Starting phenix.real_space_refine
on Sat Mar  7 05:22:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6yt5_10912/03_2026/6yt5_10912.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6yt5_10912/03_2026/6yt5_10912.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6yt5_10912/03_2026/6yt5_10912.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6yt5_10912/03_2026/6yt5_10912.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6yt5_10912/03_2026/6yt5_10912.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6yt5_10912/03_2026/6yt5_10912.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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     186      5.16       5
     C   24180      2.51       5
     N    6882      2.21       5
     O    7830      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 222 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 39078
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 642, 5116
          Classifications: {'peptide': 642}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 620}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "G"
      Number of atoms: 1397
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1397
          Classifications: {'peptide': 198}
          Incomplete info: {'truncation_to_alanine': 34}
          Link IDs: {'PTRANS': 8, 'TRANS': 189}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 127
          Unresolved non-hydrogen angles: 159
          Unresolved non-hydrogen dihedrals: 104
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 4, 'ASN:plan1': 3, 'PHE:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 63
  Restraints were copied for chains:
    B, C, D, E, F, H, I, J, K, L
  Time building chain proxies: 6.53, per 1000 atoms: 0.17
  Number of scatterers: 39078
  At special positions: 0
  Unit cell: (149.721, 147.627, 221.964, 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     186     16.00
     O    7830      8.00
     N    6882      7.00
     C   24180      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: 3.69
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  9960 Ramachandran restraints generated.
    4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  9432

