.5882 (mmp)
REVERT: N  442 VAL cc_start: 0.9005 (OUTLIER) cc_final: 0.8801 (t)
REVERT: N  494 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8870 (pp)
REVERT: B  160 LYS cc_start: 0.8623 (mtpp) cc_final: 0.8268 (ptmm)
REVERT: B  204 PHE cc_start: 0.8466 (m-80) cc_final: 0.8099 (m-80)
REVERT: B  267 MET cc_start: 0.6605 (tmm) cc_final: 0.5535 (mmp)
REVERT: B  367 GLU cc_start: 0.8417 (pp20) cc_final: 0.8105 (pp20)
REVERT: B  494 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8607 (pp)
REVERT: H   69 MET cc_start: 0.8705 (mtp) cc_final: 0.8502 (mtt)
REVERT: H  267 MET cc_start: 0.6226 (tmm) cc_final: 0.5202 (mmp)
REVERT: C   61 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8055 (pt0)
REVERT: C   69 MET cc_start: 0.8362 (mtp) cc_final: 0.8020 (ttm)
REVERT: C  267 MET cc_start: 0.6679 (tmm) cc_final: 0.6023 (mmp)
REVERT: C  322 ARG cc_start: 0.8973 (mtp-110) cc_final: 0.8599 (ttm110)
REVERT: C  367 GLU cc_start: 0.8424 (pp20) cc_final: 0.8011 (pp20)
REVERT: C  514 MET cc_start: 0.9076 (mtp) cc_final: 0.8842 (mtm)
REVERT: I  193 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8272 (ttm)
REVERT: I  204 PHE cc_start: 0.8412 (m-80) cc_final: 0.8156 (m-80)
REVERT: I  267 MET cc_start: 0.6535 (tmm) cc_final: 0.5847 (mmp)
REVERT: I  351 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8185 (pp30)
REVERT: I  494 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8803 (pp)
REVERT: I  514 MET cc_start: 0.9208 (ttm) cc_final: 0.8918 (mtp)
REVERT: D  242 LYS cc_start: 0.8043 (mmtt) cc_final: 0.7781 (mmmt)
REVERT: D  267 MET cc_start: 0.6576 (tmm) cc_final: 0.5764 (mmm)
REVERT: D  321 LYS cc_start: 0.8811 (ttpt) cc_final: 0.8462 (mmmt)
REVERT: D  367 GLU cc_start: 0.8591 (pp20) cc_final: 0.8239 (pp20)
REVERT: J   16 MET cc_start: 0.8826 (mtp) cc_final: 0.8615 (mtm)
REVERT: J  204 PHE cc_start: 0.8305 (m-80) cc_final: 0.7989 (m-80)
REVERT: J  267 MET cc_start: 0.5661 (tmm) cc_final: 0.4908 (mmm)
REVERT: J  389 MET cc_start: 0.8229 (tmm) cc_final: 0.7983 (tmm)
REVERT: E  267 MET cc_start: 0.6582 (tmm) cc_final: 0.5812 (mmp)
REVERT: E  351 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8110 (mm110)
REVERT: E  367 GLU cc_start: 0.8537 (pp20) cc_final: 0.8266 (pp20)
REVERT: E  389 MET cc_start: 0.7907 (tmm) cc_final: 0.7704 (tmm)
REVERT: E  447 MET cc_start: 0.9204 (mtm) cc_final: 0.8936 (mtp)
REVERT: E  494 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8851 (pp)
REVERT: E  514 MET cc_start: 0.9154 (ttm) cc_final: 0.8717 (mtp)
REVERT: K  142 LYS cc_start: 0.8621 (tppt) cc_final: 0.8356 (ttpp)
REVERT: K  267 MET cc_start: 0.6539 (tmm) cc_final: 0.5476 (mmp)
REVERT: F  102 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7265 (mp0)
REVERT: F  111 MET cc_start: 0.8996 (mtp) cc_final: 0.8651 (mtt)
REVERT: F  160 LYS cc_start: 0.8667 (mtpp) cc_final: 0.8383 (ptmm)
REVERT: F  234 LEU cc_start: 0.7871 (tp) cc_final: 0.7641 (tp)
REVERT: F  321 LYS cc_start: 0.8795 (mmtt) cc_final: 0.8390 (mmtp)
REVERT: F  367 GLU cc_start: 0.8362 (pp20) cc_final: 0.8057 (pp20)
REVERT: L   61 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8376 (tm-30)
REVERT: L   69 MET cc_start: 0.8511 (mtm) cc_final: 0.8068 (mtp)
REVERT: L  267 MET cc_start: 0.6114 (tmm) cc_final: 0.5370 (mmm)
REVERT: L  288 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.6654 (mpp)
REVERT: L  351 GLN cc_start: 0.8222 (tp40) cc_final: 0.7974 (tp40)
REVERT: G   61 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8085 (pt0)
REVERT: G  166 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.7900 (mtt)
REVERT: G  204 PHE cc_start: 0.8500 (m-80) cc_final: 0.8172 (m-80)
REVERT: G  267 MET cc_start: 0.6346 (tmm) cc_final: 0.5823 (mmp)
REVERT: G  367 GLU cc_start: 0.8486 (pp20) cc_final: 0.8113 (pp20)
REVERT: G  494 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8861 (pp)
REVERT: M   13 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7858 (mpt-90)
REVERT: M  267 MET cc_start: 0.6355 (tmm) cc_final: 0.5714 (mmm)
  outliers start: 164
  outliers final: 136
  residues processed: 620
  average time/residue: 0.4745
  time to fit residues: 521.3993
Evaluate side-chains