  Finding SS restraints...
    Secondary structure from input PDB file:
      264 helices and 18 sheets defined
      68.2% alpha, 1.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 61 through 78
      removed outlier: 3.776A  pdb=" N   ASP A  68 " --> pdb=" O   ARG A  64 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 87
      removed outlier: 3.629A  pdb=" N   GLU A  85 " --> pdb=" O   GLU A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 127
      removed outlier: 3.636A  pdb=" N   ALA A 112 " --> pdb=" O   THR A 108 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ASP A 119 " --> pdb=" O   LEU A 115 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   LYS A 123 " --> pdb=" O   ASP A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 155
      removed outlier: 4.104A  pdb=" N   ALA A 151 " --> pdb=" O   ALA A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 167
    Processing helix  chain 'A' and resid 170 through 201
      removed outlier: 4.350A  pdb=" N   PHE A 185 " --> pdb=" O   ALA A 181 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   VAL A 200 " --> pdb=" O   MET A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 205
    Processing helix  chain 'A' and resid 216 through 231
    Processing helix  chain 'A' and resid 236 through 253
      removed outlier: 3.501A  pdb=" N   THR A 241 " --> pdb=" O   ASP A 237 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   GLN A 242 " --> pdb=" O   ALA A 238 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   SER A 249 " --> pdb=" O   SER A 245 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   SER A 253 " --> pdb=" O   SER A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 265
      removed outlier: 4.089A  pdb=" N   PHE A 260 " --> pdb=" O   GLY A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 282
      removed outlier: 3.756A  pdb=" N   ILE A 282 " --> pdb=" O   TYR A 278 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 278 through 282'
    Processing helix  chain 'A' and resid 283 through 297
    Processing helix  chain 'A' and resid 298 through 300
      No H-bonds generated for 'chain 'A' and resid 298 through 300'
    Processing helix  chain 'A' and resid 302 through 318
      removed outlier: 3.911A  pdb=" N   ASN A 306 " --> pdb=" O   ASP A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 337
      removed outlier: 3.575A  pdb=" N   TRP A 326 " --> pdb=" O   PRO A 322 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   GLU A 327 " --> pdb=" O   ARG A 323 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   MET A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ASP A 337 " --> pdb=" O   LYS A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 372
      removed outlier: 3.740A  pdb=" N   ILE A 353 " --> pdb=" O   ARG A 349 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   ASN A 361 " --> pdb=" O   GLU A 357 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ALA A 365 " --> pdb=" O   ASN A 361 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LYS A 368 " --> pdb=" O   ASN A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 396
      removed outlier: 4.306A  pdb=" N   LEU A 384 " --> pdb=" O   SER A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 407
      removed outlier: 4.044A  pdb=" N   MET A 407 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 434
      removed outlier: 3.509A  pdb=" N   VAL A 422 " --> pdb=" O   HIS A 418 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   TYR A 424 " --> pdb=" O   ASP A 420 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU A 429 " --> pdb=" O   ALA A 425 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER A 434 " --> pdb=" O   ALA A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 452
      removed outlier: 4.281A  pdb=" N   LYS A 448 " --> pdb=" O   ALA A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 481
    Processing helix  chain 'A' and resid 487 through 500
      removed outlier: 3.604A  pdb=" N   ASP A 491 " --> pdb=" O   THR A 487 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 508
      removed outlier: 4.145A  pdb=" N   ALA A 506 " --> pdb=" O   GLN A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 523
    Processing helix  chain 'A' and resid 528 through 540
      removed outlier: 4.139A  pdb=" N   ARG A 536 " --> pdb=" O   LEU A 532 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   LEU A 537 " --> pdb=" O   ASP A 533 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LYS A 540 " --> pdb=" O   ARG A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 558
      removed outlier: 3.940A  pdb=" N   PHE A 547 " --> pdb=" O   LYS A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 562 through 567
    Processing helix  chain 'A' and resid 569 through 587
      removed outlier: 3.832A  pdb=" N   ILE A 579 " --> pdb=" O   SER A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 604
    Processing helix  chain 'A' and resid 631 through 633
      No H-bonds generated for 'chain 'A' and resid 631 through 633'
    Processing helix  chain 'A' and resid 634 through 651
      removed outlier: 3.706A  pdb=" N   ILE A 641 " --> pdb=" O   GLN A 637 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   LEU A 642 " --> pdb=" O   GLY A 638 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LYS A 647 " --> pdb=" O   GLU A 643 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 684 through 697
    Processing helix  chain 'B' and resid 61 through 78
      removed outlier: 3.775A  pdb=" N   ASP B  68 " --> pdb=" O   ARG B  64 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU B  78 " --> pdb=" O   ILE B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 87
      removed outlier: 3.629A  pdb=" N   GLU B  85 " --> pdb=" O   GLU B  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 127
      removed outlier: 3.636A  pdb=" N   ALA B 112 " --> pdb=" O   THR B 108 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ASP B 119 " --> pdb=" O   LEU B 115 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   LYS B 123 " --> pdb=" O   ASP B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 155
      removed outlier: 4.104A  pdb=" N   ALA B 151 " --> pdb=" O   ALA B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 167
    Processing helix  chain 'B' and resid 170 through 201
      removed outlier: 4.350A  pdb=" N   PHE B 185 " --> pdb=" O   ALA B 181 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   VAL B 200 " --> pdb=" O   MET B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 205
    Processing helix  chain 'B' and resid 216 through 231
    Processing helix  chain 'B' and resid 236 through 253
      removed outlier: 3.501A  pdb=" N   THR B 241 " --> pdb=" O   ASP B 237 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   GLN B 242 " --> pdb=" O   ALA B 238 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   SER B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   SER B 253 " --> pdb=" O   SER B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 265
      removed outlier: 4.089A  pdb=" N   PHE B 260 " --> pdb=" O   GLY B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 278 through 282
      removed outlier: 3.755A  pdb=" N   ILE B 282 " --> pdb=" O   TYR B 278 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 278 through 282'
    Processing helix  chain 'B' and resid 283 through 297
    Processing helix  chain 'B' and resid 298 through 300
      No H-bonds generated for 'chain 'B' and resid 298 through 300'
    Processing helix  chain 'B' and resid 302 through 318
      removed outlier: 3.910A  pdb=" N   ASN B 306 " --> pdb=" O   ASP B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 321 through 337
      removed outlier: 3.575A  pdb=" N   TRP B 326 " --> pdb=" O   PRO B 322 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   GLU B 327 " --> pdb=" O   ARG B 323 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   MET B 328 " --> pdb=" O   THR B 324 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ASP B 337 " --> pdb=" O   LYS B 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 372
      removed outlier: 3.741A  pdb=" N   ILE B 353 " --> pdb=" O   ARG B 349 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   ASN B 361 " --> pdb=" O   GLU B 357 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ALA B 365 " --> pdb=" O   ASN B 361 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LYS B 368 " --> pdb=" O   ASN B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 378 through 396
      removed outlier: 4.305A  pdb=" N   LEU B 384 " --> pdb=" O   SER B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 407
      removed outlier: 4.044A  pdb=" N   MET B 407 " --> pdb=" O   PHE B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 418 through 434
      removed outlier: 3.509A  pdb=" N   VAL B 422 " --> pdb=" O   HIS B 418 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   TYR B 424 " --> pdb=" O   ASP B 420 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU B 429 " --> pdb=" O   ALA B 425 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER B 434 " --> pdb=" O   ALA B 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 442 through 452
      removed outlier: 4.280A  pdb=" N   LYS B 448 " --> pdb=" O   ALA B 444 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 463 through 481
    Processing helix  chain 'B' and resid 487 through 500
      removed outlier: 3.604A  pdb=" N   ASP B 491 " --> pdb=" O   THR B 487 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 500 through 508
      removed outlier: 4.146A  pdb=" N   ALA B 506 " --> pdb=" O   GLN B 502 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 510 through 523
    Processing helix  chain 'B' and resid 528 through 540
      removed outlier: 4.139A  pdb=" N   ARG B 536 " --> pdb=" O   LEU B 532 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   LEU B 537 " --> pdb=" O   ASP B 533 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LYS B 540 " --> pdb=" O   ARG B 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 542 through 558
      removed outlier: 3.940A  pdb=" N   PHE B 547 " --> pdb=" O   LYS B 543 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 562 through 567
    Processing helix  chain 'B' and resid 569 through 587
      removed outlier: 3.833A  pdb=" N   ILE B 579 " --> pdb=" O   SER B 575 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 591 through 604
    Processing helix  chain 'B' and resid 631 through 633
      No H-bonds generated for 'chain 'B' and resid 631 through 633'
    Processing helix  chain 'B' and resid 634 through 651
      removed outlier: 3.706A  pdb=" N   ILE B 641 " --> pdb=" O   GLN B 637 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   LEU B 642 " --> pdb=" O   GLY B 638 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LYS B 647 " --> pdb=" O   GLU B 643 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 684 through 697
    Processing helix  chain 'C' and resid 61 through 78
      removed outlier: 3.776A  pdb=" N   ASP C  68 " --> pdb=" O   ARG C  64 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU C  78 " --> pdb=" O   ILE C  74 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 81 through 87
      removed outlier: 3.629A  pdb=" N   GLU C  85 " --> pdb=" O   GLU C  81 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 97 through 127
      removed outlier: 3.636A  pdb=" N   ALA C 112 " --> pdb=" O   THR C 108 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ASP C 119 " --> pdb=" O   LEU C 115 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   LYS C 123 " --> pdb=" O   ASP C 119 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 132 through 155
      removed outlier: 4.104A  pdb=" N   ALA C 151 " --> pdb=" O   ALA C 147 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 162 through 167
    Processing helix  chain 'C' and resid 170 through 201
      removed outlier: 4.350A  pdb=" N   PHE C 185 " --> pdb=" O   ALA C 181 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   VAL C 200 " --> pdb=" O   MET C 196 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 205
    Processing helix  chain 'C' and resid 216 through 231
    Processing helix  chain 'C' and resid 236 through 253
      removed outlier: 3.500A  pdb=" N   THR C 241 " --> pdb=" O   ASP C 237 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   GLN C 242 " --> pdb=" O   ALA C 238 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   SER C 249 " --> pdb=" O   SER C 245 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   SER C 253 " --> pdb=" O   SER C 249 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 256 through 265
      removed outlier: 4.089A  pdb=" N   PHE C 260 " --> pdb=" O   GLY C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 278 through 282
      removed outlier: 3.755A  pdb=" N   ILE C 282 " --> pdb=" O   TYR C 278 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 278 through 282'
    Processing helix  chain 'C' and resid 283 through 297
    Processing helix  chain 'C' and resid 298 through 300
      No H-bonds generated for 'chain 'C' and resid 298 through 300'
    Processing helix  chain 'C' and resid 302 through 318
      removed outlier: 3.910A  pdb=" N   ASN C 306 " --> pdb=" O   ASP C 302 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 321 through 337
      removed outlier: 3.575A  pdb=" N   TRP C 326 " --> pdb=" O   PRO C 322 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   GLU C 327 " --> pdb=" O   ARG C 323 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   MET C 328 " --> pdb=" O   THR C 324 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ASP C 337 " --> pdb=" O   LYS C 333 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 347 through 372
      removed outlier: 3.741A  pdb=" N   ILE C 353 " --> pdb=" O   ARG C 349 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   ASN C 361 " --> pdb=" O   GLU C 357 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ALA C 365 " --> pdb=" O   ASN C 361 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LYS C 368 " --> pdb=" O   ASN C 364 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 378 through 396
      removed outlier: 4.305A  pdb=" N   LEU C 384 " --> pdb=" O   SER C 380 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 403 through 407
      removed outlier: 4.044A  pdb=" N   MET C 407 " --> pdb=" O   PHE C 404 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 418 through 434
      removed outlier: 3.510A  pdb=" N   VAL C 422 " --> pdb=" O   HIS C 418 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   TYR C 424 " --> pdb=" O   ASP C 420 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU C 429 " --> pdb=" O   ALA C 425 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER C 434 " --> pdb=" O   ALA C 430 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 442 through 452
      removed outlier: 4.280A  pdb=" N   LYS C 448 " --> pdb=" O   ALA C 444 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 463 through 481
    Processing helix  chain 'C' and resid 487 through 500
      removed outlier: 3.604A  pdb=" N   ASP C 491 " --> pdb=" O   THR C 487 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 500 through 508
      removed outlier: 4.146A  pdb=" N   ALA C 506 " --> pdb=" O   GLN C 502 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 510 through 523
    Processing helix  chain 'C' and resid 528 through 540
      removed outlier: 4.139A  pdb=" N   ARG C 536 " --> pdb=" O   LEU C 532 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   LEU C 537 " --> pdb=" O   ASP C 533 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LYS C 540 " --> pdb=" O   ARG C 536 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 542 through 558
      removed outlier: 3.939A  pdb=" N   PHE C 547 " --> pdb=" O   LYS C 543 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 562 through 567
    Processing helix  chain 'C' and resid 569 through 587
      removed outlier: 3.832A  pdb=" N   ILE C 579 " --> pdb=" O   SER C 575 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 591 through 604
    Processing helix  chain 'C' and resid 631 through 633
      No H-bonds generated for 'chain 'C' and resid 631 through 633'
    Processing helix  chain 'C' and resid 634 through 651
      removed outlier: 3.706A  pdb=" N   ILE C 641 " --> pdb=" O   GLN C 637 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   LEU C 642 " --> pdb=" O   GLY C 638 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LYS C 647 " --> pdb=" O   GLU C 643 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 684 through 697
    Processing helix  chain 'D' and resid 61 through 78
      removed outlier: 3.776A  pdb=" N   ASP D  68 " --> pdb=" O   ARG D  64 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU D  78 " --> pdb=" O   ILE D  74 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 81 through 87
      removed outlier: 3.629A  pdb=" N   GLU D  85 " --> pdb=" O   GLU D  81 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 97 through 127
      removed outlier: 3.636A  pdb=" N   ALA D 112 " --> pdb=" O   THR D 108 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ASP D 119 " --> pdb=" O   LEU D 115 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   LYS D 123 " --> pdb=" O   ASP D 119 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 132 through 155
      removed outlier: 4.104A  pdb=" N   ALA D 151 " --> pdb=" O   ALA D 147 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 162 through 167
    Processing helix  chain 'D' and resid 170 through 201
      removed outlier: 4.350A  pdb=" N   PHE D 185 " --> pdb=" O   ALA D 181 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   VAL D 200 " --> pdb=" O   MET D 196 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 202 through 205
    Processing helix  chain 'D' and resid 216 through 231
    Processing helix  chain 'D' and resid 236 through 253
      removed outlier: 3.501A  pdb=" N   THR D 241 " --> pdb=" O   ASP D 237 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   GLN D 242 " --> pdb=" O   ALA D 238 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   SER D 249 " --> pdb=" O   SER D 245 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   SER D 253 " --> pdb=" O   SER D 249 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 256 through 265
      removed outlier: 4.089A  pdb=" N   PHE D 260 " --> pdb=" O   GLY D 256 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 278 through 282
      removed outlier: 3.756A  pdb=" N   ILE D 282 " --> pdb=" O   TYR D 278 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 278 through 282'
    Processing helix  chain 'D' and resid 283 through 297
    Processing helix  chain 'D' and resid 298 through 300
      No H-bonds generated for 'chain 'D' and resid 298 through 300'
    Processing helix  chain 'D' and resid 302 through 318
      removed outlier: 3.911A  pdb=" N   ASN D 306 " --> pdb=" O   ASP D 302 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 321 through 337
      removed outlier: 3.575A  pdb=" N   TRP D 326 " --> pdb=" O   PRO D 322 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   GLU D 327 " --> pdb=" O   ARG D 323 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   MET D 328 " --> pdb=" O   THR D 324 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ASP D 337 " --> pdb=" O   LYS D 333 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 347 through 372
      removed outlier: 3.740A  pdb=" N   ILE D 353 " --> pdb=" O   ARG D 349 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   ASN D 361 " --> pdb=" O   GLU D 357 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ALA D 365 " --> pdb=" O   ASN D 361 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LYS D 368 " --> pdb=" O   ASN D 364 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 378 through 396
      removed outlier: 4.306A  pdb=" N   LEU D 384 " --> pdb=" O   SER D 380 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 403 through 407
      removed outlier: 4.044A  pdb=" N   MET D 407 " --> pdb=" O   PHE D 404 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 418 through 434
      removed outlier: 3.509A  pdb=" N   VAL D 422 " --> pdb=" O   HIS D 418 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   TYR D 424 " --> pdb=" O   ASP D 420 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU D 429 " --> pdb=" O   ALA D 425 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER D 434 " --> pdb=" O   ALA D 430 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 442 through 452
      removed outlier: 4.281A  pdb=" N   LYS D 448 " --> pdb=" O   ALA D 444 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 463 through 481
    Processing helix  chain 'D' and resid 487 through 500
      removed outlier: 3.604A  pdb=" N   ASP D 491 " --> pdb=" O   THR D 487 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 500 through 508
      removed outlier: 4.145A  pdb=" N   ALA D 506 " --> pdb=" O   GLN D 502 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 510 through 523
    Processing helix  chain 'D' and resid 528 through 540
      removed outlier: 4.139A  pdb=" N   ARG D 536 " --> pdb=" O   LEU D 532 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   LEU D 537 " --> pdb=" O   ASP D 533 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LYS D 540 " --> pdb=" O   ARG D 536 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 542 through 558
      removed outlier: 3.940A  pdb=" N   PHE D 547 " --> pdb=" O   LYS D 543 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 562 through 567
    Processing helix  chain 'D' and resid 569 through 587
      removed outlier: 3.832A  pdb=" N   ILE D 579 " --> pdb=" O   SER D 575 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 591 through 604
    Processing helix  chain 'D' and resid 631 through 633
      No H-bonds generated for 'chain 'D' and resid 631 through 633'
    Processing helix  chain 'D' and resid 634 through 651
      removed outlier: 3.706A  pdb=" N   ILE D 641 " --> pdb=" O   GLN D 637 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   LEU D 642 " --> pdb=" O   GLY D 638 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LYS D 647 " --> pdb=" O   GLU D 643 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 684 through 697
    Processing helix  chain 'E' and resid 61 through 78
      removed outlier: 3.776A  pdb=" N   ASP E  68 " --> pdb=" O   ARG E  64 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 81 through 87
      removed outlier: 3.628A  pdb=" N   GLU E  85 " --> pdb=" O   GLU E  81 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 97 through 127
      removed outlier: 3.636A  pdb=" N   ALA E 112 " --> pdb=" O   THR E 108 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ASP E 119 " --> pdb=" O   LEU E 115 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   LYS E 123 " --> pdb=" O   ASP E 119 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 132 through 155
      removed outlier: 4.105A  pdb=" N   ALA E 151 " --> pdb=" O   ALA E 147 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 162 through 167
    Processing helix  chain 'E' and resid 170 through 201
      removed outlier: 4.350A  pdb=" N   PHE E 185 " --> pdb=" O   ALA E 181 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   VAL E 200 " --> pdb=" O   MET E 196 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 202 through 205
    Processing helix  chain 'E' and resid 216 through 231
    Processing helix  chain 'E' and resid 236 through 253
      removed outlier: 3.501A  pdb=" N   THR E 241 " --> pdb=" O   ASP E 237 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   GLN E 242 " --> pdb=" O   ALA E 238 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   SER E 249 " --> pdb=" O   SER E 245 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   SER E 253 " --> pdb=" O   SER E 249 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 256 through 265
      removed outlier: 4.090A  pdb=" N   PHE E 260 " --> pdb=" O   GLY E 256 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 278 through 282
      removed outlier: 3.755A  pdb=" N   ILE E 282 " --> pdb=" O   TYR E 278 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 278 through 282'
    Processing helix  chain 'E' and resid 283 through 297
    Processing helix  chain 'E' and resid 298 through 300
      No H-bonds generated for 'chain 'E' and resid 298 through 300'
    Processing helix  chain 'E' and resid 302 through 318
      removed outlier: 3.910A  pdb=" N   ASN E 306 " --> pdb=" O   ASP E 302 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 321 through 337
      removed outlier: 3.575A  pdb=" N   TRP E 326 " --> pdb=" O   PRO E 322 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   GLU E 327 " --> pdb=" O   ARG E 323 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   MET E 328 " --> pdb=" O   THR E 324 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ASP E 337 " --> pdb=" O   LYS E 333 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 347 through 372
      removed outlier: 3.741A  pdb=" N   ILE E 353 " --> pdb=" O   ARG E 349 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   ASN E 361 " --> pdb=" O   GLU E 357 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ALA E 365 " --> pdb=" O   ASN E 361 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LYS E 368 " --> pdb=" O   ASN E 364 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 378 through 396
      removed outlier: 4.306A  pdb=" N   LEU E 384 " --> pdb=" O   SER E 380 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 403 through 407
      removed outlier: 4.044A  pdb=" N   MET E 407 " --> pdb=" O   PHE E 404 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 418 through 434
      removed outlier: 3.509A  pdb=" N   VAL E 422 " --> pdb=" O   HIS E 418 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   TYR E 424 " --> pdb=" O   ASP E 420 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU E 429 " --> pdb=" O   ALA E 425 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER E 434 " --> pdb=" O   ALA E 430 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 442 through 452
      removed outlier: 4.281A  pdb=" N   LYS E 448 " --> pdb=" O   ALA E 444 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 463 through 481
    Processing helix  chain 'E' and resid 487 through 500
      removed outlier: 3.604A  pdb=" N   ASP E 491 " --> pdb=" O   THR E 487 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 500 through 508
      removed outlier: 4.145A  pdb=" N   ALA E 506 " --> pdb=" O   GLN E 502 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 510 through 523
    Processing helix  chain 'E' and resid 528 through 540
      removed outlier: 4.139A  pdb=" N   ARG E 536 " --> pdb=" O   LEU E 532 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   LEU E 537 " --> pdb=" O   ASP E 533 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LYS E 540 " --> pdb=" O   ARG E 536 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 542 through 558
      removed outlier: 3.940A  pdb=" N   PHE E 547 " --> pdb=" O   LYS E 543 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 562 through 567
    Processing helix  chain 'E' and resid 569 through 587
      removed outlier: 3.832A  pdb=" N   ILE E 579 " --> pdb=" O   SER E 575 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 591 through 604
    Processing helix  chain 'E' and resid 631 through 633
      No H-bonds generated for 'chain 'E' and resid 631 through 633'
    Processing helix  chain 'E' and resid 634 through 651
      removed outlier: 3.706A  pdb=" N   ILE E 641 " --> pdb=" O   GLN E 637 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   LEU E 642 " --> pdb=" O   GLY E 638 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LYS E 647 " --> pdb=" O   GLU E 643 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 684 through 697
    Processing helix  chain 'F' and resid 61 through 78
      removed outlier: 3.776A  pdb=" N   ASP F  68 " --> pdb=" O   ARG F  64 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU F  78 " --> pdb=" O   ILE F  74 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 81 through 87
      removed outlier: 3.628A  pdb=" N   GLU F  85 " --> pdb=" O   GLU F  81 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 97 through 127
      removed outlier: 3.636A  pdb=" N   ALA F 112 " --> pdb=" O   THR F 108 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ASP F 119 " --> pdb=" O   LEU F 115 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   LYS F 123 " --> pdb=" O   ASP F 119 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 132 through 155
      removed outlier: 4.104A  pdb=" N   ALA F 151 " --> pdb=" O   ALA F 147 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 162 through 167
    Processing helix  chain 'F' and resid 170 through 201
      removed outlier: 4.351A  pdb=" N   PHE F 185 " --> pdb=" O   ALA F 181 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   VAL F 200 " --> pdb=" O   MET F 196 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 202 through 205
    Processing helix  chain 'F' and resid 216 through 231
    Processing helix  chain 'F' and resid 236 through 253
      removed outlier: 3.501A  pdb=" N   THR F 241 " --> pdb=" O   ASP F 237 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   GLN F 242 " --> pdb=" O   ALA F 238 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   SER F 249 " --> pdb=" O   SER F 245 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   SER F 253 " --> pdb=" O   SER F 249 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 256 through 265
      removed outlier: 4.088A  pdb=" N   PHE F 260 " --> pdb=" O   GLY F 256 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 278 through 282
      removed outlier: 3.756A  pdb=" N   ILE F 282 " --> pdb=" O   TYR F 278 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 278 through 282'
    Processing helix  chain 'F' and resid 283 through 297
    Processing helix  chain 'F' and resid 298 through 300
      No H-bonds generated for 'chain 'F' and resid 298 through 300'
    Processing helix  chain 'F' and resid 302 through 318
      removed outlier: 3.910A  pdb=" N   ASN F 306 " --> pdb=" O   ASP F 302 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 321 through 337
      removed outlier: 3.576A  pdb=" N   TRP F 326 " --> pdb=" O   PRO F 322 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   GLU F 327 " --> pdb=" O   ARG F 323 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   MET F 328 " --> pdb=" O   THR F 324 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ASP F 337 " --> pdb=" O   LYS F 333 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 347 through 372
      removed outlier: 3.741A  pdb=" N   ILE F 353 " --> pdb=" O   ARG F 349 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   ASN F 361 " --> pdb=" O   GLU F 357 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ALA F 365 " --> pdb=" O   ASN F 361 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LYS F 368 " --> pdb=" O   ASN F 364 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 378 through 396
      removed outlier: 4.305A  pdb=" N   LEU F 384 " --> pdb=" O   SER F 380 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 403 through 407
      removed outlier: 4.043A  pdb=" N   MET F 407 " --> pdb=" O   PHE F 404 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 418 through 434
      removed outlier: 3.510A  pdb=" N   VAL F 422 " --> pdb=" O   HIS F 418 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   TYR F 424 " --> pdb=" O   ASP F 420 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU F 429 " --> pdb=" O   ALA F 425 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER F 434 " --> pdb=" O   ALA F 430 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 442 through 452
      removed outlier: 4.280A  pdb=" N   LYS F 448 " --> pdb=" O   ALA F 444 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 463 through 481
    Processing helix  chain 'F' and resid 487 through 500
      removed outlier: 3.604A  pdb=" N   ASP F 491 " --> pdb=" O   THR F 487 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 500 through 508
      removed outlier: 4.145A  pdb=" N   ALA F 506 " --> pdb=" O   GLN F 502 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 510 through 523
    Processing helix  chain 'F' and resid 528 through 540
      removed outlier: 4.139A  pdb=" N   ARG F 536 " --> pdb=" O   LEU F 532 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   LEU F 537 " --> pdb=" O   ASP F 533 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LYS F 540 " --> pdb=" O   ARG F 536 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 542 through 558
      removed outlier: 3.940A  pdb=" N   PHE F 547 " --> pdb=" O   LYS F 543 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 562 through 567
    Processing helix  chain 'F' and resid 569 through 587
      removed outlier: 3.832A  pdb=" N   ILE F 579 " --> pdb=" O   SER F 575 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 591 through 604
    Processing helix  chain 'F' and resid 631 through 633
      No H-bonds generated for 'chain 'F' and resid 631 through 633'
    Processing helix  chain 'F' and resid 634 through 651
      removed outlier: 3.705A  pdb=" N   ILE F 641 " --> pdb=" O   GLN F 637 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   LEU F 642 " --> pdb=" O   GLY F 638 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LYS F 647 " --> pdb=" O   GLU F 643 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 684 through 697
    Processing helix  chain 'G' and resid 11 through 21
      removed outlier: 3.780A  pdb=" N   LYS G  18 " --> pdb=" O   GLY G  14 " (cutoff:3.500A)
      removed outlier: 5.034A  pdb=" N   ALA G  19 " --> pdb=" O   LEU G  15 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 26 through 38
      removed outlier: 3.605A  pdb=" N   ALA G  34 " --> pdb=" O   LEU G  30 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   TRP G  35 " --> pdb=" O   ARG G  31 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   GLU G  37 " --> pdb=" O   VAL G  33 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 58 through 66
    Processing helix  chain 'G' and resid 81 through 94
    Processing helix  chain 'G' and resid 100 through 110
      removed outlier: 3.754A  pdb=" N   ASN G 109 " --> pdb=" O   ALA G 105 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 116 through 124
      removed outlier: 3.619A  pdb=" N   ALA G 122 " --> pdb=" O   PRO G 118 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   SER G 124 " --> pdb=" O   LEU G 120 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 127 through 131
      removed outlier: 3.563A  pdb=" N   ILE G 131 " --> pdb=" O   PHE G 128 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 134 through 143
      removed outlier: 3.585A  pdb=" N   ASN G 141 " --> pdb=" O   ASN G 137 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 150 through 155
    Processing helix  chain 'G' and resid 168 through 173
      removed outlier: 3.541A  pdb=" N   GLY G 172 " --> pdb=" O   PRO G 168 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 205 through 215
    Processing helix  chain 'G' and resid 217 through 223
    Processing helix  chain 'H' and resid 11 through 21
      removed outlier: 3.781A  pdb=" N   LYS H  18 " --> pdb=" O   GLY H  14 " (cutoff:3.500A)
      removed outlier: 5.034A  pdb=" N   ALA H  19 " --> pdb=" O   LEU H  15 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 26 through 38
      removed outlier: 3.604A  pdb=" N   ALA H  34 " --> pdb=" O   LEU H  30 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   TRP H  35 " --> pdb=" O   ARG H  31 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   GLU H  37 " --> pdb=" O   VAL H  33 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 58 through 66
    Processing helix  chain 'H' and resid 81 through 94
    Processing helix  chain 'H' and resid 100 through 110
      removed outlier: 3.755A  pdb=" N   ASN H 109 " --> pdb=" O   ALA H 105 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 116 through 124
      removed outlier: 3.619A  pdb=" N   ALA H 122 " --> pdb=" O   PRO H 118 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   SER H 124 " --> pdb=" O   LEU H 120 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 127 through 131
      removed outlier: 3.563A  pdb=" N   ILE H 131 " --> pdb=" O   PHE H 128 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 134 through 143
      removed outlier: 3.586A  pdb=" N   ASN H 141 " --> pdb=" O   ASN H 137 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 150 through 155
    Processing helix  chain 'H' and resid 168 through 173
      removed outlier: 3.540A  pdb=" N   GLY H 172 " --> pdb=" O   PRO H 168 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 205 through 215
    Processing helix  chain 'H' and resid 217 through 223
    Processing helix  chain 'I' and resid 11 through 21
      removed outlier: 3.780A  pdb=" N   LYS I  18 " --> pdb=" O   GLY I  14 " (cutoff:3.500A)
      removed outlier: 5.034A  pdb=" N   ALA I  19 " --> pdb=" O   LEU I  15 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 26 through 38
      removed outlier: 3.605A  pdb=" N   ALA I  34 " --> pdb=" O   LEU I  30 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   TRP I  35 " --> pdb=" O   ARG I  31 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   GLU I  37 " --> pdb=" O   VAL I  33 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 58 through 66
    Processing helix  chain 'I' and resid 81 through 94
    Processing helix  chain 'I' and resid 100 through 110
      removed outlier: 3.754A  pdb=" N   ASN I 109 " --> pdb=" O   ALA I 105 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 116 through 124
      removed outlier: 3.619A  pdb=" N   ALA I 122 " --> pdb=" O   PRO I 118 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   SER I 124 " --> pdb=" O   LEU I 120 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 127 through 131
      removed outlier: 3.563A  pdb=" N   ILE I 131 " --> pdb=" O   PHE I 128 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 134 through 143
      removed outlier: 3.585A  pdb=" N   ASN I 141 " --> pdb=" O   ASN I 137 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 150 through 155
    Processing helix  chain 'I' and resid 168 through 173
      removed outlier: 3.542A  pdb=" N   GLY I 172 " --> pdb=" O   PRO I 168 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 205 through 215
    Processing helix  chain 'I' and resid 217 through 223
    Processing helix  chain 'J' and resid 11 through 21
      removed outlier: 3.781A  pdb=" N   LYS J  18 " --> pdb=" O   GLY J  14 " (cutoff:3.500A)
      removed outlier: 5.034A  pdb=" N   ALA J  19 " --> pdb=" O   LEU J  15 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 26 through 38
      removed outlier: 3.604A  pdb=" N   ALA J  34 " --> pdb=" O   LEU J  30 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   TRP J  35 " --> pdb=" O   ARG J  31 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   GLU J  37 " --> pdb=" O   VAL J  33 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 58 through 66
    Processing helix  chain 'J' and resid 81 through 94
    Processing helix  chain 'J' and resid 100 through 110
      removed outlier: 3.754A  pdb=" N   ASN J 109 " --> pdb=" O   ALA J 105 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 116 through 124
      removed outlier: 3.620A  pdb=" N   ALA J 122 " --> pdb=" O   PRO J 118 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   SER J 124 " --> pdb=" O   LEU J 120 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 127 through 131
      removed outlier: 3.564A  pdb=" N   ILE J 131 " --> pdb=" O   PHE J 128 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 134 through 143
      removed outlier: 3.585A  pdb=" N   ASN J 141 " --> pdb=" O   ASN J 137 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 150 through 155
    Processing helix  chain 'J' and resid 168 through 173
      removed outlier: 3.541A  pdb=" N   GLY J 172 " --> pdb=" O   PRO J 168 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 205 through 215
    Processing helix  chain 'J' and resid 217 through 223
    Processing helix  chain 'K' and resid 11 through 21
      removed outlier: 3.780A  pdb=" N   LYS K  18 " --> pdb=" O   GLY K  14 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   ALA K  19 " --> pdb=" O   LEU K  15 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 26 through 38
      removed outlier: 3.605A  pdb=" N   ALA K  34 " --> pdb=" O   LEU K  30 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   TRP K  35 " --> pdb=" O   ARG K  31 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   GLU K  37 " --> pdb=" O   VAL K  33 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 58 through 66
    Processing helix  chain 'K' and resid 81 through 94
    Processing helix  chain 'K' and resid 100 through 110
      removed outlier: 3.753A  pdb=" N   ASN K 109 " --> pdb=" O   ALA K 105 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 116 through 124
      removed outlier: 3.620A  pdb=" N   ALA K 122 " --> pdb=" O   PRO K 118 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   SER K 124 " --> pdb=" O   LEU K 120 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 127 through 131
      removed outlier: 3.564A  pdb=" N   ILE K 131 " --> pdb=" O   PHE K 128 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 134 through 143
      removed outlier: 3.585A  pdb=" N   ASN K 141 " --> pdb=" O   ASN K 137 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 150 through 155
    Processing helix  chain 'K' and resid 168 through 173
      removed outlier: 3.541A  pdb=" N   GLY K 172 " --> pdb=" O   PRO K 168 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 205 through 215
    Processing helix  chain 'K' and resid 217 through 223
    Processing helix  chain 'L' and resid 11 through 21
      removed outlier: 3.781A  pdb=" N   LYS L  18 " --> pdb=" O   GLY L  14 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   ALA L  19 " --> pdb=" O   LEU L  15 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 26 through 38
      removed outlier: 3.605A  pdb=" N   ALA L  34 " --> pdb=" O   LEU L  30 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   TRP L  35 " --> pdb=" O   ARG L  31 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   GLU L  37 " --> pdb=" O   VAL L  33 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 58 through 66
    Processing helix  chain 'L' and resid 81 through 94
    Processing helix  chain 'L' and resid 100 through 110
      removed outlier: 3.753A  pdb=" N   ASN L 109 " --> pdb=" O   ALA L 105 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 116 through 124
      removed outlier: 3.619A  pdb=" N   ALA L 122 " --> pdb=" O   PRO L 118 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   SER L 124 " --> pdb=" O   LEU L 120 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 127 through 131
      removed outlier: 3.563A  pdb=" N   ILE L 131 " --> pdb=" O   PHE L 128 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 134 through 143
      removed outlier: 3.585A  pdb=" N   ASN L 141 " --> pdb=" O   ASN L 137 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 150 through 155
    Processing helix  chain 'L' and resid 168 through 173
      removed outlier: 3.541A  pdb=" N   GLY L 172 " --> pdb=" O   PRO L 168 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 205 through 215
    Processing helix  chain 'L' and resid 217 through 223
    Processing sheet with id=AA1, first strand: chain 'A' and resid 268 through 271
    Processing sheet with id=AA2, first strand: chain 'A' and resid 605 through 607
    Processing sheet with id=AA3, first strand: chain 'A' and resid 670 through 671
    Processing sheet with id=AA4, first strand: chain 'B' and resid 268 through 271
    Processing sheet with id=AA5, first strand: chain 'B' and resid 605 through 607
    Processing sheet with id=AA6, first strand: chain 'B' and resid 670 through 671
    Processing sheet with id=AA7, first strand: chain 'C' and resid 268 through 271
    Processing sheet with id=AA8, first strand: chain 'C' and resid 605 through 607
    Processing sheet with id=AA9, first strand: chain 'C' and resid 670 through 671
    Processing sheet with id=AB1, first strand: chain 'D' and resid 268 through 271
    Processing sheet with id=AB2, first strand: chain 'D' and resid 605 through 607
    Processing sheet with id=AB3, first strand: chain 'D' and resid 670 through 671
    Processing sheet with id=AB4, first strand: chain 'E' and resid 268 through 271
    Processing sheet with id=AB5, first strand: chain 'E' and resid 605 through 607
    Processing sheet with id=AB6, first strand: chain 'E' and resid 670 through 671
    Processing sheet with id=AB7, first strand: chain 'F' and resid 268 through 271
    Processing sheet with id=AB8, first strand: chain 'F' and resid 605 through 607
    Processing sheet with id=AB9, first strand: chain 'F' and resid 670 through 671

    2148 hydrogen bonds defined for protein.
    6354 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: 7.34

  Time building geometry restraints manager: 4.89 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 13456
        1.34 -     1.45: 4938
        1.45 -     1.57: 20912
        1.57 -     1.69: 0
        1.69 -     1.81: 372
  Bond restraints: 39678
  Sorted by residual:
  bond pdb=" CB  TRP C 326 "
       pdb=" CG  TRP C 326 "
    ideal  model  delta    sigma   weight residual
    1.498  1.432  0.066 3.10e-02 1.04e+03 4.52e+00
  bond pdb=" CB  TRP D 326 "
       pdb=" CG  TRP D 326 "
    ideal  model  delta    sigma   weight residual
    1.498  1.432  0.066 3.10e-02 1.04e+03 4.50e+00
  bond pdb=" CB  TRP A 326 "
       pdb=" CG  TRP A 326 "
    ideal  model  delta    sigma   weight residual
    1.498  1.432  0.066 3.10e-02 1.04e+03 4.50e+00
  bond pdb=" CB  TRP F 326 "
       pdb=" CG  TRP F 326 "
    ideal  model  delta    sigma   weight residual
    1.498  1.432  0.066 3.10e-02 1.04e+03 4.47e+00
  bond pdb=" CB  TRP E 326 "
       pdb=" CG  TRP E 326 "
    ideal  model  delta    sigma   weight residual
    1.498  1.433  0.065 3.10e-02 1.04e+03 4.44e+00
  ... (remaining 39673 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 52080
        1.95 -     3.90: 1292
        3.90 -     5.84: 118
        5.84 -     7.79: 0
        7.79 -     9.74: 6
  Bond angle restraints: 53496
  Sorted by residual:
  angle pdb=" CA  LYS E 584 "
        pdb=" CB  LYS E 584 "
        pdb=" CG  LYS E 584 "
      ideal   model   delta    sigma   weight residual
     114.10  119.40   -5.30 2.00e+00 2.50e-01 7.03e+00
  angle pdb=" CA  LYS C 584 "
        pdb=" CB  LYS C 584 "
        pdb=" CG  LYS C 584 "
      ideal   model   delta    sigma   weight residual
     114.10  119.38   -5.28 2.00e+00 2.50e-01 6.98e+00
  angle pdb=" CA  LYS A 584 "
        pdb=" CB  LYS A 584 "
        pdb=" CG  LYS A 584 "
      ideal   model   delta    sigma   weight residual
     114.10  119.37   -5.27 2.00e+00 2.50e-01 6.95e+00
  angle pdb=" CA  LYS D 584 "
        pdb=" CB  LYS D 584 "
        pdb=" CG  LYS D 584 "
      ideal   model   delta    sigma   weight residual
     114.10  119.37   -5.27 2.00e+00 2.50e-01 6.95e+00
  angle pdb=" CA  LYS B 584 "
        pdb=" CB  LYS B 584 "
        pdb=" CG  LYS B 584 "
      ideal   model   delta    sigma   weight residual
     114.10  119.35   -5.25 2.00e+00 2.50e-01 6.89e+00
  ... (remaining 53491 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 21473
       17.96 -    35.93: 2461
       35.93 -    53.89: 384
       53.89 -    71.86: 78
       71.86 -    89.82: 48
  Dihedral angle restraints: 24444
    sinusoidal: 9852
      harmonic: 14592
  Sorted by residual:
  dihedral pdb=" CA  GLU L 170 "
           pdb=" C   GLU L 170 "
           pdb=" N   VAL L 171 "
           pdb=" CA  VAL L 171 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.45   24.55     0      5.00e+00 4.00e-02 2.41e+01
  dihedral pdb=" CA  GLU I 170 "
           pdb=" C   GLU I 170 "
           pdb=" N   VAL I 171 "
           pdb=" CA  VAL I 171 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.46   24.54     0      5.00e+00 4.00e-02 2.41e+01
  dihedral pdb=" CA  GLU G 170 "
           pdb=" C   GLU G 170 "
           pdb=" N   VAL G 171 "
           pdb=" CA  VAL G 171 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.49   24.51     0      5.00e+00 4.00e-02 2.40e+01
  ... (remaining 24441 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 2659
       0.030 -    0.061: 1965
       0.061 -    0.091: 785
       0.091 -    0.121: 256
       0.121 -    0.151: 89
  Chirality restraints: 5754
  Sorted by residual:
  chirality pdb=" CB  VAL J 171 "
            pdb=" CA  VAL J 171 "
            pdb=" CG1 VAL J 171 "
            pdb=" CG2 VAL J 171 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.73e-01
  chirality pdb=" CA  ILE B 437 "
            pdb=" N   ILE B 437 "
            pdb=" C   ILE B 437 "
            pdb=" CB  ILE B 437 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.72e-01
  chirality pdb=" CB  VAL H 171 "
            pdb=" CA  VAL H 171 "
            pdb=" CG1 VAL H 171 "
            pdb=" CG2 VAL H 171 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.70e-01
  ... (remaining 5751 not shown)

  Planarity restraints: 7182
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR E  79 "    0.038 5.00e-02 4.00e+02   5.71e-02 5.22e+00
        pdb=" N   PRO E  80 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO E  80 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO E  80 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C  79 "    0.038 5.00e-02 4.00e+02   5.71e-02 5.21e+00
        pdb=" N   PRO C  80 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO C  80 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO C  80 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  79 "    0.038 5.00e-02 4.00e+02   5.70e-02 5.20e+00
        pdb=" N   PRO A  80 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A  80 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A  80 "    0.031 5.00e-02 4.00e+02
  ... (remaining 7179 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 5665
        2.74 -     3.28: 40053
        3.28 -     3.82: 64517
        3.82 -     4.36: 78058
        4.36 -     4.90: 132339
  Nonbonded interactions: 320632
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP C 403 "
            pdb=" NZ  LYS C 405 "
     model   vdw
     2.196 3.120
  nonbonded pdb=" OD2 ASP F 403 "
            pdb=" NZ  LYS F 405 "
     model   vdw
     2.196 3.120
  nonbonded pdb=" OD2 ASP E 403 "
            pdb=" NZ  LYS E 405 "
     model   vdw
     2.196 3.120
  nonbonded pdb=" OD2 ASP B 403 "
            pdb=" NZ  LYS B 405 "
     model   vdw
     2.196 3.120
  nonbonded pdb=" OD2 ASP A 403 "
            pdb=" NZ  LYS A 405 "
     model   vdw
     2.197 3.120
  ... (remaining 320627 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: 0.10
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
}

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:             2.960
  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:             0.040
  Extract box with map and model:          0.640
  Check model and map are aligned:         0.120
  Set scattering table:                    0.100
  Process input model:                     33.380
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:7.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
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      :  0.010   0.072  39678  Z= 0.403
  Angle     :  0.731   9.740  53496  Z= 0.407
  Chirality :  0.049   0.151   5754
  Planarity :  0.005   0.057   7182
  Dihedral  : 15.513  89.819  15012
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  8.23 %
    Favored  : 91.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.28 (0.09), residues: 4980
  helix: -2.56 (0.07), residues: 3270
  sheet:  None (None), residues: 0
  loop : -3.09 (0.12), residues: 1710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 394 
 TYR   0.017   0.002   TYR E 664 
 PHE   0.014   0.002   PHE C 404 
 TRP   0.020   0.002   TRP F 366 
 HIS   0.005   0.002   HIS E 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00959 (39678)
  covalent geometry    : angle       0.73096 (53496)
  hydrogen bonds       : bond        0.18088 ( 2148)
  hydrogen bonds       : angle       7.53291 ( 6354)

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

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

  9960 Ramachandran restraints generated.
    4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  9960 Ramachandran restraints generated.
    4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  962 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 956
  time to evaluate  : 1.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 VAL cc_start: 0.8359 (t) cc_final: 0.8125 (p)
REVERT: A  519 ASP cc_start: 0.7294 (m-30) cc_final: 0.6848 (m-30)
REVERT: B  149 VAL cc_start: 0.8483 (t) cc_final: 0.8229 (p)
REVERT: B  496 ILE cc_start: 0.8453 (mt) cc_final: 0.8239 (mp)
REVERT: B  698 LYS cc_start: 0.8592 (mttm) cc_final: 0.8387 (mttp)
REVERT: C  149 VAL cc_start: 0.8462 (t) cc_final: 0.8228 (p)
REVERT: C  421 MET cc_start: 0.7789 (tpp) cc_final: 0.7527 (tpp)
REVERT: D  149 VAL cc_start: 0.8345 (t) cc_final: 0.8105 (p)
REVERT: D  519 ASP cc_start: 0.7302 (m-30) cc_final: 0.6856 (m-30)
REVERT: D  661 LEU cc_start: 0.8519 (mt) cc_final: 0.8277 (mt)
REVERT: E  149 VAL cc_start: 0.8478 (t) cc_final: 0.8229 (p)
REVERT: E  496 ILE cc_start: 0.8452 (mt) cc_final: 0.8237 (mp)
REVERT: E  698 LYS cc_start: 0.8588 (mttm) cc_final: 0.8385 (mttp)
REVERT: F  149 VAL cc_start: 0.8463 (t) cc_final: 0.8231 (p)
REVERT: F  421 MET cc_start: 0.7786 (tpp) cc_final: 0.7533 (tpp)
REVERT: G  136 ARG cc_start: 0.6857 (mtm180) cc_final: 0.6638 (mtp180)
REVERT: H  112 GLU cc_start: 0.7736 (mt-10) cc_final: 0.6648 (tm-30)
REVERT: H  134 GLU cc_start: 0.7527 (mp0) cc_final: 0.7255 (mp0)
REVERT: I  102 LEU cc_start: 0.8462 (mm) cc_final: 0.8260 (mm)
REVERT: I  134 GLU cc_start: 0.7439 (mp0) cc_final: 0.7052 (mp0)
REVERT: J  112 GLU cc_start: 0.7736 (mt-10) cc_final: 0.6648 (tm-30)
REVERT: J  134 GLU cc_start: 0.7526 (mp0) cc_final: 0.7250 (mp0)
REVERT: K  136 ARG cc_start: 0.6912 (mtm180) cc_final: 0.6679 (mtp180)
REVERT: L  102 LEU cc_start: 0.8458 (mm) cc_final: 0.8255 (mm)
REVERT: L  134 GLU cc_start: 0.7437 (mp0) cc_final: 0.7048 (mp0)
  outliers start: 6
  outliers final: 6
  residues processed: 960
  average time/residue: 0.8369
  time to fit residues: 946.6423
Evaluate side-chains
  741 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 735
  time to evaluate  : 1.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 THR
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  411 GLU
Chi-restraints excluded: chain D residue  131 THR
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain E residue  411 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 498
   random chunks:
   chunk 432 optimal weight:    0.6980
   chunk 197 optimal weight:    0.8980
   chunk 388 optimal weight:    4.9990
   chunk 455 optimal weight:    2.9990
   chunk 215 optimal weight:    0.3980
   chunk 20 optimal weight:    0.6980
   chunk 132 optimal weight:    0.3980
   chunk 494 optimal weight:    0.8980
   chunk 261 optimal weight:    0.9990
   chunk 248 optimal weight:    0.6980
   chunk 207 optimal weight:    0.9980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 164 GLN
A 189 GLN
A 286 GLN
A 314 ASN
A 318 ASN
A 356 GLN
A 418 HIS
A 426 ASN
A 472 GLN
A 529 GLN
B 140 HIS
B 189 GLN
B 314 ASN
B 318 ASN
B 356 GLN
B 418 HIS
B 426 ASN
B 472 GLN
B 529 GLN
B 658 ASN
B 696 GLN
C 189 GLN
C 286 GLN
C 314 ASN
C 318 ASN
C 356 GLN
C 418 HIS
C 426 ASN
C 472 GLN
C 529 GLN
** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 164 GLN
D 189 GLN
D 286 GLN
D 314 ASN
D 318 ASN
D 356 GLN
D 418 HIS
D 426 ASN
D 472 GLN
D 529 GLN
E 140 HIS
E 189 GLN
E 314 ASN
E 318 ASN
E 356 GLN
E 418 HIS
E 426 ASN
E 472 GLN
E 529 GLN
E 658 ASN
E 696 GLN
** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 189 GLN
F 272 ASN
F 286 GLN
F 314 ASN
F 318 ASN
F 356 GLN
F 418 HIS
F 426 ASN
F 472 GLN
F 529 GLN
G   7 ASN
** G 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H   7 ASN
H 214 HIS
I   7 ASN
** I 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J   7 ASN
J 214 HIS
K   7 ASN
** K 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L   7 ASN
** L 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 69

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.140905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.116310 restraints weight = 58144.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3818 rms_B_bonded: 2.26
r_work: 0.3684 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3527 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  39678  Z= 0.130
  Angle     :  0.558   8.738  53496  Z= 0.296
  Chirality :  0.040   0.157   5754
  Planarity :  0.005   0.059   7182
  Dihedral  :  5.723 164.346   5452
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 18.16 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.39 (0.11), residues: 4980
  helix: -1.04 (0.08), residues: 3366
  sheet: -4.10 (0.58), residues: 60
  loop : -2.46 (0.14), residues: 1554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG L 136 
 TYR   0.018   0.001   TYR L 138 
 PHE   0.009   0.001   PHE B 167 
 TRP   0.010   0.001   TRP E 326 
 HIS   0.002   0.001   HIS A 140 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (39678)
  covalent geometry    : angle       0.55824 (53496)
  hydrogen bonds       : bond        0.04101 ( 2148)
  hydrogen bonds       : angle       4.38652 ( 6354)