  620 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 151
    poor density    : 469
  time to evaluate  : 5.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  331 THR
Chi-restraints excluded: chain A residue  463 SER
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain N residue   11 ASP
Chi-restraints excluded: chain N residue   50 THR
Chi-restraints excluded: chain N residue  111 MET
Chi-restraints excluded: chain N residue  213 VAL
Chi-restraints excluded: chain N residue  230 ILE
Chi-restraints excluded: chain N residue  234 LEU
Chi-restraints excluded: chain N residue  240 VAL
Chi-restraints excluded: chain N residue  442 VAL
Chi-restraints excluded: chain N residue  494 LEU
Chi-restraints excluded: chain N residue  499 VAL
Chi-restraints excluded: chain N residue  517 THR
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  261 THR
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  307 MET
Chi-restraints excluded: chain B residue  331 THR
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  517 THR
Chi-restraints excluded: chain H residue   61 GLU
Chi-restraints excluded: chain H residue  146 GLN
Chi-restraints excluded: chain H residue  213 VAL
Chi-restraints excluded: chain H residue  240 VAL
Chi-restraints excluded: chain H residue  300 VAL
Chi-restraints excluded: chain H residue  442 VAL
Chi-restraints excluded: chain H residue  517 THR
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  174 VAL
Chi-restraints excluded: chain C residue  205 ILE
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  228 SER
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  261 THR
Chi-restraints excluded: chain C residue  271 VAL
Chi-restraints excluded: chain C residue  300 VAL
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  331 THR
Chi-restraints excluded: chain C residue  517 THR
Chi-restraints excluded: chain I residue   61 GLU
Chi-restraints excluded: chain I residue  124 VAL
Chi-restraints excluded: chain I residue  146 GLN
Chi-restraints excluded: chain I residue  193 MET
Chi-restraints excluded: chain I residue  213 VAL
Chi-restraints excluded: chain I residue  234 LEU
Chi-restraints excluded: chain I residue  240 VAL
Chi-restraints excluded: chain I residue  351 GLN
Chi-restraints excluded: chain I residue  442 VAL
Chi-restraints excluded: chain I residue  494 LEU
Chi-restraints excluded: chain I residue  499 VAL
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue   48 THR
Chi-restraints excluded: chain D residue   61 GLU
Chi-restraints excluded: chain D residue  124 VAL
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  259 LEU
Chi-restraints excluded: chain D residue  331 THR
Chi-restraints excluded: chain D residue  351 GLN
Chi-restraints excluded: chain D residue  447 MET
Chi-restraints excluded: chain D residue  517 THR
Chi-restraints excluded: chain J residue   11 ASP
Chi-restraints excluded: chain J residue  146 GLN
Chi-restraints excluded: chain J residue  213 VAL
Chi-restraints excluded: chain J residue  273 VAL
Chi-restraints excluded: chain J residue  388 GLU
Chi-restraints excluded: chain J residue  433 ASN
Chi-restraints excluded: chain J residue  517 THR
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   50 THR
Chi-restraints excluded: chain E residue  177 VAL
Chi-restraints excluded: chain E residue  205 ILE
Chi-restraints excluded: chain E residue  213 VAL
Chi-restraints excluded: chain E residue  240 VAL
Chi-restraints excluded: chain E residue  271 VAL
Chi-restraints excluded: chain E residue  288 MET
Chi-restraints excluded: chain E residue  300 VAL
Chi-restraints excluded: chain E residue  331 THR
Chi-restraints excluded: chain E residue  351 GLN
Chi-restraints excluded: chain E residue  494 LEU
Chi-restraints excluded: chain E residue  517 THR
Chi-restraints excluded: chain K residue   43 SER
Chi-restraints excluded: chain K residue   62 LEU
Chi-restraints excluded: chain K residue  146 GLN
Chi-restraints excluded: chain K residue  213 VAL
Chi-restraints excluded: chain K residue  240 VAL
Chi-restraints excluded: chain K residue  273 VAL
Chi-restraints excluded: chain K residue  288 MET
Chi-restraints excluded: chain K residue  307 MET