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

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

  9960 Ramachandran restraints generated.
    4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  9960 Ramachandran restraints generated.
    4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  937 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 118
    poor density    : 819
  time to evaluate  : 1.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ASP cc_start: 0.8017 (m-30) cc_final: 0.7800 (m-30)
REVERT: A  121 MET cc_start: 0.8365 (tpp) cc_final: 0.8118 (tpp)
REVERT: A  149 VAL cc_start: 0.7763 (t) cc_final: 0.7370 (p)
REVERT: A  214 ARG cc_start: 0.8339 (mmm160) cc_final: 0.8011 (ttm-80)
REVERT: A  323 ARG cc_start: 0.7902 (mpp80) cc_final: 0.7596 (mtt-85)
REVERT: A  372 LYS cc_start: 0.8691 (ttpp) cc_final: 0.8408 (ttpt)
REVERT: A  519 ASP cc_start: 0.7601 (m-30) cc_final: 0.7015 (m-30)
REVERT: A  550 ASP cc_start: 0.6842 (OUTLIER) cc_final: 0.6625 (t70)
REVERT: A  574 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7509 (mm-30)
REVERT: A  625 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8240 (mtt)
REVERT: A  663 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.8061 (ttp)
REVERT: B  119 ASP cc_start: 0.8064 (m-30) cc_final: 0.7819 (m-30)
REVERT: B  149 VAL cc_start: 0.7748 (t) cc_final: 0.7241 (p)
REVERT: B  196 MET cc_start: 0.7086 (mtm) cc_final: 0.6885 (mtt)
REVERT: B  335 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6924 (mt-10)
REVERT: B  455 LYS cc_start: 0.9050 (ptmm) cc_final: 0.8518 (pmtt)
REVERT: B  550 ASP cc_start: 0.6748 (OUTLIER) cc_final: 0.6165 (t70)
REVERT: B  581 ASP cc_start: 0.8344 (m-30) cc_final: 0.8104 (m-30)
REVERT: B  590 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6727 (pm20)
REVERT: B  602 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8420 (ttmm)
REVERT: B  647 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7269 (mtpt)
REVERT: B  698 LYS cc_start: 0.7778 (mttm) cc_final: 0.7514 (mttp)
REVERT: C   73 GLU cc_start: 0.8023 (tp30) cc_final: 0.7815 (tp30)
REVERT: C  149 VAL cc_start: 0.7880 (t) cc_final: 0.7361 (p)
REVERT: C  214 ARG cc_start: 0.8512 (ttm-80) cc_final: 0.8054 (mtp85)
REVERT: C  282 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7596 (mp)
REVERT: C  372 LYS cc_start: 0.8621 (ttpp) cc_final: 0.8259 (tppp)
REVERT: C  490 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7356 (ttm)
REVERT: C  494 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7711 (mtt-85)
REVERT: C  513 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7474 (mm-30)
REVERT: C  625 MET cc_start: 0.8499 (mtt) cc_final: 0.8294 (mtt)
REVERT: D  121 MET cc_start: 0.8343 (tpp) cc_final: 0.8100 (tpp)
REVERT: D  149 VAL cc_start: 0.7770 (t) cc_final: 0.7380 (p)
REVERT: D  214 ARG cc_start: 0.8342 (mmm160) cc_final: 0.8023 (ttm-80)
REVERT: D  323 ARG cc_start: 0.7905 (mpp80) cc_final: 0.7595 (mtt-85)
REVERT: D  372 LYS cc_start: 0.8708 (ttpp) cc_final: 0.8424 (ttpt)
REVERT: D  451 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7966 (tm-30)
REVERT: D  519 ASP cc_start: 0.7603 (m-30) cc_final: 0.7005 (m-30)
REVERT: D  550 ASP cc_start: 0.6849 (OUTLIER) cc_final: 0.6630 (t70)
REVERT: D  574 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7524 (mm-30)
REVERT: D  611 ASP cc_start: 0.7395 (p0) cc_final: 0.6849 (p0)
REVERT: D  625 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8247 (mtt)
REVERT: D  663 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.8025 (ttp)
REVERT: D  664 TYR cc_start: 0.8079 (t80) cc_final: 0.7604 (t80)
REVERT: D  673 MET cc_start: 0.8834 (ttp) cc_final: 0.8576 (ttt)
REVERT: E  119 ASP cc_start: 0.8100 (m-30) cc_final: 0.7879 (m-30)
REVERT: E  126 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7274 (mm-30)
REVERT: E  149 VAL cc_start: 0.7740 (t) cc_final: 0.7239 (p)
REVERT: E  196 MET cc_start: 0.7151 (mtm) cc_final: 0.6941 (mtt)
REVERT: E  335 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6912 (mt-10)
REVERT: E  378 MET cc_start: 0.8214 (ttm) cc_final: 0.8009 (ttp)
REVERT: E  455 LYS cc_start: 0.9044 (ptmm) cc_final: 0.8516 (pmtt)
REVERT: E  519 ASP cc_start: 0.7360 (m-30) cc_final: 0.7145 (m-30)
REVERT: E  550 ASP cc_start: 0.6755 (OUTLIER) cc_final: 0.6204 (t70)
REVERT: E  581 ASP cc_start: 0.8350 (m-30) cc_final: 0.8109 (m-30)
REVERT: E  590 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6734 (pm20)
REVERT: E  602 LYS cc_start: 0.8671 (ttmm) cc_final: 0.8420 (ttmm)
REVERT: E  647 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7267 (mtpt)
REVERT: E  698 LYS cc_start: 0.7746 (mttm) cc_final: 0.7504 (mtpp)
REVERT: F   73 GLU cc_start: 0.8039 (tp30) cc_final: 0.7814 (tp30)
REVERT: F  149 VAL cc_start: 0.7892 (t) cc_final: 0.7369 (p)
REVERT: F  214 ARG cc_start: 0.8487 (ttm-80) cc_final: 0.8012 (mtp85)
REVERT: F  282 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7607 (mp)
REVERT: F  372 LYS cc_start: 0.8616 (ttpp) cc_final: 0.8254 (tppp)
REVERT: F  490 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7363 (ttm)
REVERT: F  494 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7700 (mtt-85)
REVERT: F  513 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7482 (mm-30)
REVERT: F  625 MET cc_start: 0.8487 (mtt) cc_final: 0.8267 (mtt)
REVERT: G  216 GLU cc_start: 0.7976 (pt0) cc_final: 0.7653 (pm20)
REVERT: H  115 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7293 (tm)
REVERT: H  136 ARG cc_start: 0.6801 (OUTLIER) cc_final: 0.6599 (mtp-110)
REVERT: H  170 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7368 (tp30)
REVERT: H  210 PHE cc_start: 0.7997 (t80) cc_final: 0.7687 (t80)
REVERT: H  216 GLU cc_start: 0.7945 (pt0) cc_final: 0.7420 (pm20)
REVERT: I  102 LEU cc_start: 0.7999 (mm) cc_final: 0.7780 (mm)
REVERT: I  112 GLU cc_start: 0.8031 (mp0) cc_final: 0.7818 (mp0)
REVERT: I  216 GLU cc_start: 0.7942 (pt0) cc_final: 0.7704 (pm20)
REVERT: J  115 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7283 (tm)
REVERT: J  136 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.6604 (mtp-110)
REVERT: J  170 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7400 (mm-30)
REVERT: J  210 PHE cc_start: 0.8009 (t80) cc_final: 0.7719 (t80)
REVERT: J  216 GLU cc_start: 0.7944 (pt0) cc_final: 0.7424 (pm20)
REVERT: K  216 GLU cc_start: 0.7970 (pt0) cc_final: 0.7661 (pm20)
REVERT: L  102 LEU cc_start: 0.7990 (mm) cc_final: 0.7773 (mm)
REVERT: L  112 GLU cc_start: 0.8030 (mp0) cc_final: 0.7817 (mp0)
REVERT: L  216 GLU cc_start: 0.7928 (pt0) cc_final: 0.7689 (pm20)
  outliers start: 118
  outliers final: 24
  residues processed: 876
  average time/residue: 0.7640
  time to fit residues: 799.8892
Evaluate side-chains
  781 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 733
  time to evaluate  : 1.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  131 THR
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  550 ASP
Chi-restraints excluded: chain A residue  625 MET
Chi-restraints excluded: chain A residue  663 MET
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  335 GLU
Chi-restraints excluded: chain B residue  550 ASP
Chi-restraints excluded: chain B residue  574 GLU
Chi-restraints excluded: chain B residue  590 GLU
Chi-restraints excluded: chain B residue  647 LYS
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  282 ILE
Chi-restraints excluded: chain C residue  411 GLU
Chi-restraints excluded: chain C residue  482 LYS
Chi-restraints excluded: chain C residue  490 MET
Chi-restraints excluded: chain C residue  494 ARG
Chi-restraints excluded: chain C residue  574 GLU
Chi-restraints excluded: chain C residue  688 LEU
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  131 THR
Chi-restraints excluded: chain D residue  282 ILE
Chi-restraints excluded: chain D residue  550 ASP
Chi-restraints excluded: chain D residue  625 MET
Chi-restraints excluded: chain D residue  663 MET
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain E residue  335 GLU
Chi-restraints excluded: chain E residue  550 ASP
Chi-restraints excluded: chain E residue  574 GLU
Chi-restraints excluded: chain E residue  590 GLU
Chi-restraints excluded: chain E residue  647 LYS
Chi-restraints excluded: chain F residue   91 THR
Chi-restraints excluded: chain F residue  245 SER
Chi-restraints excluded: chain F residue  282 ILE
Chi-restraints excluded: chain F residue  411 GLU
Chi-restraints excluded: chain F residue  482 LYS
Chi-restraints excluded: chain F residue  490 MET
Chi-restraints excluded: chain F residue  494 ARG
Chi-restraints excluded: chain F residue  574 GLU
Chi-restraints excluded: chain F residue  688 LEU
Chi-restraints excluded: chain H residue  115 LEU
Chi-restraints excluded: chain H residue  136 ARG
Chi-restraints excluded: chain J residue  115 LEU
Chi-restraints excluded: chain J residue  136 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 498
   random chunks:
   chunk 269 optimal weight:    0.6980
   chunk 451 optimal weight:    3.9990
   chunk 474 optimal weight:    0.6980
   chunk 392 optimal weight:   20.0000
   chunk 119 optimal weight:    0.9980
   chunk 118 optimal weight:    0.7980
   chunk 207 optimal weight:    0.8980
   chunk 10 optimal weight:    0.3980
   chunk 126 optimal weight:    3.9990
   chunk 114 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 140 HIS
A 164 GLN
A 191 GLN
C 140 HIS
C 272 ASN
D 140 HIS
D 191 GLN
** D 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 140 HIS
G 214 HIS
H 180 GLN
** I 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 214 HIS
J 180 GLN
K 214 HIS
** L 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 214 HIS

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.141667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.117056 restraints weight = 57917.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.3844 rms_B_bonded: 2.26
r_work: 0.3709 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3552 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.2384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  39678  Z= 0.124
  Angle     :  0.533   8.128  53496  Z= 0.277
  Chirality :  0.040   0.169   5754
  Planarity :  0.004   0.056   7182
  Dihedral  :  4.411  34.337   5446
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 19.91 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.11), residues: 4980
  helix: -0.28 (0.09), residues: 3390
  sheet: -3.74 (0.55), residues: 60
  loop : -1.87 (0.14), residues: 1530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG F 586 
 TYR   0.023   0.001   TYR L 138 
 PHE   0.018   0.001   PHE F 167 
 TRP   0.008   0.001   TRP E 366 
 HIS   0.003   0.001   HIS B 140 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (39678)
  covalent geometry    : angle       0.53296 (53496)
  hydrogen bonds       : bond        0.03649 ( 2148)
  hydrogen bonds       : angle       3.90662 ( 6354)

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

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

  9960 Ramachandran restraints generated.
    4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  9960 Ramachandran restraints generated.
    4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  938 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 148
    poor density    : 790
  time to evaluate  : 1.585 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ASP cc_start: 0.7955 (m-30) cc_final: 0.7675 (m-30)
REVERT: A  149 VAL cc_start: 0.7859 (t) cc_final: 0.7385 (p)
REVERT: A  214 ARG cc_start: 0.8319 (mmm160) cc_final: 0.8015 (ttm-80)
REVERT: A  323 ARG cc_start: 0.7832 (mpp80) cc_final: 0.7509 (mtt-85)
REVERT: A  407 MET cc_start: 0.8708 (mmt) cc_final: 0.8497 (mmt)
REVERT: A  431 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7552 (tm-30)
REVERT: A  456 ASP cc_start: 0.8477 (t0) cc_final: 0.7703 (p0)
REVERT: A  519 ASP cc_start: 0.7568 (m-30) cc_final: 0.7033 (m-30)
REVERT: A  561 LYS cc_start: 0.9149 (pmtt) cc_final: 0.8717 (mmmt)
REVERT: A  574 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7463 (mm-30)
REVERT: A  625 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8252 (mtt)
REVERT: B  119 ASP cc_start: 0.8016 (m-30) cc_final: 0.7708 (m-30)
REVERT: B  149 VAL cc_start: 0.7746 (t) cc_final: 0.7296 (p)
REVERT: B  431 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7629 (tm-30)
REVERT: B  455 LYS cc_start: 0.9081 (ptmm) cc_final: 0.8535 (pmtt)
REVERT: B  568 MET cc_start: 0.7518 (mtm) cc_final: 0.7156 (mtp)
REVERT: B  574 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7333 (mp0)
REVERT: B  581 ASP cc_start: 0.8405 (m-30) cc_final: 0.8135 (m-30)
REVERT: B  602 LYS cc_start: 0.8685 (ttmm) cc_final: 0.8436 (ttmm)
REVERT: B  625 MET cc_start: 0.8634 (mtt) cc_final: 0.8404 (mtt)
REVERT: B  647 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.7182 (mtpt)
REVERT: C   73 GLU cc_start: 0.8173 (tp30) cc_final: 0.7841 (tp30)
REVERT: C  126 GLU cc_start: 0.8040 (tt0) cc_final: 0.7704 (tm-30)
REVERT: C  149 VAL cc_start: 0.7876 (t) cc_final: 0.7432 (p)
REVERT: C  214 ARG cc_start: 0.8331 (ttm-80) cc_final: 0.8034 (mmm-85)
REVERT: C  323 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7754 (mtt-85)
REVERT: C  335 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6791 (mt-10)
REVERT: C  372 LYS cc_start: 0.8635 (ttpp) cc_final: 0.8289 (tppp)
REVERT: C  494 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7507 (mtt-85)
REVERT: C  513 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7393 (mm-30)
REVERT: C  519 ASP cc_start: 0.7212 (m-30) cc_final: 0.7006 (m-30)
REVERT: C  564 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7851 (mp0)
REVERT: C  581 ASP cc_start: 0.8413 (m-30) cc_final: 0.8196 (m-30)
REVERT: C  594 MET cc_start: 0.7165 (tpp) cc_final: 0.5821 (tpt)
REVERT: D  149 VAL cc_start: 0.7875 (t) cc_final: 0.7394 (p)
REVERT: D  323 ARG cc_start: 0.7813 (mpp80) cc_final: 0.7487 (mtt-85)
REVERT: D  407 MET cc_start: 0.8714 (mmt) cc_final: 0.8499 (mmt)
REVERT: D  431 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7552 (tm-30)
REVERT: D  456 ASP cc_start: 0.8488 (t0) cc_final: 0.7722 (p0)
REVERT: D  519 ASP cc_start: 0.7578 (m-30) cc_final: 0.7038 (m-30)
REVERT: D  561 LYS cc_start: 0.9138 (pmtt) cc_final: 0.8763 (mmmt)
REVERT: D  574 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7462 (mm-30)
REVERT: D  625 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8237 (mtm)
REVERT: E  119 ASP cc_start: 0.8047 (m-30) cc_final: 0.7738 (m-30)
REVERT: E  126 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7243 (mm-30)
REVERT: E  149 VAL cc_start: 0.7742 (t) cc_final: 0.7193 (p)
REVERT: E  152 GLU cc_start: 0.7562 (pp20) cc_final: 0.7342 (pp20)
REVERT: E  378 MET cc_start: 0.8183 (ttm) cc_final: 0.7831 (ttt)
REVERT: E  455 LYS cc_start: 0.9083 (ptmm) cc_final: 0.8541 (pmtt)
REVERT: E  519 ASP cc_start: 0.7272 (m-30) cc_final: 0.7031 (m-30)
REVERT: E  574 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7321 (mp0)
REVERT: E  581 ASP cc_start: 0.8398 (m-30) cc_final: 0.8130 (m-30)
REVERT: E  602 LYS cc_start: 0.8685 (ttmm) cc_final: 0.8456 (ttmm)
REVERT: E  625 MET cc_start: 0.8633 (mtt) cc_final: 0.8391 (mtt)
REVERT: E  647 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.7166 (mtpt)
REVERT: E  698 LYS cc_start: 0.7559 (mttm) cc_final: 0.7340 (mttm)
REVERT: F   73 GLU cc_start: 0.8165 (tp30) cc_final: 0.7877 (tp30)
REVERT: F  117 ASP cc_start: 0.8327 (t0) cc_final: 0.7923 (m-30)
REVERT: F  126 GLU cc_start: 0.8030 (tt0) cc_final: 0.7700 (tm-30)
REVERT: F  149 VAL cc_start: 0.7873 (t) cc_final: 0.7430 (p)
REVERT: F  214 ARG cc_start: 0.8333 (ttm-80) cc_final: 0.7924 (mtp85)
REVERT: F  323 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7739 (mtt-85)
REVERT: F  335 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6780 (mt-10)
REVERT: F  372 LYS cc_start: 0.8634 (ttpp) cc_final: 0.8291 (tppp)
REVERT: F  421 MET cc_start: 0.8319 (tpp) cc_final: 0.8021 (mmm)
REVERT: F  494 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7505 (mtt-85)
REVERT: F  513 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7396 (mm-30)
REVERT: F  564 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7877 (mp0)
REVERT: F  581 ASP cc_start: 0.8435 (m-30) cc_final: 0.8216 (m-30)
REVERT: F  594 MET cc_start: 0.7155 (tpp) cc_final: 0.5806 (tpt)
REVERT: G  165 LYS cc_start: 0.8682 (mmtt) cc_final: 0.8447 (mmtp)
REVERT: G  216 GLU cc_start: 0.8002 (pt0) cc_final: 0.7653 (pm20)
REVERT: H  136 ARG cc_start: 0.6871 (OUTLIER) cc_final: 0.6583 (mtp-110)
REVERT: H  210 PHE cc_start: 0.7994 (t80) cc_final: 0.7784 (t80)
REVERT: H  216 GLU cc_start: 0.7999 (pt0) cc_final: 0.7515 (pm20)
REVERT: I  102 LEU cc_start: 0.8058 (mm) cc_final: 0.7843 (mm)
REVERT: I  112 GLU cc_start: 0.8099 (mp0) cc_final: 0.7897 (mp0)
REVERT: I  208 LYS cc_start: 0.7445 (tttm) cc_final: 0.7118 (tttp)
REVERT: I  216 GLU cc_start: 0.8043 (pt0) cc_final: 0.7616 (pm20)
REVERT: J  136 ARG cc_start: 0.6870 (OUTLIER) cc_final: 0.6577 (mtp-110)
REVERT: J  210 PHE cc_start: 0.7990 (t80) cc_final: 0.7648 (t80)
REVERT: J  216 GLU cc_start: 0.8011 (pt0) cc_final: 0.7458 (pm20)
REVERT: K  165 LYS cc_start: 0.8684 (mmtt) cc_final: 0.8450 (mmtp)
REVERT: K  216 GLU cc_start: 0.7965 (pt0) cc_final: 0.7656 (pm20)
REVERT: L  102 LEU cc_start: 0.8075 (mm) cc_final: 0.7858 (mm)
REVERT: L  208 LYS cc_start: 0.7445 (tttm) cc_final: 0.7121 (tttp)
REVERT: L  216 GLU cc_start: 0.8037 (pt0) cc_final: 0.7601 (pm20)
  outliers start: 148
  outliers final: 42
  residues processed: 862
  average time/residue: 0.7499
  time to fit residues: 771.7104
Evaluate side-chains
  786 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 728
  time to evaluate  : 1.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  131 THR
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  625 MET
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  162 ASP
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  346 THR
Chi-restraints excluded: chain B residue  574 GLU
Chi-restraints excluded: chain B residue  647 LYS
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  162 ASP
Chi-restraints excluded: chain C residue  323 ARG
Chi-restraints excluded: chain C residue  335 GLU
Chi-restraints excluded: chain C residue  411 GLU
Chi-restraints excluded: chain C residue  445 MET
Chi-restraints excluded: chain C residue  482 LYS
Chi-restraints excluded: chain C residue  494 ARG
Chi-restraints excluded: chain C residue  564 GLU
Chi-restraints excluded: chain C residue  574 GLU
Chi-restraints excluded: chain C residue  688 LEU
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  131 THR
Chi-restraints excluded: chain D residue  245 SER
Chi-restraints excluded: chain D residue  324 THR
Chi-restraints excluded: chain D residue  625 MET
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain E residue  282 ILE
Chi-restraints excluded: chain E residue  346 THR
Chi-restraints excluded: chain E residue  574 GLU
Chi-restraints excluded: chain E residue  647 LYS
Chi-restraints excluded: chain F residue   91 THR
Chi-restraints excluded: chain F residue  162 ASP
Chi-restraints excluded: chain F residue  323 ARG
Chi-restraints excluded: chain F residue  335 GLU
Chi-restraints excluded: chain F residue  411 GLU
Chi-restraints excluded: chain F residue  445 MET
Chi-restraints excluded: chain F residue  482 LYS
Chi-restraints excluded: chain F residue  494 ARG
Chi-restraints excluded: chain F residue  564 GLU
Chi-restraints excluded: chain F residue  574 GLU
Chi-restraints excluded: chain F residue  688 LEU
Chi-restraints excluded: chain G residue  131 ILE
Chi-restraints excluded: chain G residue  209 ASP
Chi-restraints excluded: chain H residue  136 ARG
Chi-restraints excluded: chain I residue  131 ILE
Chi-restraints excluded: chain I residue  136 ARG
Chi-restraints excluded: chain I residue  143 LEU
Chi-restraints excluded: chain I residue  218 LEU
Chi-restraints excluded: chain J residue  136 ARG
Chi-restraints excluded: chain K residue  131 ILE
Chi-restraints excluded: chain K residue  209 ASP
Chi-restraints excluded: chain L residue  131 ILE
Chi-restraints excluded: chain L residue  136 ARG
Chi-restraints excluded: chain L residue  143 LEU
Chi-restraints excluded: chain L residue  218 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 498
   random chunks:
   chunk 226 optimal weight:    4.9990
   chunk 176 optimal weight:    5.9990
   chunk 164 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 413 optimal weight:    2.9990
   chunk 165 optimal weight:    0.8980
   chunk 492 optimal weight:    2.9990
   chunk 119 optimal weight:    2.9990
   chunk 489 optimal weight:    0.9990
   chunk 470 optimal weight:    2.9990
   chunk 277 optimal weight:    2.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 164 GLN
A 358 GLN
A 390 GLN
** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 660 GLN
D 358 GLN
E 358 GLN
F 660 GLN
G 180 GLN
H 180 GLN
** I 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 180 GLN
K 180 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.140188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.114886 restraints weight = 58097.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.3803 rms_B_bonded: 2.35
r_work: 0.3663 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.2451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  39678  Z= 0.165
  Angle     :  0.560   8.072  53496  Z= 0.289
  Chirality :  0.042   0.230   5754
  Planarity :  0.004   0.059   7182
  Dihedral  :  4.335  33.787   5445
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 20.81 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.83 (0.11), residues: 4980
  helix:  0.10 (0.09), residues: 3360
  sheet: -3.42 (0.55), residues: 60
  loop : -1.73 (0.14), residues: 1560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 323 
 TYR   0.023   0.001   TYR I 138 
 PHE   0.019   0.001   PHE F 220 
 TRP   0.011   0.001   TRP A 351 
 HIS   0.003   0.001   HIS C 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 (39678)
  covalent geometry    : angle       0.56010 (53496)
  hydrogen bonds       : bond        0.03782 ( 2148)
  hydrogen bonds       : angle       3.81638 ( 6354)

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

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

  9960 Ramachandran restraints generated.
    4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  9960 Ramachandran restraints generated.
    4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  949 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 184
    poor density    : 765
  time to evaluate  : 1.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ASP cc_start: 0.7737 (m-30) cc_final: 0.7475 (m-30)
REVERT: A  149 VAL cc_start: 0.7701 (t) cc_final: 0.7297 (p)
REVERT: A  188 GLN cc_start: 0.7341 (pp30) cc_final: 0.7115 (pp30)
REVERT: A  207 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7545 (tt0)
REVERT: A  214 ARG cc_start: 0.8253 (mmm160) cc_final: 0.7964 (ttm-80)
REVERT: A  262 MET cc_start: 0.7844 (ttp) cc_final: 0.7571 (mtp)
REVERT: A  431 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7350 (tm-30)
REVERT: A  456 ASP cc_start: 0.8393 (t0) cc_final: 0.7628 (p0)
REVERT: A  519 ASP cc_start: 0.7390 (m-30) cc_final: 0.6862 (m-30)
REVERT: A  561 LYS cc_start: 0.9128 (pmtt) cc_final: 0.8692 (mmmt)
REVERT: A  574 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7315 (mm-30)
REVERT: A  664 TYR cc_start: 0.7297 (t80) cc_final: 0.7042 (t80)
REVERT: B  119 ASP cc_start: 0.7759 (m-30) cc_final: 0.7444 (m-30)
REVERT: B  149 VAL cc_start: 0.7699 (t) cc_final: 0.7269 (p)
REVERT: B  335 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6797 (mt-10)
REVERT: B  363 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.6960 (ttt)
REVERT: B  431 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7406 (tm-30)
REVERT: B  455 LYS cc_start: 0.9043 (ptmm) cc_final: 0.8514 (pmtt)
REVERT: B  550 ASP cc_start: 0.6685 (OUTLIER) cc_final: 0.6279 (t70)
REVERT: B  568 MET cc_start: 0.7303 (mtm) cc_final: 0.6971 (mtp)
REVERT: B  574 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7042 (mp0)
REVERT: B  581 ASP cc_start: 0.8118 (m-30) cc_final: 0.7784 (m-30)
REVERT: B  625 MET cc_start: 0.8609 (mtt) cc_final: 0.8366 (mtt)
REVERT: B  684 ASP cc_start: 0.8039 (p0) cc_final: 0.7715 (p0)
REVERT: B  688 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.6229 (mp)
REVERT: B  698 LYS cc_start: 0.7871 (mtmm) cc_final: 0.7657 (mtpp)
REVERT: C   73 GLU cc_start: 0.8033 (tp30) cc_final: 0.7732 (tp30)
REVERT: C  117 ASP cc_start: 0.8225 (t0) cc_final: 0.7818 (m-30)
REVERT: C  214 ARG cc_start: 0.8288 (ttm-80) cc_final: 0.7880 (mtp85)
REVERT: C  335 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6606 (mt-10)
REVERT: C  372 LYS cc_start: 0.8519 (ttpp) cc_final: 0.8196 (ttpt)
REVERT: C  421 MET cc_start: 0.8235 (tpp) cc_final: 0.7854 (mmm)
REVERT: C  513 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7234 (mm-30)
REVERT: C  532 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7559 (mm)
REVERT: C  581 ASP cc_start: 0.8156 (m-30) cc_final: 0.7904 (m-30)
REVERT: C  592 MET cc_start: 0.6169 (tmm) cc_final: 0.5790 (tmm)
REVERT: C  594 MET cc_start: 0.7060 (OUTLIER) cc_final: 0.5814 (tpt)
REVERT: D  149 VAL cc_start: 0.7695 (t) cc_final: 0.7291 (p)
REVERT: D  188 GLN cc_start: 0.7351 (pp30) cc_final: 0.7128 (pp30)
REVERT: D  207 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7538 (tt0)
REVERT: D  262 MET cc_start: 0.7805 (ttp) cc_final: 0.7597 (mtp)
REVERT: D  431 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7361 (tm-30)
REVERT: D  456 ASP cc_start: 0.8419 (t0) cc_final: 0.7650 (p0)
REVERT: D  519 ASP cc_start: 0.7404 (m-30) cc_final: 0.6879 (m-30)
REVERT: D  561 LYS cc_start: 0.9103 (pmtt) cc_final: 0.8727 (mmmt)
REVERT: D  574 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7239 (mm-30)
REVERT: D  592 MET cc_start: 0.6293 (OUTLIER) cc_final: 0.5525 (tmt)
REVERT: E  117 ASP cc_start: 0.8348 (t0) cc_final: 0.8125 (m-30)
REVERT: E  149 VAL cc_start: 0.7682 (t) cc_final: 0.7199 (p)
REVERT: E  335 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6802 (mt-10)
REVERT: E  363 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.7025 (ttt)
REVERT: E  378 MET cc_start: 0.7953 (ttm) cc_final: 0.7641 (ttt)
REVERT: E  431 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7401 (tm-30)
REVERT: E  455 LYS cc_start: 0.9038 (ptmm) cc_final: 0.8514 (pmtt)
REVERT: E  550 ASP cc_start: 0.6684 (OUTLIER) cc_final: 0.6237 (t70)
REVERT: E  574 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7031 (mp0)
REVERT: E  581 ASP cc_start: 0.8098 (m-30) cc_final: 0.7765 (m-30)
REVERT: E  625 MET cc_start: 0.8614 (mtt) cc_final: 0.8353 (mtt)
REVERT: E  684 ASP cc_start: 0.8040 (p0) cc_final: 0.7820 (p0)
REVERT: F   73 GLU cc_start: 0.8083 (tp30) cc_final: 0.7757 (tp30)
REVERT: F  117 ASP cc_start: 0.8265 (t0) cc_final: 0.7838 (m-30)
REVERT: F  214 ARG cc_start: 0.8290 (ttm-80) cc_final: 0.7864 (mtp85)
REVERT: F  335 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6590 (mt-10)
REVERT: F  372 LYS cc_start: 0.8520 (ttpp) cc_final: 0.8200 (ttpt)
REVERT: F  421 MET cc_start: 0.8323 (tpp) cc_final: 0.7897 (mmm)
REVERT: F  494 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7404 (mtt-85)
REVERT: F  513 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7283 (mm-30)
REVERT: F  532 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7506 (mm)
REVERT: F  544 GLU cc_start: 0.8230 (mp0) cc_final: 0.8029 (pm20)
REVERT: F  594 MET cc_start: 0.7057 (OUTLIER) cc_final: 0.5782 (tpt)
REVERT: G  103 LYS cc_start: 0.5390 (OUTLIER) cc_final: 0.4554 (tttt)
REVERT: G  112 GLU cc_start: 0.7995 (mp0) cc_final: 0.7248 (pp20)
REVERT: G  216 GLU cc_start: 0.7856 (pt0) cc_final: 0.7554 (pm20)
REVERT: H  103 LYS cc_start: 0.5121 (OUTLIER) cc_final: 0.4699 (tmtt)
REVERT: H  136 ARG cc_start: 0.6727 (OUTLIER) cc_final: 0.6477 (mtp-110)
REVERT: H  150 MET cc_start: 0.6371 (mpp) cc_final: 0.6009 (mpt)
REVERT: H  210 PHE cc_start: 0.7974 (t80) cc_final: 0.7601 (t80)
REVERT: H  216 GLU cc_start: 0.7923 (pt0) cc_final: 0.7413 (pm20)
REVERT: I  102 LEU cc_start: 0.7970 (mm) cc_final: 0.7741 (mm)
REVERT: I  112 GLU cc_start: 0.8066 (mp0) cc_final: 0.7841 (mp0)
REVERT: I  216 GLU cc_start: 0.7974 (pt0) cc_final: 0.7524 (pm20)
REVERT: J  136 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6797 (mtp-110)
REVERT: J  150 MET cc_start: 0.6372 (mpp) cc_final: 0.6003 (mpt)
REVERT: J  210 PHE cc_start: 0.7997 (t80) cc_final: 0.7627 (t80)
REVERT: J  216 GLU cc_start: 0.7929 (pt0) cc_final: 0.7429 (pm20)
REVERT: K  103 LYS cc_start: 0.5372 (OUTLIER) cc_final: 0.4543 (tttt)
REVERT: K  112 GLU cc_start: 0.7982 (mp0) cc_final: 0.7242 (pp20)
REVERT: K  216 GLU cc_start: 0.7846 (pt0) cc_final: 0.7546 (pm20)
REVERT: L  102 LEU cc_start: 0.7958 (mm) cc_final: 0.7730 (mm)
REVERT: L  112 GLU cc_start: 0.7866 (mp0) cc_final: 0.6978 (tm-30)
REVERT: L  216 GLU cc_start: 0.7965 (pt0) cc_final: 0.7524 (pm20)
  outliers start: 184
  outliers final: 61
  residues processed: 853
  average time/residue: 0.7374
  time to fit residues: 754.4451
Evaluate side-chains
  810 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 85
    poor density    : 725
  time to evaluate  : 1.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  131 THR
Chi-restraints excluded: chain A residue  207 GLN
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  161 VAL
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  335 GLU
Chi-restraints excluded: chain B residue  346 THR
Chi-restraints excluded: chain B residue  357 GLU
Chi-restraints excluded: chain B residue  363 MET
Chi-restraints excluded: chain B residue  482 LYS
Chi-restraints excluded: chain B residue  490 MET
Chi-restraints excluded: chain B residue  550 ASP
Chi-restraints excluded: chain B residue  574 GLU
Chi-restraints excluded: chain B residue  688 LEU
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  335 GLU
Chi-restraints excluded: chain C residue  445 MET
Chi-restraints excluded: chain C residue  454 SER
Chi-restraints excluded: chain C residue  482 LYS
Chi-restraints excluded: chain C residue  532 LEU
Chi-restraints excluded: chain C residue  574 GLU
Chi-restraints excluded: chain C residue  594 MET
Chi-restraints excluded: chain C residue  688 LEU
Chi-restraints excluded: chain D residue   66 LEU
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  131 THR
Chi-restraints excluded: chain D residue  207 GLN
Chi-restraints excluded: chain D residue  245 SER
Chi-restraints excluded: chain D residue  282 ILE
Chi-restraints excluded: chain D residue  324 THR
Chi-restraints excluded: chain D residue  346 THR
Chi-restraints excluded: chain D residue  592 MET
Chi-restraints excluded: chain D residue  688 LEU
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain E residue  282 ILE
Chi-restraints excluded: chain E residue  324 THR
Chi-restraints excluded: chain E residue  335 GLU
Chi-restraints excluded: chain E residue  346 THR
Chi-restraints excluded: chain E residue  357 GLU
Chi-restraints excluded: chain E residue  363 MET
Chi-restraints excluded: chain E residue  482 LYS
Chi-restraints excluded: chain E residue  490 MET
Chi-restraints excluded: chain E residue  550 ASP
Chi-restraints excluded: chain E residue  574 GLU
Chi-restraints excluded: chain F residue   66 LEU
Chi-restraints excluded: chain F residue   91 THR
Chi-restraints excluded: chain F residue  245 SER
Chi-restraints excluded: chain F residue  335 GLU
Chi-restraints excluded: chain F residue  411 GLU
Chi-restraints excluded: chain F residue  445 MET
Chi-restraints excluded: chain F residue  454 SER
Chi-restraints excluded: chain F residue  482 LYS
Chi-restraints excluded: chain F residue  494 ARG
Chi-restraints excluded: chain F residue  532 LEU
Chi-restraints excluded: chain F residue  574 GLU
Chi-restraints excluded: chain F residue  594 MET
Chi-restraints excluded: chain F residue  673 MET
Chi-restraints excluded: chain F residue  688 LEU
Chi-restraints excluded: chain G residue  103 LYS
Chi-restraints excluded: chain G residue  131 ILE
Chi-restraints excluded: chain H residue  103 LYS
Chi-restraints excluded: chain H residue  115 LEU
Chi-restraints excluded: chain H residue  136 ARG
Chi-restraints excluded: chain I residue  131 ILE
Chi-restraints excluded: chain I residue  136 ARG
Chi-restraints excluded: chain J residue  115 LEU
Chi-restraints excluded: chain J residue  136 ARG
Chi-restraints excluded: chain J residue  143 LEU
Chi-restraints excluded: chain K residue  103 LYS
Chi-restraints excluded: chain K residue  131 ILE
Chi-restraints excluded: chain K residue  143 LEU
Chi-restraints excluded: chain L residue  131 ILE
Chi-restraints excluded: chain L residue  136 ARG
Chi-restraints excluded: chain L residue  143 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 498
   random chunks:
   chunk 400 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   chunk 496 optimal weight:    3.9990
   chunk 18 optimal weight:    0.5980
   chunk 145 optimal weight:    7.9990
   chunk 125 optimal weight:    3.9990
   chunk 451 optimal weight:    1.9990
   chunk 119 optimal weight:    0.0770
   chunk 134 optimal weight:    1.9990
   chunk 238 optimal weight:    4.9990
   chunk 277 optimal weight:    1.9990
   overall best weight:    1.1344