Chi-restraints excluded: chain K residue  463 SER
Chi-restraints excluded: chain F residue   11 ASP
Chi-restraints excluded: chain F residue   48 THR
Chi-restraints excluded: chain F residue  124 VAL
Chi-restraints excluded: chain F residue  169 VAL
Chi-restraints excluded: chain F residue  193 MET
Chi-restraints excluded: chain F residue  205 ILE
Chi-restraints excluded: chain F residue  213 VAL
Chi-restraints excluded: chain F residue  255 GLU
Chi-restraints excluded: chain F residue  270 ILE
Chi-restraints excluded: chain F residue  300 VAL
Chi-restraints excluded: chain F residue  331 THR
Chi-restraints excluded: chain F residue  351 GLN
Chi-restraints excluded: chain F residue  369 VAL
Chi-restraints excluded: chain F residue  463 SER
Chi-restraints excluded: chain F residue  491 MET
Chi-restraints excluded: chain F residue  494 LEU
Chi-restraints excluded: chain F residue  517 THR
Chi-restraints excluded: chain F residue  524 LEU
Chi-restraints excluded: chain L residue   50 THR
Chi-restraints excluded: chain L residue  124 VAL
Chi-restraints excluded: chain L residue  146 GLN
Chi-restraints excluded: chain L residue  213 VAL
Chi-restraints excluded: chain L residue  288 MET
Chi-restraints excluded: chain L residue  494 LEU
Chi-restraints excluded: chain L residue  517 THR
Chi-restraints excluded: chain G residue   11 ASP
Chi-restraints excluded: chain G residue   48 THR
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue  160 LYS
Chi-restraints excluded: chain G residue  166 MET
Chi-restraints excluded: chain G residue  169 VAL
Chi-restraints excluded: chain G residue  300 VAL
Chi-restraints excluded: chain G residue  307 MET
Chi-restraints excluded: chain G residue  331 THR
Chi-restraints excluded: chain G residue  494 LEU
Chi-restraints excluded: chain M residue   11 ASP
Chi-restraints excluded: chain M residue   13 ARG
Chi-restraints excluded: chain M residue   61 GLU
Chi-restraints excluded: chain M residue  124 VAL
Chi-restraints excluded: chain M residue  146 GLN
Chi-restraints excluded: chain M residue  205 ILE
Chi-restraints excluded: chain M residue  259 LEU
Chi-restraints excluded: chain M residue  262 LEU
Chi-restraints excluded: chain M residue  442 VAL
Chi-restraints excluded: chain M residue  463 SER
Chi-restraints excluded: chain M residue  517 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 728
   random chunks:
   chunk 581 optimal weight:    1.9990
   chunk 646 optimal weight:    6.9990
   chunk 253 optimal weight:    0.9980
   chunk 543 optimal weight:    0.0970
   chunk 334 optimal weight:   20.0000
   chunk 255 optimal weight:    4.9990
   chunk 600 optimal weight:    1.9990
   chunk 371 optimal weight:    0.8980
   chunk 381 optimal weight:    6.9990
   chunk 92 optimal weight:    2.9990
   chunk 27 optimal weight:   10.0000
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
E 467 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.151666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.109829 restraints weight = 68309.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 1.74
r_work: 0.3161 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3009 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.2323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048  54362  Z= 0.161
  Angle     :  0.488  13.079  73402  Z= 0.255
  Chirality :  0.040   0.170   8932
  Planarity :  0.003   0.037   9618
  Dihedral  :  3.771  18.721   7729
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 15.51 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.10), residues: 7308
  helix:  2.31 (0.08), residues: 4088
  sheet:  0.65 (0.17), residues: 938
  loop : -0.41 (0.12), residues: 2282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.000   0.000   HIS N 401 
 PHE   0.007   0.001   PHE N 195 
 TYR   0.010   0.001   TYR J 476 
 ARG   0.004   0.000   ARG I 345 

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

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

  14616 Ramachandran restraints generated.
    7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  14616 Ramachandran restraints generated.