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

Flipped N/Q/H residues before XYZ refinement:
A 596 GLN
B 358 GLN
** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 358 GLN
** C 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 658 ASN
** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 658 ASN
G 180 GLN
H 180 GLN
J 180 GLN
K 180 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.140898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.116007 restraints weight = 57921.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.3812 rms_B_bonded: 2.26
r_work: 0.3675 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3512 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.2637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  39678  Z= 0.150
  Angle     :  0.558   8.289  53496  Z= 0.285
  Chirality :  0.041   0.231   5754
  Planarity :  0.004   0.067   7182
  Dihedral  :  4.255  34.011   5445
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 22.60 %
    Favored  : 73.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.44 (0.12), residues: 4980
  helix:  0.37 (0.09), residues: 3360
  sheet: -3.09 (0.58), residues: 60
  loop : -1.52 (0.14), residues: 1560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C 586 
 TYR   0.020   0.001   TYR L 138 
 PHE   0.015   0.001   PHE F 167 
 TRP   0.013   0.001   TRP D 351 
 HIS   0.003   0.001   HIS F 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (39678)
  covalent geometry    : angle       0.55805 (53496)
  hydrogen bonds       : bond        0.03644 ( 2148)
  hydrogen bonds       : angle       3.71501 ( 6354)

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

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

  9960 Ramachandran restraints generated.
    4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  9960 Ramachandran restraints generated.
    4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  944 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 173
    poor density    : 771
  time to evaluate  : 1.487 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ASP cc_start: 0.7988 (m-30) cc_final: 0.7699 (m-30)
REVERT: A  149 VAL cc_start: 0.7800 (t) cc_final: 0.7424 (p)
REVERT: A  167 PHE cc_start: 0.7998 (t80) cc_final: 0.7655 (t80)
REVERT: A  188 GLN cc_start: 0.7509 (pp30) cc_final: 0.7280 (pp30)
REVERT: A  207 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7637 (tp40)
REVERT: A  214 ARG cc_start: 0.8326 (mmm160) cc_final: 0.7971 (ttm-80)
REVERT: A  262 MET cc_start: 0.7996 (ttp) cc_final: 0.7764 (mtp)
REVERT: A  431 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7533 (tm-30)
REVERT: A  456 ASP cc_start: 0.8555 (t0) cc_final: 0.7699 (p0)
REVERT: A  519 ASP cc_start: 0.7539 (m-30) cc_final: 0.6970 (m-30)
REVERT: A  561 LYS cc_start: 0.9179 (pmtt) cc_final: 0.8743 (mmmt)
REVERT: A  574 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7587 (mm-30)
REVERT: A  625 MET cc_start: 0.8559 (mtt) cc_final: 0.8225 (mtt)
REVERT: A  664 TYR cc_start: 0.7555 (t80) cc_final: 0.7187 (t80)
REVERT: B  117 ASP cc_start: 0.8450 (t0) cc_final: 0.8151 (m-30)
REVERT: B  149 VAL cc_start: 0.7783 (t) cc_final: 0.7301 (p)
REVERT: B  152 GLU cc_start: 0.7493 (pp20) cc_final: 0.7287 (pp20)
REVERT: B  363 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7373 (ttt)
REVERT: B  388 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.8016 (t0)
REVERT: B  431 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7714 (tm-30)
REVERT: B  455 LYS cc_start: 0.9073 (ptmm) cc_final: 0.8528 (pmtt)
REVERT: B  519 ASP cc_start: 0.7117 (m-30) cc_final: 0.6896 (m-30)
REVERT: B  550 ASP cc_start: 0.6743 (OUTLIER) cc_final: 0.6282 (t70)
REVERT: B  574 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7332 (mp0)
REVERT: B  581 ASP cc_start: 0.8415 (m-30) cc_final: 0.8119 (m-30)
REVERT: B  602 LYS cc_start: 0.8714 (ttmm) cc_final: 0.8383 (tptt)
REVERT: B  625 MET cc_start: 0.8670 (mtt) cc_final: 0.8283 (mtm)
REVERT: B  647 LYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6911 (mtpt)
REVERT: B  684 ASP cc_start: 0.8103 (p0) cc_final: 0.7768 (p0)
REVERT: B  688 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6193 (mp)
REVERT: B  698 LYS cc_start: 0.7748 (mtmm) cc_final: 0.7462 (mttp)
REVERT: C   73 GLU cc_start: 0.8242 (tp30) cc_final: 0.7900 (tp30)
REVERT: C  117 ASP cc_start: 0.8350 (t0) cc_final: 0.7969 (m-30)
REVERT: C  149 VAL cc_start: 0.7868 (t) cc_final: 0.7467 (p)
REVERT: C  214 ARG cc_start: 0.8388 (ttm-80) cc_final: 0.7871 (mtp85)
REVERT: C  335 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6878 (mt-10)
REVERT: C  372 LYS cc_start: 0.8611 (ttpp) cc_final: 0.8283 (ttpt)
REVERT: C  421 MET cc_start: 0.8492 (tpp) cc_final: 0.8113 (mmm)
REVERT: C  431 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7765 (tm-30)
REVERT: C  513 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7485 (mm-30)
REVERT: C  532 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7767 (mm)
REVERT: C  550 ASP cc_start: 0.7049 (OUTLIER) cc_final: 0.6257 (t70)
REVERT: C  581 ASP cc_start: 0.8456 (m-30) cc_final: 0.8236 (m-30)
REVERT: C  592 MET cc_start: 0.6525 (tmm) cc_final: 0.6070 (tmm)
REVERT: C  594 MET cc_start: 0.7216 (OUTLIER) cc_final: 0.5990 (tpt)
REVERT: C  673 MET cc_start: 0.8497 (tpp) cc_final: 0.8266 (tpp)
REVERT: D  149 VAL cc_start: 0.7803 (t) cc_final: 0.7424 (p)
REVERT: D  207 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7628 (tp40)
REVERT: D  262 MET cc_start: 0.7949 (ttp) cc_final: 0.7745 (mtp)
REVERT: D  431 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7533 (tm-30)
REVERT: D  519 ASP cc_start: 0.7558 (m-30) cc_final: 0.6996 (m-30)
REVERT: D  561 LYS cc_start: 0.9170 (pmtt) cc_final: 0.8774 (mmmt)
REVERT: D  574 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7593 (mm-30)
REVERT: D  625 MET cc_start: 0.8577 (mtt) cc_final: 0.8245 (mtt)
REVERT: E  119 ASP cc_start: 0.8117 (m-30) cc_final: 0.7864 (m-30)
REVERT: E  149 VAL cc_start: 0.7771 (t) cc_final: 0.7268 (p)
REVERT: E  152 GLU cc_start: 0.7498 (pp20) cc_final: 0.7259 (pp20)
REVERT: E  363 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7391 (ttt)
REVERT: E  378 MET cc_start: 0.8178 (ttm) cc_final: 0.7963 (ttp)
REVERT: E  388 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.8012 (t0)
REVERT: E  431 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7706 (tm-30)
REVERT: E  455 LYS cc_start: 0.9092 (ptmm) cc_final: 0.8562 (pmtt)
REVERT: E  519 ASP cc_start: 0.7146 (m-30) cc_final: 0.6893 (m-30)
REVERT: E  521 MET cc_start: 0.7778 (mmt) cc_final: 0.6879 (mmt)
REVERT: E  550 ASP cc_start: 0.6734 (OUTLIER) cc_final: 0.6263 (t70)
REVERT: E  574 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7322 (mp0)
REVERT: E  581 ASP cc_start: 0.8419 (m-30) cc_final: 0.8122 (m-30)
REVERT: E  602 LYS cc_start: 0.8722 (ttmm) cc_final: 0.8381 (tptt)
REVERT: E  625 MET cc_start: 0.8695 (mtt) cc_final: 0.8332 (mtm)
REVERT: E  647 LYS cc_start: 0.7130 (OUTLIER) cc_final: 0.6895 (mtpt)
REVERT: E  673 MET cc_start: 0.8826 (ttp) cc_final: 0.8620 (ttp)
REVERT: E  684 ASP cc_start: 0.8097 (p0) cc_final: 0.7771 (p0)
REVERT: E  688 LEU cc_start: 0.6611 (OUTLIER) cc_final: 0.6154 (mp)
REVERT: E  698 LYS cc_start: 0.7690 (mtmm) cc_final: 0.7422 (mttm)
REVERT: F   73 GLU cc_start: 0.8262 (tp30) cc_final: 0.7931 (tp30)
REVERT: F  117 ASP cc_start: 0.8362 (t0) cc_final: 0.7936 (m-30)
REVERT: F  149 VAL cc_start: 0.7853 (t) cc_final: 0.7467 (p)
REVERT: F  214 ARG cc_start: 0.8400 (ttm-80) cc_final: 0.8062 (mmm-85)
REVERT: F  335 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6849 (mt-10)
REVERT: F  372 LYS cc_start: 0.8591 (ttpp) cc_final: 0.8257 (ttpt)
REVERT: F  421 MET cc_start: 0.8472 (tpp) cc_final: 0.8080 (mmm)
REVERT: F  431 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7789 (tm-30)
REVERT: F  513 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7494 (mm-30)
REVERT: F  532 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7661 (mm)
REVERT: F  544 GLU cc_start: 0.8359 (mp0) cc_final: 0.8118 (pm20)
REVERT: F  594 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6027 (tpt)
REVERT: G  103 LYS cc_start: 0.5468 (OUTLIER) cc_final: 0.4619 (tttt)
REVERT: G  112 GLU cc_start: 0.8081 (mp0) cc_final: 0.7244 (pp20)
REVERT: G  216 GLU cc_start: 0.8043 (pt0) cc_final: 0.7581 (pm20)
REVERT: H  103 LYS cc_start: 0.5421 (OUTLIER) cc_final: 0.4955 (tmtt)
REVERT: H  136 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.6599 (mtp-110)
REVERT: H  163 LYS cc_start: 0.8879 (mtpp) cc_final: 0.8550 (mtmm)
REVERT: H  210 PHE cc_start: 0.8037 (t80) cc_final: 0.7782 (t80)
REVERT: H  216 GLU cc_start: 0.8110 (pt0) cc_final: 0.7527 (pm20)
REVERT: I  102 LEU cc_start: 0.8023 (mm) cc_final: 0.7780 (mm)
REVERT: I  163 LYS cc_start: 0.8870 (mtpp) cc_final: 0.8555 (mtmm)
REVERT: I  216 GLU cc_start: 0.8134 (pt0) cc_final: 0.7659 (pm20)
REVERT: J  103 LYS cc_start: 0.5408 (OUTLIER) cc_final: 0.4930 (tmtt)
REVERT: J  136 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6948 (mtp-110)
REVERT: J  216 GLU cc_start: 0.8122 (pt0) cc_final: 0.7487 (pm20)
REVERT: K  103 LYS cc_start: 0.5490 (OUTLIER) cc_final: 0.4622 (tttt)
REVERT: K  112 GLU cc_start: 0.8044 (mp0) cc_final: 0.7253 (pp20)
REVERT: K  216 GLU cc_start: 0.8037 (pt0) cc_final: 0.7559 (pm20)
REVERT: L  102 LEU cc_start: 0.8009 (mm) cc_final: 0.7766 (mm)
REVERT: L  216 GLU cc_start: 0.8147 (pt0) cc_final: 0.7672 (pm20)
  outliers start: 173
  outliers final: 81
  residues processed: 858
  average time/residue: 0.7648
  time to fit residues: 787.0545
Evaluate side-chains
  838 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 108
    poor density    : 730
  time to evaluate  : 1.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  131 THR
Chi-restraints excluded: chain A residue  207 GLN
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  594 MET
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  346 THR
Chi-restraints excluded: chain B residue  357 GLU
Chi-restraints excluded: chain B residue  363 MET
Chi-restraints excluded: chain B residue  388 ASP
Chi-restraints excluded: chain B residue  411 GLU
Chi-restraints excluded: chain B residue  482 LYS
Chi-restraints excluded: chain B residue  490 MET
Chi-restraints excluded: chain B residue  550 ASP
Chi-restraints excluded: chain B residue  574 GLU
Chi-restraints excluded: chain B residue  647 LYS
Chi-restraints excluded: chain B residue  688 LEU
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  282 ILE
Chi-restraints excluded: chain C residue  335 GLU
Chi-restraints excluded: chain C residue  445 MET
Chi-restraints excluded: chain C residue  454 SER
Chi-restraints excluded: chain C residue  482 LYS
Chi-restraints excluded: chain C residue  532 LEU
Chi-restraints excluded: chain C residue  550 ASP
Chi-restraints excluded: chain C residue  574 GLU
Chi-restraints excluded: chain C residue  594 MET
Chi-restraints excluded: chain C residue  613 VAL
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  131 THR
Chi-restraints excluded: chain D residue  207 GLN
Chi-restraints excluded: chain D residue  245 SER
Chi-restraints excluded: chain D residue  282 ILE
Chi-restraints excluded: chain D residue  324 THR
Chi-restraints excluded: chain D residue  346 THR
Chi-restraints excluded: chain D residue  688 LEU
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  104 LEU
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain E residue  161 VAL
Chi-restraints excluded: chain E residue  282 ILE
Chi-restraints excluded: chain E residue  324 THR
Chi-restraints excluded: chain E residue  346 THR
Chi-restraints excluded: chain E residue  357 GLU
Chi-restraints excluded: chain E residue  363 MET
Chi-restraints excluded: chain E residue  388 ASP
Chi-restraints excluded: chain E residue  411 GLU
Chi-restraints excluded: chain E residue  482 LYS
Chi-restraints excluded: chain E residue  490 MET
Chi-restraints excluded: chain E residue  550 ASP
Chi-restraints excluded: chain E residue  574 GLU
Chi-restraints excluded: chain E residue  647 LYS
Chi-restraints excluded: chain E residue  688 LEU
Chi-restraints excluded: chain F residue   91 THR
Chi-restraints excluded: chain F residue  245 SER
Chi-restraints excluded: chain F residue  282 ILE
Chi-restraints excluded: chain F residue  335 GLU
Chi-restraints excluded: chain F residue  445 MET
Chi-restraints excluded: chain F residue  454 SER
Chi-restraints excluded: chain F residue  482 LYS
Chi-restraints excluded: chain F residue  532 LEU
Chi-restraints excluded: chain F residue  574 GLU
Chi-restraints excluded: chain F residue  594 MET
Chi-restraints excluded: chain F residue  613 VAL
Chi-restraints excluded: chain F residue  673 MET
Chi-restraints excluded: chain G residue  103 LYS
Chi-restraints excluded: chain G residue  131 ILE
Chi-restraints excluded: chain G residue  143 LEU
Chi-restraints excluded: chain G residue  148 SER
Chi-restraints excluded: chain G residue  180 GLN
Chi-restraints excluded: chain G residue  209 ASP
Chi-restraints excluded: chain H residue  103 LYS
Chi-restraints excluded: chain H residue  115 LEU
Chi-restraints excluded: chain H residue  131 ILE
Chi-restraints excluded: chain H residue  136 ARG
Chi-restraints excluded: chain H residue  143 LEU
Chi-restraints excluded: chain H residue  185 GLU
Chi-restraints excluded: chain I residue   30 LEU
Chi-restraints excluded: chain I residue  131 ILE
Chi-restraints excluded: chain I residue  136 ARG
Chi-restraints excluded: chain I residue  143 LEU
Chi-restraints excluded: chain I residue  194 VAL
Chi-restraints excluded: chain I residue  218 LEU
Chi-restraints excluded: chain J residue  103 LYS
Chi-restraints excluded: chain J residue  115 LEU
Chi-restraints excluded: chain J residue  131 ILE
Chi-restraints excluded: chain J residue  136 ARG
Chi-restraints excluded: chain J residue  185 GLU
Chi-restraints excluded: chain K residue  103 LYS
Chi-restraints excluded: chain K residue  131 ILE
Chi-restraints excluded: chain K residue  148 SER
Chi-restraints excluded: chain K residue  180 GLN
Chi-restraints excluded: chain K residue  209 ASP
Chi-restraints excluded: chain L residue  131 ILE
Chi-restraints excluded: chain L residue  136 ARG
Chi-restraints excluded: chain L residue  143 LEU
Chi-restraints excluded: chain L residue  185 GLU
Chi-restraints excluded: chain L residue  194 VAL
Chi-restraints excluded: chain L residue  218 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 498
   random chunks:
   chunk 157 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 156 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 251 optimal weight:    0.4980
   chunk 34 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 114 optimal weight:    3.9990
   chunk 242 optimal weight:    4.9990
   chunk 270 optimal weight:    0.8980
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 298 GLN
** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 660 GLN
C 480 ASN
** C 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 298 GLN
D 390 GLN
D 596 GLN
D 653 ASN
F 358 GLN
** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 180 GLN
J 180 GLN
** L 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.140801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.115300 restraints weight = 57944.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3816 rms_B_bonded: 2.36
r_work: 0.3674 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.2770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  39678  Z= 0.146
  Angle     :  0.574   8.997  53496  Z= 0.291
  Chirality :  0.041   0.233   5754
  Planarity :  0.004   0.061   7182
  Dihedral  :  4.171  33.927   5445
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 23.23 %
    Favored  : 72.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.12), residues: 4980
  helix:  0.53 (0.09), residues: 3420
  sheet: -2.75 (0.60), residues: 60
  loop : -1.10 (0.15), residues: 1500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 323 
 TYR   0.018   0.001   TYR J 138 
 PHE   0.013   0.001   PHE F 167 
 TRP   0.017   0.001   TRP A 351 
 HIS   0.003   0.001   HIS F 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (39678)
  covalent geometry    : angle       0.57367 (53496)
  hydrogen bonds       : bond        0.03563 ( 2148)
  hydrogen bonds       : angle       3.66117 ( 6354)

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

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

  9960 Ramachandran restraints generated.
    4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  9960 Ramachandran restraints generated.
    4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  933 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 166
    poor density    : 767
  time to evaluate  : 1.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ASP cc_start: 0.7719 (m-30) cc_final: 0.7444 (m-30)
REVERT: A  149 VAL cc_start: 0.7696 (t) cc_final: 0.7394 (p)
REVERT: A  188 GLN cc_start: 0.7349 (pp30) cc_final: 0.7112 (pp30)
REVERT: A  207 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7564 (tp-100)
REVERT: A  214 ARG cc_start: 0.8215 (mmm160) cc_final: 0.7965 (ttm-80)
REVERT: A  262 MET cc_start: 0.7827 (ttp) cc_final: 0.7578 (mtp)
REVERT: A  357 GLU cc_start: 0.7435 (tt0) cc_final: 0.7213 (tt0)
REVERT: A  363 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.7032 (ttt)
REVERT: A  403 ASP cc_start: 0.7281 (t0) cc_final: 0.7065 (t0)
REVERT: A  431 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7352 (tm-30)
REVERT: A  456 ASP cc_start: 0.8382 (t0) cc_final: 0.7683 (p0)
REVERT: A  519 ASP cc_start: 0.7318 (m-30) cc_final: 0.6806 (m-30)
REVERT: A  574 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7329 (mm-30)
REVERT: A  625 MET cc_start: 0.8485 (mtt) cc_final: 0.8026 (mtm)
REVERT: A  664 TYR cc_start: 0.7255 (t80) cc_final: 0.6998 (t80)
REVERT: B  117 ASP cc_start: 0.8331 (t0) cc_final: 0.7875 (m-30)
REVERT: B  119 ASP cc_start: 0.7805 (m-30) cc_final: 0.7602 (m-30)
REVERT: B  149 VAL cc_start: 0.7671 (t) cc_final: 0.7234 (p)
REVERT: B  363 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.6983 (ttt)
REVERT: B  388 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7851 (t0)
REVERT: B  405 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8803 (mtmm)
REVERT: B  431 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7467 (tm-30)
REVERT: B  455 LYS cc_start: 0.8999 (ptmm) cc_final: 0.8480 (pmtt)
REVERT: B  550 ASP cc_start: 0.6684 (OUTLIER) cc_final: 0.6216 (t70)
REVERT: B  574 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6974 (mp0)
REVERT: B  581 ASP cc_start: 0.8105 (m-30) cc_final: 0.7778 (m-30)
REVERT: B  602 LYS cc_start: 0.8645 (ttmm) cc_final: 0.8266 (tptt)
REVERT: B  625 MET cc_start: 0.8618 (mtt) cc_final: 0.8238 (mtm)
REVERT: B  647 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6901 (mtpt)
REVERT: B  673 MET cc_start: 0.8692 (ttp) cc_final: 0.8486 (ttp)
REVERT: B  684 ASP cc_start: 0.7963 (p0) cc_final: 0.7648 (p0)
REVERT: B  688 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6185 (mp)
REVERT: B  698 LYS cc_start: 0.7788 (mtmm) cc_final: 0.7535 (mttp)
REVERT: C   73 GLU cc_start: 0.8133 (tp30) cc_final: 0.7823 (tp30)
REVERT: C  117 ASP cc_start: 0.8224 (t0) cc_final: 0.7785 (m-30)
REVERT: C  145 GLU cc_start: 0.7360 (mm-30) cc_final: 0.7148 (pp20)
REVERT: C  214 ARG cc_start: 0.8291 (ttm-80) cc_final: 0.7886 (mtp85)
REVERT: C  323 ARG cc_start: 0.7466 (mtt-85) cc_final: 0.7092 (mtt90)
REVERT: C  372 LYS cc_start: 0.8556 (ttpp) cc_final: 0.8218 (ttpt)
REVERT: C  421 MET cc_start: 0.8349 (tpp) cc_final: 0.7880 (mmm)
REVERT: C  513 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7285 (mm-30)
REVERT: C  543 LYS cc_start: 0.7242 (tppt) cc_final: 0.6728 (tppt)
REVERT: C  550 ASP cc_start: 0.7026 (OUTLIER) cc_final: 0.6222 (t70)
REVERT: C  592 MET cc_start: 0.6260 (tmm) cc_final: 0.5945 (tmm)
REVERT: C  594 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6446 (tpp)
REVERT: C  673 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8188 (tpp)
REVERT: D  149 VAL cc_start: 0.7693 (t) cc_final: 0.7401 (p)
REVERT: D  196 MET cc_start: 0.6815 (mtt) cc_final: 0.6561 (ttm)
REVERT: D  207 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7603 (tp40)
REVERT: D  262 MET cc_start: 0.7767 (ttp) cc_final: 0.7495 (mtp)
REVERT: D  403 ASP cc_start: 0.7350 (t0) cc_final: 0.7143 (t0)
REVERT: D  431 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7359 (tm-30)
REVERT: D  456 ASP cc_start: 0.8320 (t0) cc_final: 0.7687 (p0)
REVERT: D  519 ASP cc_start: 0.7333 (m-30) cc_final: 0.6823 (m-30)
REVERT: D  561 LYS cc_start: 0.9104 (pmtt) cc_final: 0.8751 (mmmt)
REVERT: D  574 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7334 (mm-30)
REVERT: D  592 MET cc_start: 0.6440 (tmm) cc_final: 0.5767 (tmt)
REVERT: D  625 MET cc_start: 0.8493 (mtt) cc_final: 0.8139 (mtt)
REVERT: E  149 VAL cc_start: 0.7647 (t) cc_final: 0.7099 (p)
REVERT: E  152 GLU cc_start: 0.7406 (pp20) cc_final: 0.7168 (pp20)
REVERT: E  363 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.6962 (ttt)
REVERT: E  378 MET cc_start: 0.7962 (ttm) cc_final: 0.7646 (ttt)
REVERT: E  388 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7846 (t0)
REVERT: E  431 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7464 (tm-30)
REVERT: E  455 LYS cc_start: 0.9004 (ptmm) cc_final: 0.8485 (pmtt)
REVERT: E  513 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7212 (mm-30)
REVERT: E  550 ASP cc_start: 0.6658 (OUTLIER) cc_final: 0.6182 (t70)
REVERT: E  574 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6997 (mp0)
REVERT: E  581 ASP cc_start: 0.8113 (m-30) cc_final: 0.7795 (m-30)
REVERT: E  602 LYS cc_start: 0.8634 (ttmm) cc_final: 0.8281 (tptt)
REVERT: E  625 MET cc_start: 0.8620 (mtt) cc_final: 0.8239 (mtm)
REVERT: E  647 LYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6882 (mtpt)
REVERT: E  673 MET cc_start: 0.8651 (ttp) cc_final: 0.8419 (ttp)
REVERT: E  684 ASP cc_start: 0.7970 (p0) cc_final: 0.7657 (p0)
REVERT: E  688 LEU cc_start: 0.6606 (OUTLIER) cc_final: 0.6143 (mp)
REVERT: E  698 LYS cc_start: 0.7751 (mtmm) cc_final: 0.7480 (mttp)
REVERT: F   73 GLU cc_start: 0.8142 (tp30) cc_final: 0.7845 (tp30)
REVERT: F  117 ASP cc_start: 0.8212 (t0) cc_final: 0.7834 (m-30)
REVERT: F  145 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7153 (pp20)
REVERT: F  214 ARG cc_start: 0.8298 (ttm-80) cc_final: 0.7829 (mtp85)
REVERT: F  323 ARG cc_start: 0.7485 (mtt-85) cc_final: 0.7146 (mtt90)
REVERT: F  405 LYS cc_start: 0.9072 (mtmp) cc_final: 0.8737 (ptpt)
REVERT: F  421 MET cc_start: 0.8345 (tpp) cc_final: 0.7919 (mmm)
REVERT: F  513 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7296 (mm-30)
REVERT: F  544 GLU cc_start: 0.8183 (mp0) cc_final: 0.7940 (pm20)
REVERT: F  594 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.5853 (tpt)
REVERT: G  112 GLU cc_start: 0.8020 (mp0) cc_final: 0.7234 (pp20)
REVERT: G  216 GLU cc_start: 0.7894 (pt0) cc_final: 0.7494 (pm20)
REVERT: H  150 MET cc_start: 0.6581 (mpp) cc_final: 0.6372 (mpt)
REVERT: H  163 LYS cc_start: 0.8768 (mtpp) cc_final: 0.8469 (mtmm)
REVERT: H  210 PHE cc_start: 0.7977 (t80) cc_final: 0.7705 (t80)
REVERT: H  216 GLU cc_start: 0.7973 (pt0) cc_final: 0.7375 (pm20)
REVERT: I  102 LEU cc_start: 0.7996 (mm) cc_final: 0.7766 (mm)
REVERT: I  112 GLU cc_start: 0.7826 (mp0) cc_final: 0.7017 (tm-30)
REVERT: I  208 LYS cc_start: 0.7241 (tttm) cc_final: 0.6914 (tttp)
REVERT: I  216 GLU cc_start: 0.8056 (pt0) cc_final: 0.7587 (pm20)
REVERT: J  103 LYS cc_start: 0.5369 (OUTLIER) cc_final: 0.4922 (tmtt)
REVERT: J  136 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.6820 (mtp-110)
REVERT: J  150 MET cc_start: 0.6507 (mpp) cc_final: 0.6305 (mpt)
REVERT: J  163 LYS cc_start: 0.8791 (mtpp) cc_final: 0.8485 (mtmm)
REVERT: J  210 PHE cc_start: 0.7865 (t80) cc_final: 0.7617 (t80)
REVERT: J  216 GLU cc_start: 0.7941 (pt0) cc_final: 0.7335 (pm20)
REVERT: K  103 LYS cc_start: 0.5405 (OUTLIER) cc_final: 0.4578 (tttt)
REVERT: K  112 GLU cc_start: 0.8019 (mp0) cc_final: 0.7233 (pp20)
REVERT: K  216 GLU cc_start: 0.7889 (pt0) cc_final: 0.7451 (pm20)
REVERT: L  102 LEU cc_start: 0.7990 (mm) cc_final: 0.7760 (mm)
REVERT: L  112 GLU cc_start: 0.8070 (mp0) cc_final: 0.6935 (tm-30)
REVERT: L  208 LYS cc_start: 0.7246 (tttm) cc_final: 0.6923 (tttp)
REVERT: L  216 GLU cc_start: 0.8056 (pt0) cc_final: 0.7585 (pm20)
  outliers start: 166
  outliers final: 80
  residues processed: 849
  average time/residue: 0.7749
  time to fit residues: 789.5834
Evaluate side-chains
  841 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 103
    poor density    : 738
  time to evaluate  : 1.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  131 THR
Chi-restraints excluded: chain A residue  207 GLN
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  490 MET
Chi-restraints excluded: chain A residue  594 MET
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  161 VAL
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  346 THR
Chi-restraints excluded: chain B residue  363 MET
Chi-restraints excluded: chain B residue  388 ASP
Chi-restraints excluded: chain B residue  405 LYS
Chi-restraints excluded: chain B residue  454 SER
Chi-restraints excluded: chain B residue  482 LYS
Chi-restraints excluded: chain B residue  550 ASP
Chi-restraints excluded: chain B residue  574 GLU
Chi-restraints excluded: chain B residue  647 LYS
Chi-restraints excluded: chain B residue  688 LEU
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  282 ILE
Chi-restraints excluded: chain C residue  445 MET
Chi-restraints excluded: chain C residue  454 SER
Chi-restraints excluded: chain C residue  482 LYS
Chi-restraints excluded: chain C residue  490 MET
Chi-restraints excluded: chain C residue  550 ASP
Chi-restraints excluded: chain C residue  574 GLU
Chi-restraints excluded: chain C residue  594 MET
Chi-restraints excluded: chain C residue  673 MET
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  131 THR
Chi-restraints excluded: chain D residue  207 GLN
Chi-restraints excluded: chain D residue  245 SER
Chi-restraints excluded: chain D residue  282 ILE
Chi-restraints excluded: chain D residue  324 THR
Chi-restraints excluded: chain D residue  346 THR
Chi-restraints excluded: chain D residue  688 LEU
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  104 LEU
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain E residue  161 VAL
Chi-restraints excluded: chain E residue  282 ILE
Chi-restraints excluded: chain E residue  324 THR
Chi-restraints excluded: chain E residue  346 THR
Chi-restraints excluded: chain E residue  363 MET
Chi-restraints excluded: chain E residue  388 ASP
Chi-restraints excluded: chain E residue  454 SER
Chi-restraints excluded: chain E residue  482 LYS
Chi-restraints excluded: chain E residue  490 MET
Chi-restraints excluded: chain E residue  550 ASP
Chi-restraints excluded: chain E residue  574 GLU
Chi-restraints excluded: chain E residue  647 LYS
Chi-restraints excluded: chain E residue  688 LEU
Chi-restraints excluded: chain F residue   91 THR
Chi-restraints excluded: chain F residue  245 SER
Chi-restraints excluded: chain F residue  282 ILE
Chi-restraints excluded: chain F residue  445 MET
Chi-restraints excluded: chain F residue  454 SER
Chi-restraints excluded: chain F residue  482 LYS
Chi-restraints excluded: chain F residue  490 MET
Chi-restraints excluded: chain F residue  565 ILE
Chi-restraints excluded: chain F residue  574 GLU
Chi-restraints excluded: chain F residue  594 MET
Chi-restraints excluded: chain F residue  673 MET
Chi-restraints excluded: chain G residue  131 ILE
Chi-restraints excluded: chain G residue  143 LEU
Chi-restraints excluded: chain G residue  148 SER
Chi-restraints excluded: chain G residue  209 ASP
Chi-restraints excluded: chain H residue  115 LEU
Chi-restraints excluded: chain H residue  131 ILE
Chi-restraints excluded: chain H residue  143 LEU
Chi-restraints excluded: chain H residue  185 GLU
Chi-restraints excluded: chain H residue  194 VAL
Chi-restraints excluded: chain I residue   30 LEU
Chi-restraints excluded: chain I residue  131 ILE
Chi-restraints excluded: chain I residue  136 ARG
Chi-restraints excluded: chain I residue  143 LEU
Chi-restraints excluded: chain I residue  194 VAL
Chi-restraints excluded: chain J residue  103 LYS
Chi-restraints excluded: chain J residue  115 LEU
Chi-restraints excluded: chain J residue  131 ILE
Chi-restraints excluded: chain J residue  136 ARG
Chi-restraints excluded: chain J residue  143 LEU
Chi-restraints excluded: chain J residue  185 GLU
Chi-restraints excluded: chain K residue  103 LYS
Chi-restraints excluded: chain K residue  131 ILE
Chi-restraints excluded: chain K residue  143 LEU
Chi-restraints excluded: chain K residue  148 SER
Chi-restraints excluded: chain K residue  194 VAL
Chi-restraints excluded: chain K residue  209 ASP
Chi-restraints excluded: chain L residue  131 ILE
Chi-restraints excluded: chain L residue  136 ARG
Chi-restraints excluded: chain L residue  143 LEU
Chi-restraints excluded: chain L residue  185 GLU
Chi-restraints excluded: chain L residue  194 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 498
   random chunks:
   chunk 302 optimal weight:    5.9990
   chunk 194 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 485 optimal weight:    7.9990
   chunk 241 optimal weight:    0.8980
   chunk 223 optimal weight:    0.8980
   chunk 239 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0870
   chunk 252 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9990
   chunk 262 optimal weight:    2.9990
   overall best weight:    0.7760