    7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  650 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 149
    poor density    : 501
  time to evaluate  : 4.852 
Fit side-chains
REVERT: A  238 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6870 (mm-30)
REVERT: A  267 MET cc_start: 0.6010 (mmm) cc_final: 0.5058 (mmm)
REVERT: A  367 GLU cc_start: 0.8366 (pp20) cc_final: 0.8056 (pp20)
REVERT: N   69 MET cc_start: 0.7900 (mtm) cc_final: 0.7472 (mtp)
REVERT: N  111 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8372 (mtt)
REVERT: N  201 SER cc_start: 0.8109 (t) cc_final: 0.7807 (m)
REVERT: N  267 MET cc_start: 0.6702 (tmm) cc_final: 0.5921 (mmp)
REVERT: N  494 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8878 (pp)
REVERT: N  514 MET cc_start: 0.9126 (ttm) cc_final: 0.8742 (mtp)
REVERT: N  520 MET cc_start: 0.8805 (mmm) cc_final: 0.8429 (mtt)
REVERT: B  160 LYS cc_start: 0.8614 (mtpp) cc_final: 0.8269 (ptmm)
REVERT: B  204 PHE cc_start: 0.8461 (m-80) cc_final: 0.8080 (m-80)
REVERT: B  267 MET cc_start: 0.6479 (tmm) cc_final: 0.5467 (mmp)
REVERT: B  367 GLU cc_start: 0.8429 (pp20) cc_final: 0.8196 (pp20)
REVERT: B  494 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8629 (pp)
REVERT: H  238 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6736 (mm-30)
REVERT: H  267 MET cc_start: 0.6264 (tmm) cc_final: 0.5335 (mmp)
REVERT: H  514 MET cc_start: 0.9052 (mtp) cc_final: 0.8803 (mtm)
REVERT: C   61 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8120 (pt0)
REVERT: C   69 MET cc_start: 0.8271 (mtp) cc_final: 0.7987 (ttm)
REVERT: C  267 MET cc_start: 0.6577 (tmm) cc_final: 0.5931 (mmp)
REVERT: C  322 ARG cc_start: 0.8957 (mtp-110) cc_final: 0.8701 (ttm110)
REVERT: C  367 GLU cc_start: 0.8435 (pp20) cc_final: 0.8024 (pp20)
REVERT: I  193 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8246 (ttm)
REVERT: I  204 PHE cc_start: 0.8412 (m-80) cc_final: 0.8133 (m-80)
REVERT: I  267 MET cc_start: 0.6457 (tmm) cc_final: 0.5900 (mmp)
REVERT: I  288 MET cc_start: 0.7784 (mmp) cc_final: 0.7581 (mmp)
REVERT: I  351 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8108 (pp30)
REVERT: I  494 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8771 (pp)
REVERT: I  514 MET cc_start: 0.9172 (ttm) cc_final: 0.8904 (mtp)
REVERT: D  267 MET cc_start: 0.6526 (tmm) cc_final: 0.5726 (mmm)
REVERT: D  321 LYS cc_start: 0.8799 (ttpt) cc_final: 0.8495 (mmmt)
REVERT: D  367 GLU cc_start: 0.8600 (pp20) cc_final: 0.8251 (pp20)
REVERT: J  204 PHE cc_start: 0.8296 (m-80) cc_final: 0.7971 (m-80)
REVERT: J  267 MET cc_start: 0.5577 (tmm) cc_final: 0.4896 (mmm)
REVERT: J  389 MET cc_start: 0.8179 (tmm) cc_final: 0.7928 (tmm)
REVERT: E  267 MET cc_start: 0.6471 (tmm) cc_final: 0.5853 (mmp)
REVERT: E  367 GLU cc_start: 0.8487 (pp20) cc_final: 0.8194 (pp20)
REVERT: E  389 MET cc_start: 0.7886 (tmm) cc_final: 0.7671 (tmm)
REVERT: E  447 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8894 (mtp)
REVERT: E  494 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8839 (pp)
REVERT: E  514 MET cc_start: 0.9086 (ttm) cc_final: 0.8719 (mtp)
REVERT: K  204 PHE cc_start: 0.8283 (m-80) cc_final: 0.7892 (m-80)
REVERT: K  267 MET cc_start: 0.6451 (tmm) cc_final: 0.5518 (mmp)
REVERT: F  102 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7174 (mp0)
REVERT: F  111 MET cc_start: 0.8945 (mtp) cc_final: 0.8640 (mtt)
REVERT: F  160 LYS cc_start: 0.8645 (mtpp) cc_final: 0.8372 (ptmm)
REVERT: F  234 LEU cc_start: 0.7904 (tp) cc_final: 0.7671 (tp)
REVERT: F  321 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8425 (mmtp)
REVERT: F  367 GLU cc_start: 0.8359 (pp20) cc_final: 0.8157 (pp20)
REVERT: L   61 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8436 (tm-30)
REVERT: L   69 MET cc_start: 0.8379 (mtm) cc_final: 0.7940 (mtp)
REVERT: L   76 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8558 (tm-30)
REVERT: L  267 MET cc_start: 0.6067 (tmm) cc_final: 0.5379 (mmm)
REVERT: L  288 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.6650 (mpp)
REVERT: L  351 GLN cc_start: 0.8188 (tp40) cc_final: 0.7951 (tp40)
REVERT: G   61 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8062 (pt0)
REVERT: G  166 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.7910 (mtt)
REVERT: G  204 PHE cc_start: 0.8488 (m-80) cc_final: 0.8213 (m-80)
REVERT: G  267 MET cc_start: 0.6191 (tmm) cc_final: 0.5856 (mmp)
REVERT: G  367 GLU cc_start: 0.8487 (pp20) cc_final: 0.8194 (pp20)
REVERT: G  494 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8861 (pp)
REVERT: M  267 MET cc_start: 0.6288 (tmm) cc_final: 0.5727 (mmm)
  outliers start: 149
  outliers final: 121
  residues processed: 624
  average time/residue: 0.4669
  time to fit residues: 516.4114
Evaluate side-chains
  606 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 134
    poor density    : 472
  time to evaluate  : 5.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  331 THR
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain N residue   11 ASP
Chi-restraints excluded: chain N residue   50 THR
Chi-restraints excluded: chain N residue  111 MET
Chi-restraints excluded: chain N residue  213 VAL
Chi-restraints excluded: chain N residue  230 ILE
Chi-restraints excluded: chain N residue  234 LEU
Chi-restraints excluded: chain N residue  240 VAL
Chi-restraints excluded: chain N residue  494 LEU
Chi-restraints excluded: chain N residue  499 VAL
Chi-restraints excluded: chain N residue  517 THR
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  261 THR
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  307 MET
Chi-restraints excluded: chain B residue  331 THR
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  517 THR
Chi-restraints excluded: chain H residue   61 GLU
Chi-restraints excluded: chain H residue  213 VAL
Chi-restraints excluded: chain H residue  240 VAL
Chi-restraints excluded: chain H residue  300 VAL
Chi-restraints excluded: chain H residue  442 VAL
Chi-restraints excluded: chain H residue  517 THR
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  174 VAL
Chi-restraints excluded: chain C residue  205 ILE
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  228 SER
Chi-restraints excluded: chain C residue  271 VAL
Chi-restraints excluded: chain C residue  300 VAL
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  331 THR
Chi-restraints excluded: chain C residue  517 THR
Chi-restraints excluded: chain I residue   61 GLU
Chi-restraints excluded: chain I residue  124 VAL
Chi-restraints excluded: chain I residue  146 GLN
Chi-restraints excluded: chain I residue  193 MET
Chi-restraints excluded: chain I residue  213 VAL
Chi-restraints excluded: chain I residue  240 VAL
Chi-restraints excluded: chain I residue  351 GLN
Chi-restraints excluded: chain I residue  442 VAL
Chi-restraints excluded: chain I residue  494 LEU
Chi-restraints excluded: chain I residue  499 VAL
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue   48 THR
Chi-restraints excluded: chain D residue   61 GLU
Chi-restraints excluded: chain D residue  124 VAL
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  205 ILE
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  259 LEU
Chi-restraints excluded: chain D residue  331 THR
Chi-restraints excluded: chain D residue  351 GLN
Chi-restraints excluded: chain D residue  447 MET
Chi-restraints excluded: chain D residue  517 THR
Chi-restraints excluded: chain J residue   11 ASP
Chi-restraints excluded: chain J residue  146 GLN
Chi-restraints excluded: chain J residue  213 VAL
Chi-restraints excluded: chain J residue  273 VAL
Chi-restraints excluded: chain J residue  388 GLU
Chi-restraints excluded: chain J residue  433 ASN
Chi-restraints excluded: chain J residue  517 THR
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   50 THR
Chi-restraints excluded: chain E residue  205 ILE
Chi-restraints excluded: chain E residue  213 VAL
Chi-restraints excluded: chain E residue  240 VAL
Chi-restraints excluded: chain E residue  288 MET
Chi-restraints excluded: chain E residue  300 VAL
Chi-restraints excluded: chain E residue  331 THR
Chi-restraints excluded: chain E residue  447 MET
Chi-restraints excluded: chain E residue  491 MET
Chi-restraints excluded: chain E residue  494 LEU
Chi-restraints excluded: chain E residue  517 THR
Chi-restraints excluded: chain K residue   43 SER
Chi-restraints excluded: chain K residue   62 LEU
Chi-restraints excluded: chain K residue  213 VAL
Chi-restraints excluded: chain K residue  240 VAL
Chi-restraints excluded: chain K residue  273 VAL
Chi-restraints excluded: chain K residue  288 MET
Chi-restraints excluded: chain K residue  307 MET
Chi-restraints excluded: chain K residue  463 SER
Chi-restraints excluded: chain K residue  517 THR
Chi-restraints excluded: chain F residue   48 THR
Chi-restraints excluded: chain F residue   50 THR
Chi-restraints excluded: chain F residue  169 VAL
Chi-restraints excluded: chain F residue  193 MET
Chi-restraints excluded: chain F residue  213 VAL
Chi-restraints excluded: chain F residue  255 GLU
Chi-restraints excluded: chain F residue  270 ILE
Chi-restraints excluded: chain F residue  300 VAL
Chi-restraints excluded: chain F residue  331 THR
Chi-restraints excluded: chain F residue  351 GLN
Chi-restraints excluded: chain F residue  369 VAL
Chi-restraints excluded: chain F residue  463 SER
Chi-restraints excluded: chain F residue  494 LEU
Chi-restraints excluded: chain F residue  517 THR
Chi-restraints excluded: chain F residue  524 LEU
Chi-restraints excluded: chain L residue   50 THR
Chi-restraints excluded: chain L residue  124 VAL
Chi-restraints excluded: chain L residue  146 GLN
Chi-restraints excluded: chain L residue  213 VAL
Chi-restraints excluded: chain L residue  288 MET
Chi-restraints excluded: chain L residue  494 LEU
Chi-restraints excluded: chain G residue   11 ASP
Chi-restraints excluded: chain G residue   48 THR
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue  160 LYS
Chi-restraints excluded: chain G residue  166 MET
Chi-restraints excluded: chain G residue  169 VAL
Chi-restraints excluded: chain G residue  300 VAL
Chi-restraints excluded: chain G residue  307 MET
Chi-restraints excluded: chain G residue  331 THR
Chi-restraints excluded: chain G residue  494 LEU
Chi-restraints excluded: chain M residue   61 GLU
Chi-restraints excluded: chain M residue  124 VAL
Chi-restraints excluded: chain M residue  146 GLN
Chi-restraints excluded: chain M residue  205 ILE
Chi-restraints excluded: chain M residue  442 VAL
Chi-restraints excluded: chain M residue  463 SER
Chi-restraints excluded: chain M residue  517 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 728
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 387 optimal weight:    0.9980
   chunk 478 optimal weight:    5.9990
   chunk 119 optimal weight:    7.9990
   chunk 583 optimal weight:    1.9990
   chunk 147 optimal weight:    3.9990
   chunk 317 optimal weight:    3.9990
   chunk 543 optimal weight:    4.9990
   chunk 157 optimal weight:    1.9990
   chunk 327 optimal weight:   10.0000
   chunk 29 optimal weight:    8.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
B 351 GLN
J 351 GLN
E 351 GLN
G 351 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.149426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.107173 restraints weight = 68619.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 1.74
r_work: 0.3122 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.2408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  54362  Z= 0.254
  Angle     :  0.524  11.678  73402  Z= 0.273
  Chirality :  0.042   0.155   8932
  Planarity :  0.003   0.041   9618
  Dihedral  :  3.847  19.209   7729
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 15.61 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.10), residues: 7308
  helix:  2.27 (0.08), residues: 4060
  sheet:  0.62 (0.17), residues: 938
  loop : -0.44 (0.12), residues: 2310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS C 401 
 PHE   0.009   0.001   PHE H   8 
 TYR   0.010   0.001   TYR J 476 
 ARG   0.004   0.000   ARG I 345 

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

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

  14616 Ramachandran restraints generated.
    7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  14616 Ramachandran restraints generated.
    7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  626 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 148
    poor density    : 478
  time to evaluate  : 4.848 
Fit side-chains
REVERT: A  267 MET cc_start: 0.5966 (mmm) cc_final: 0.5054 (mmm)
REVERT: A  367 GLU cc_start: 0.8398 (pp20) cc_final: 0.8088 (pp20)
REVERT: N  111 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8443 (mtt)
REVERT: N  201 SER cc_start: 0.8213 (t) cc_final: 0.7899 (m)
REVERT: N  267 MET cc_start: 0.6759 (tmm) cc_final: 0.5953 (mmp)
REVERT: N  494 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8881 (pp)
REVERT: B  160 LYS cc_start: 0.8629 (mtpp) cc_final: 0.8276 (ptmm)
REVERT: B  204 PHE cc_start: 0.8456 (m-80) cc_final: 0.8083 (m-80)
REVERT: B  267 MET cc_start: 0.6605 (tmm) cc_final: 0.5588 (mmp)
REVERT: B  367 GLU cc_start: 0.8449 (pp20) cc_final: 0.8177 (pp20)
REVERT: B  494 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8679 (pp)
REVERT: H   69 MET cc_start: 0.8611 (mtp) cc_final: 0.8373 (mtt)
REVERT: H  267 MET cc_start: 0.6315 (tmm) cc_final: 0.5342 (mmp)
REVERT: H  514 MET cc_start: 0.9160 (mtp) cc_final: 0.8884 (mtm)
REVERT: C   61 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8054 (pt0)
REVERT: C   69 MET cc_start: 0.8401 (mtp) cc_final: 0.8009 (ttm)
REVERT: C  267 MET cc_start: 0.6650 (tmm) cc_final: 0.6007 (mmp)
REVERT: C  322 ARG cc_start: 0.8918 (mtp-110) cc_final: 0.8708 (ttm110)
REVERT: C  367 GLU cc_start: 0.8416 (pp20) cc_final: 0.7997 (pp20)
REVERT: I  193 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8268 (ttm)
REVERT: I  204 PHE cc_start: 0.8439 (m-80) cc_final: 0.8233 (m-80)
REVERT: I  267 MET cc_start: 0.6433 (tmm) cc_final: 0.5882 (mmp)
REVERT: I  288 MET cc_start: 0.7822 (mmp) cc_final: 0.7605 (mmp)
REVERT: I  351 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8118 (pp30)
REVERT: I  494 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8816 (pp)
REVERT: I  514 MET cc_start: 0.9157 (ttm) cc_final: 0.8894 (mtp)
REVERT: D  267 MET cc_start: 0.6564 (tmm) cc_final: 0.5769 (mmp)
REVERT: D  321 LYS cc_start: 0.8778 (ttpt) cc_final: 0.8503 (mmmt)
REVERT: D  367 GLU cc_start: 0.8589 (pp20) cc_final: 0.8235 (pp20)
REVERT: J  204 PHE cc_start: 0.8326 (m-80) cc_final: 0.8015 (m-80)
REVERT: J  267 MET cc_start: 0.5615 (tmm) cc_final: 0.4921 (mmm)
REVERT: J  389 MET cc_start: 0.8303 (tmm) cc_final: 0.8072 (tmm)
REVERT: E  267 MET cc_start: 0.6439 (tmm) cc_final: 0.5840 (mmp)
REVERT: E  367 GLU cc_start: 0.8482 (pp20) cc_final: 0.8193 (pp20)
REVERT: E  389 MET cc_start: 0.7918 (tmm) cc_final: 0.7688 (tmm)
REVERT: E  447 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8918 (mtp)
REVERT: E  514 MET cc_start: 0.9108 (ttm) cc_final: 0.8741 (mtp)
REVERT: K  142 LYS cc_start: 0.8632 (tppt) cc_final: 0.8377 (ttpp)
REVERT: K  204 PHE cc_start: 0.8320 (m-80) cc_final: 0.7921 (m-80)
REVERT: K  267 MET cc_start: 0.6462 (tmm) cc_final: 0.5487 (mmp)
REVERT: F  102 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7241 (mp0)
REVERT: F  111 MET cc_start: 0.8974 (mtp) cc_final: 0.8656 (mtt)
REVERT: F  160 LYS cc_start: 0.8705 (mtpp) cc_final: 0.8394 (ptmm)
REVERT: F  234 LEU cc_start: 0.7909 (tp) cc_final: 0.7681 (tp)
REVERT: F  321 LYS cc_start: 0.8786 (mmtt) cc_final: 0.8381 (mmtp)
REVERT: F  367 GLU cc_start: 0.8366 (pp20) cc_final: 0.8160 (pp20)
REVERT: L   61 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8377 (tm-30)
REVERT: L   69 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8095 (mtp)
REVERT: L   76 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8599 (tm-30)
REVERT: L  267 MET cc_start: 0.6114 (tmm) cc_final: 0.5393 (mmm)
REVERT: L  288 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.6640 (mpp)
REVERT: L  351 GLN cc_start: 0.8215 (tp40) cc_final: 0.7966 (tp40)
REVERT: G   61 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.7905 (pt0)
REVERT: G  166 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.7968 (mtt)
REVERT: G  204 PHE cc_start: 0.8506 (m-80) cc_final: 0.8199 (m-80)
REVERT: G  267 MET cc_start: 0.6180 (tmm) cc_final: 0.5813 (mmp)
REVERT: G  367 GLU cc_start: 0.8477 (pp20) cc_final: 0.8178 (pp20)
REVERT: G  494 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8873 (pp)
REVERT: M   13 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7889 (mpt-90)
REVERT: M   76 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8727 (tm-30)
REVERT: M  267 MET cc_start: 0.6369 (tmm) cc_final: 0.5863 (mmm)
  outliers start: 148
  outliers final: 124
  residues processed: 603
  average time/residue: 0.5119
  time to fit residues: 548.2854
Evaluate side-chains
  601 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 138
    poor density    : 463
  time to evaluate  : 4.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  331 THR
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain N residue   11 ASP
Chi-restraints excluded: chain N residue   50 THR
Chi-restraints excluded: chain N residue  111 MET
Chi-restraints excluded: chain N residue  213 VAL
Chi-restraints excluded: chain N residue  234 LEU
Chi-restraints excluded: chain N residue  240 VAL
Chi-restraints excluded: chain N residue  494 LEU
Chi-restraints excluded: chain N residue  499 VAL
Chi-restraints excluded: chain N residue  517 THR
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  261 THR
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  307 MET
Chi-restraints excluded: chain B residue  331 THR
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  517 THR
Chi-restraints excluded: chain H residue   61 GLU
Chi-restraints excluded: chain H residue  213 VAL
Chi-restraints excluded: chain H residue  240 VAL
Chi-restraints excluded: chain H residue  300 VAL
Chi-restraints excluded: chain H residue  517 THR
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  174 VAL
Chi-restraints excluded: chain C residue  205 ILE
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  228 SER
Chi-restraints excluded: chain C residue  271 VAL
Chi-restraints excluded: chain C residue  300 VAL
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  331 THR
Chi-restraints excluded: chain C residue  517 THR
Chi-restraints excluded: chain I residue   61 GLU
Chi-restraints excluded: chain I residue  124 VAL
Chi-restraints excluded: chain I residue  146 GLN
Chi-restraints excluded: chain I residue  193 MET
Chi-restraints excluded: chain I residue  213 VAL
Chi-restraints excluded: chain I residue  240 VAL
Chi-restraints excluded: chain I residue  351 GLN
Chi-restraints excluded: chain I residue  442 VAL
Chi-restraints excluded: chain I residue  494 LEU
Chi-restraints excluded: chain I residue  499 VAL
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue   48 THR
Chi-restraints excluded: chain D residue   61 GLU
Chi-restraints excluded: chain D residue  124 VAL
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  205 ILE
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  240 VAL
Chi-restraints excluded: chain D residue  259 LEU
Chi-restraints excluded: chain D residue  331 THR
Chi-restraints excluded: chain D residue  351 GLN
Chi-restraints excluded: chain D residue  517 THR
Chi-restraints excluded: chain J residue   11 ASP
Chi-restraints excluded: chain J residue  146 GLN
Chi-restraints excluded: chain J residue  213 VAL
Chi-restraints excluded: chain J residue  273 VAL
Chi-restraints excluded: chain J residue  388 GLU
Chi-restraints excluded: chain J residue  433 ASN
Chi-restraints excluded: chain E residue   11 ASP
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   50 THR
Chi-restraints excluded: chain E residue  177 VAL
Chi-restraints excluded: chain E residue  205 ILE
Chi-restraints excluded: chain E residue  213 VAL
Chi-restraints excluded: chain E residue  240 VAL
Chi-restraints excluded: chain E residue  288 MET
Chi-restraints excluded: chain E residue  300 VAL
Chi-restraints excluded: chain E residue  331 THR
Chi-restraints excluded: chain E residue  447 MET
Chi-restraints excluded: chain E residue  517 THR
Chi-restraints excluded: chain K residue   43 SER
Chi-restraints excluded: chain K residue   62 LEU
Chi-restraints excluded: chain K residue  146 GLN
Chi-restraints excluded: chain K residue  213 VAL
Chi-restraints excluded: chain K residue  240 VAL
Chi-restraints excluded: chain K residue  273 VAL
Chi-restraints excluded: chain K residue  288 MET
Chi-restraints excluded: chain K residue  307 MET
Chi-restraints excluded: chain K residue  463 SER
Chi-restraints excluded: chain K residue  517 THR
Chi-restraints excluded: chain F residue   11 ASP
Chi-restraints excluded: chain F residue   48 THR
Chi-restraints excluded: chain F residue   50 THR
Chi-restraints excluded: chain F residue  124 VAL
Chi-restraints excluded: chain F residue  169 VAL
Chi-restraints excluded: chain F residue  193 MET
Chi-restraints excluded: chain F residue  213 VAL
Chi-restraints excluded: chain F residue  255 GLU
Chi-restraints excluded: chain F residue  270 ILE
Chi-restraints excluded: chain F residue  300 VAL
Chi-restraints excluded: chain F residue  331 THR
Chi-restraints excluded: chain F residue  351 GLN
Chi-restraints excluded: chain F residue  369 VAL
Chi-restraints excluded: chain F residue  463 SER
Chi-restraints excluded: chain F residue  494 LEU
Chi-restraints excluded: chain F residue  517 THR
Chi-restraints excluded: chain F residue  524 LEU
Chi-restraints excluded: chain L residue   50 THR
Chi-restraints excluded: chain L residue   69 MET
Chi-restraints excluded: chain L residue  124 VAL
Chi-restraints excluded: chain L residue  146 GLN
Chi-restraints excluded: chain L residue  213 VAL
Chi-restraints excluded: chain L residue  288 MET
Chi-restraints excluded: chain L residue  494 LEU
Chi-restraints excluded: chain L residue  517 THR
Chi-restraints excluded: chain G residue   11 ASP
Chi-restraints excluded: chain G residue   48 THR
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue  160 LYS
Chi-restraints excluded: chain G residue  166 MET
Chi-restraints excluded: chain G residue  169 VAL
Chi-restraints excluded: chain G residue  300 VAL
Chi-restraints excluded: chain G residue  307 MET
Chi-restraints excluded: chain G residue  494 LEU
Chi-restraints excluded: chain M residue   13 ARG
Chi-restraints excluded: chain M residue   61 GLU
Chi-restraints excluded: chain M residue  124 VAL
Chi-restraints excluded: chain M residue  146 GLN
Chi-restraints excluded: chain M residue  205 ILE
Chi-restraints excluded: chain M residue  442 VAL
Chi-restraints excluded: chain M residue  463 SER
Chi-restraints excluded: chain M residue  517 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 728
   random chunks:
   chunk 250 optimal weight:    1.9990
   chunk 138 optimal weight:    5.9990
   chunk 546 optimal weight:   30.0000
   chunk 389 optimal weight:   20.0000
   chunk 473 optimal weight:    0.9980
   chunk 477 optimal weight:    0.7980
   chunk 248 optimal weight:    5.9990
   chunk 725 optimal weight:    0.0770
   chunk 207 optimal weight:    7.9990
   chunk 34 optimal weight:    9.9990
   chunk 430 optimal weight:    0.9990
   overall best weight:    0.9742

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.151799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.111953 restraints weight = 68658.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 1.77
r_work: 0.3187 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.2426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  54362  Z= 0.155
  Angle     :  0.489  11.779  73402  Z= 0.254
  Chirality :  0.040   0.182   8932
  Planarity :  0.003   0.042   9618
  Dihedral  :  3.771  17.999   7728
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 16.00 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.10), residues: 7308
  helix:  2.33 (0.08), residues: 4088
  sheet:  0.65 (0.17), residues: 938
  loop : -0.41 (0.12), residues: 2282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.000   0.000   HIS N 401 
 PHE   0.007   0.001   PHE N 195 
 TYR   0.010   0.001   TYR C 476 
 ARG   0.004   0.000   ARG I 345 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 23076.01 seconds
wall clock time: 397 minutes 40.00 seconds (23860.00 seconds total)