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

Flipped N/Q/H residues before XYZ refinement:
B 498 ASN
** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 298 GLN
** C 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 653 ASN
** E 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 180 GLN
J 180 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.142521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.116916 restraints weight = 57876.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3830 rms_B_bonded: 2.37
r_work: 0.3688 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.2968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  39678  Z= 0.130
  Angle     :  0.580   9.410  53496  Z= 0.292
  Chirality :  0.040   0.225   5754
  Planarity :  0.004   0.058   7182
  Dihedral  :  4.082  33.916   5445
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 24.78 %
    Favored  : 71.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.12), residues: 4980
  helix:  0.79 (0.09), residues: 3414
  sheet: -2.48 (0.65), residues: 60
  loop : -1.06 (0.15), residues: 1506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG E 586 
 TYR   0.017   0.001   TYR H 138 
 PHE   0.013   0.001   PHE F 167 
 TRP   0.021   0.001   TRP A 351 
 HIS   0.002   0.001   HIS E 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (39678)
  covalent geometry    : angle       0.58023 (53496)
  hydrogen bonds       : bond        0.03396 ( 2148)
  hydrogen bonds       : angle       3.57804 ( 6354)

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

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

  9960 Ramachandran restraints generated.
    4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  9960 Ramachandran restraints generated.
    4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  918 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 144
    poor density    : 774
  time to evaluate  : 1.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ASP cc_start: 0.7664 (m-30) cc_final: 0.7414 (m-30)
REVERT: A  149 VAL cc_start: 0.7796 (t) cc_final: 0.7528 (p)
REVERT: A  167 PHE cc_start: 0.7855 (t80) cc_final: 0.7577 (t80)
REVERT: A  196 MET cc_start: 0.6836 (mtt) cc_final: 0.6597 (ttm)
REVERT: A  207 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7605 (tp-100)
REVERT: A  214 ARG cc_start: 0.8204 (mmm160) cc_final: 0.7996 (ttm-80)
REVERT: A  262 MET cc_start: 0.7784 (ttp) cc_final: 0.7541 (mtp)
REVERT: A  363 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.7032 (ttt)
REVERT: A  431 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7329 (tm-30)
REVERT: A  456 ASP cc_start: 0.8334 (t0) cc_final: 0.7706 (p0)
REVERT: A  519 ASP cc_start: 0.7296 (m-30) cc_final: 0.6803 (m-30)
REVERT: A  561 LYS cc_start: 0.9090 (pmtt) cc_final: 0.8678 (mmmt)
REVERT: A  574 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7257 (mm-30)
REVERT: A  625 MET cc_start: 0.8482 (mtt) cc_final: 0.8043 (mtm)
REVERT: B  117 ASP cc_start: 0.8298 (t0) cc_final: 0.7865 (m-30)
REVERT: B  119 ASP cc_start: 0.7721 (m-30) cc_final: 0.7461 (m-30)
REVERT: B  149 VAL cc_start: 0.7718 (t) cc_final: 0.7302 (p)
REVERT: B  335 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6875 (mp0)
REVERT: B  363 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.7038 (ttt)
REVERT: B  378 MET cc_start: 0.7832 (ttp) cc_final: 0.7603 (ttt)
REVERT: B  388 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7771 (t70)
REVERT: B  431 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7483 (tm-30)
REVERT: B  455 LYS cc_start: 0.8997 (ptmm) cc_final: 0.8486 (pmtt)
REVERT: B  550 ASP cc_start: 0.6809 (OUTLIER) cc_final: 0.6372 (t70)
REVERT: B  574 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6905 (mp0)
REVERT: B  581 ASP cc_start: 0.8133 (m-30) cc_final: 0.7804 (m-30)
REVERT: B  590 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6681 (pm20)
REVERT: B  592 MET cc_start: 0.6410 (tmm) cc_final: 0.5520 (tmt)
REVERT: B  594 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6337 (tpp)
REVERT: B  602 LYS cc_start: 0.8664 (ttmm) cc_final: 0.8263 (tptt)
REVERT: B  625 MET cc_start: 0.8617 (mtt) cc_final: 0.8264 (mtm)
REVERT: B  647 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6895 (mtpt)
REVERT: B  661 LEU cc_start: 0.8592 (mp) cc_final: 0.8336 (mt)
REVERT: B  673 MET cc_start: 0.8638 (ttp) cc_final: 0.8330 (ttp)
REVERT: B  684 ASP cc_start: 0.7967 (p0) cc_final: 0.7683 (p0)
REVERT: B  688 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6238 (mp)
REVERT: B  698 LYS cc_start: 0.7869 (mtmm) cc_final: 0.7656 (mttp)
REVERT: C   73 GLU cc_start: 0.8117 (tp30) cc_final: 0.7872 (tp30)
REVERT: C  117 ASP cc_start: 0.8151 (t0) cc_final: 0.7828 (m-30)
REVERT: C  214 ARG cc_start: 0.8251 (ttm-80) cc_final: 0.7988 (mmm-85)
REVERT: C  335 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6801 (mp0)
REVERT: C  405 LYS cc_start: 0.9063 (mtmp) cc_final: 0.8742 (ptpt)
REVERT: C  421 MET cc_start: 0.8340 (tpp) cc_final: 0.7934 (mmm)
REVERT: C  451 GLN cc_start: 0.7791 (tm-30) cc_final: 0.7481 (tm-30)
REVERT: C  513 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7216 (mm-30)
REVERT: C  533 ASP cc_start: 0.7856 (m-30) cc_final: 0.7610 (m-30)
REVERT: C  543 LYS cc_start: 0.7222 (tppt) cc_final: 0.6731 (tppt)
REVERT: C  550 ASP cc_start: 0.7080 (OUTLIER) cc_final: 0.6351 (t70)
REVERT: C  592 MET cc_start: 0.6521 (tmm) cc_final: 0.6058 (tmm)
REVERT: C  594 MET cc_start: 0.6983 (OUTLIER) cc_final: 0.6499 (tpp)
REVERT: C  663 MET cc_start: 0.8069 (ttp) cc_final: 0.7705 (ttp)
REVERT: D  149 VAL cc_start: 0.7771 (t) cc_final: 0.7507 (p)
REVERT: D  167 PHE cc_start: 0.7850 (t80) cc_final: 0.7567 (t80)
REVERT: D  196 MET cc_start: 0.6829 (mtt) cc_final: 0.6585 (ttm)
REVERT: D  207 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7605 (tp-100)
REVERT: D  262 MET cc_start: 0.7737 (ttp) cc_final: 0.7510 (mtp)
REVERT: D  431 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7325 (tm-30)
REVERT: D  456 ASP cc_start: 0.8308 (t0) cc_final: 0.7673 (p0)
REVERT: D  519 ASP cc_start: 0.7305 (m-30) cc_final: 0.6811 (m-30)
REVERT: D  561 LYS cc_start: 0.9061 (pmtt) cc_final: 0.8690 (mmmt)
REVERT: D  574 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7266 (mm-30)
REVERT: D  625 MET cc_start: 0.8487 (mtt) cc_final: 0.8128 (mtt)
REVERT: E  119 ASP cc_start: 0.7803 (m-30) cc_final: 0.7564 (m-30)
REVERT: E  149 VAL cc_start: 0.7721 (t) cc_final: 0.7248 (p)
REVERT: E  335 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6898 (mp0)
REVERT: E  363 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.7037 (ttt)
REVERT: E  378 MET cc_start: 0.7988 (ttm) cc_final: 0.7763 (ttp)
REVERT: E  388 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7855 (t70)
REVERT: E  431 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7439 (tm-30)
REVERT: E  455 LYS cc_start: 0.9006 (ptmm) cc_final: 0.8488 (pmtt)
REVERT: E  513 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7224 (mm-30)
REVERT: E  550 ASP cc_start: 0.6717 (OUTLIER) cc_final: 0.6199 (t70)
REVERT: E  574 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6986 (mp0)
REVERT: E  581 ASP cc_start: 0.8132 (m-30) cc_final: 0.7804 (m-30)
REVERT: E  590 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6692 (pm20)
REVERT: E  592 MET cc_start: 0.6390 (tmm) cc_final: 0.5525 (tmt)
REVERT: E  594 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.6282 (tpp)
REVERT: E  625 MET cc_start: 0.8612 (mtt) cc_final: 0.8270 (mtm)
REVERT: E  647 LYS cc_start: 0.7151 (OUTLIER) cc_final: 0.6876 (mtpt)
REVERT: E  673 MET cc_start: 0.8627 (ttp) cc_final: 0.8344 (ttp)
REVERT: E  684 ASP cc_start: 0.7984 (p0) cc_final: 0.7696 (p0)
REVERT: E  688 LEU cc_start: 0.6693 (OUTLIER) cc_final: 0.6245 (mp)
REVERT: E  690 LYS cc_start: 0.8038 (tmtt) cc_final: 0.7794 (tmmm)
REVERT: E  698 LYS cc_start: 0.7837 (mtmm) cc_final: 0.7599 (mttp)
REVERT: F   73 GLU cc_start: 0.8118 (tp30) cc_final: 0.7879 (tp30)
REVERT: F  117 ASP cc_start: 0.8173 (t0) cc_final: 0.7807 (m-30)
REVERT: F  149 VAL cc_start: 0.7863 (t) cc_final: 0.7553 (p)
REVERT: F  214 ARG cc_start: 0.8257 (ttm-80) cc_final: 0.7984 (mmm-85)
REVERT: F  405 LYS cc_start: 0.9079 (mtmp) cc_final: 0.8724 (ptpt)
REVERT: F  421 MET cc_start: 0.8325 (tpp) cc_final: 0.7965 (mmm)
REVERT: F  482 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8275 (ptpt)
REVERT: F  513 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7282 (mm-30)
REVERT: F  543 LYS cc_start: 0.7424 (tppt) cc_final: 0.7071 (tppt)
REVERT: F  544 GLU cc_start: 0.8123 (mp0) cc_final: 0.7892 (pm20)
REVERT: F  550 ASP cc_start: 0.7057 (OUTLIER) cc_final: 0.6349 (t70)
REVERT: F  594 MET cc_start: 0.7036 (OUTLIER) cc_final: 0.5989 (tpt)
REVERT: G  216 GLU cc_start: 0.7911 (pt0) cc_final: 0.7504 (pm20)
REVERT: H  163 LYS cc_start: 0.8730 (mtpp) cc_final: 0.8457 (mtmm)
REVERT: H  210 PHE cc_start: 0.8053 (t80) cc_final: 0.7750 (t80)
REVERT: H  216 GLU cc_start: 0.7948 (pt0) cc_final: 0.7477 (pm20)
REVERT: I  102 LEU cc_start: 0.7974 (mm) cc_final: 0.7759 (mm)
REVERT: I  208 LYS cc_start: 0.7276 (tttm) cc_final: 0.6973 (tttp)
REVERT: I  216 GLU cc_start: 0.8083 (pt0) cc_final: 0.7615 (pm20)
REVERT: J  136 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6730 (mtp-110)
REVERT: J  163 LYS cc_start: 0.8776 (mtpp) cc_final: 0.8479 (mtmm)
REVERT: J  210 PHE cc_start: 0.7923 (t80) cc_final: 0.7697 (t80)
REVERT: J  216 GLU cc_start: 0.7907 (pt0) cc_final: 0.7463 (pm20)
REVERT: K  216 GLU cc_start: 0.7900 (pt0) cc_final: 0.7501 (pm20)
REVERT: L  102 LEU cc_start: 0.7978 (mm) cc_final: 0.7763 (mm)
REVERT: L  112 GLU cc_start: 0.8074 (mp0) cc_final: 0.6988 (tm-30)
REVERT: L  163 LYS cc_start: 0.8727 (mtpp) cc_final: 0.8402 (mtmm)
REVERT: L  208 LYS cc_start: 0.7268 (tttm) cc_final: 0.6964 (tttp)
REVERT: L  216 GLU cc_start: 0.8080 (pt0) cc_final: 0.7610 (pm20)
  outliers start: 144
  outliers final: 66
  residues processed: 841
  average time/residue: 0.7796
  time to fit residues: 784.2085
Evaluate side-chains
  838 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 94
    poor density    : 744
  time to evaluate  : 1.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  131 THR
Chi-restraints excluded: chain A residue  207 GLN
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  454 SER
Chi-restraints excluded: chain A residue  490 MET
Chi-restraints excluded: chain A residue  594 MET
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  335 GLU
Chi-restraints excluded: chain B residue  346 THR
Chi-restraints excluded: chain B residue  363 MET
Chi-restraints excluded: chain B residue  388 ASP
Chi-restraints excluded: chain B residue  411 GLU
Chi-restraints excluded: chain B residue  454 SER
Chi-restraints excluded: chain B residue  482 LYS
Chi-restraints excluded: chain B residue  550 ASP
Chi-restraints excluded: chain B residue  574 GLU
Chi-restraints excluded: chain B residue  590 GLU
Chi-restraints excluded: chain B residue  594 MET
Chi-restraints excluded: chain B residue  647 LYS
Chi-restraints excluded: chain B residue  688 LEU
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  335 GLU
Chi-restraints excluded: chain C residue  454 SER
Chi-restraints excluded: chain C residue  482 LYS
Chi-restraints excluded: chain C residue  490 MET
Chi-restraints excluded: chain C residue  550 ASP
Chi-restraints excluded: chain C residue  574 GLU
Chi-restraints excluded: chain C residue  594 MET
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  131 THR
Chi-restraints excluded: chain D residue  207 GLN
Chi-restraints excluded: chain D residue  245 SER
Chi-restraints excluded: chain D residue  282 ILE
Chi-restraints excluded: chain D residue  346 THR
Chi-restraints excluded: chain D residue  688 LEU
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  104 LEU
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain E residue  282 ILE
Chi-restraints excluded: chain E residue  335 GLU
Chi-restraints excluded: chain E residue  346 THR
Chi-restraints excluded: chain E residue  363 MET
Chi-restraints excluded: chain E residue  388 ASP
Chi-restraints excluded: chain E residue  454 SER
Chi-restraints excluded: chain E residue  482 LYS
Chi-restraints excluded: chain E residue  550 ASP
Chi-restraints excluded: chain E residue  574 GLU
Chi-restraints excluded: chain E residue  590 GLU
Chi-restraints excluded: chain E residue  594 MET
Chi-restraints excluded: chain E residue  647 LYS
Chi-restraints excluded: chain E residue  688 LEU
Chi-restraints excluded: chain F residue   91 THR
Chi-restraints excluded: chain F residue  245 SER
Chi-restraints excluded: chain F residue  445 MET
Chi-restraints excluded: chain F residue  454 SER
Chi-restraints excluded: chain F residue  482 LYS
Chi-restraints excluded: chain F residue  490 MET
Chi-restraints excluded: chain F residue  550 ASP
Chi-restraints excluded: chain F residue  565 ILE
Chi-restraints excluded: chain F residue  574 GLU
Chi-restraints excluded: chain F residue  594 MET
Chi-restraints excluded: chain G residue  143 LEU
Chi-restraints excluded: chain G residue  148 SER
Chi-restraints excluded: chain G residue  209 ASP
Chi-restraints excluded: chain H residue  115 LEU
Chi-restraints excluded: chain H residue  136 ARG
Chi-restraints excluded: chain H residue  194 VAL
Chi-restraints excluded: chain I residue   30 LEU
Chi-restraints excluded: chain I residue  131 ILE
Chi-restraints excluded: chain I residue  143 LEU
Chi-restraints excluded: chain I residue  185 GLU
Chi-restraints excluded: chain I residue  194 VAL
Chi-restraints excluded: chain I residue  218 LEU
Chi-restraints excluded: chain J residue  115 LEU
Chi-restraints excluded: chain J residue  136 ARG
Chi-restraints excluded: chain J residue  194 VAL
Chi-restraints excluded: chain K residue  143 LEU
Chi-restraints excluded: chain K residue  148 SER
Chi-restraints excluded: chain K residue  194 VAL
Chi-restraints excluded: chain K residue  209 ASP
Chi-restraints excluded: chain L residue  131 ILE
Chi-restraints excluded: chain L residue  136 ARG
Chi-restraints excluded: chain L residue  143 LEU
Chi-restraints excluded: chain L residue  218 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 498
   random chunks:
   chunk 243 optimal weight:    0.9990
   chunk 318 optimal weight:    5.9990
   chunk 162 optimal weight:    1.9990
   chunk 447 optimal weight:    7.9990
   chunk 466 optimal weight:    8.9990
   chunk 182 optimal weight:    1.9990
   chunk 131 optimal weight:    0.8980
   chunk 170 optimal weight:    0.6980
   chunk 233 optimal weight:    1.9990
   chunk 142 optimal weight:    0.9980
   chunk 388 optimal weight:   20.0000
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 298 GLN
** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 653 ASN
G 137 ASN
G 180 GLN
H 180 GLN
J 141 ASN
J 180 GLN
K 137 ASN
K 180 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.141695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.116704 restraints weight = 57584.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3819 rms_B_bonded: 2.25
r_work: 0.3684 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3528 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.2993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  39678  Z= 0.156
  Angle     :  0.615  11.386  53496  Z= 0.308
  Chirality :  0.042   0.212   5754
  Planarity :  0.004   0.050   7182
  Dihedral  :  4.096  33.487   5445
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 25.30 %
    Favored  : 70.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.38 (0.12), residues: 4980
  helix:  0.93 (0.09), residues: 3378
  sheet: -2.37 (0.65), residues: 60
  loop : -1.05 (0.15), residues: 1542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG E 586 
 TYR   0.020   0.001   TYR F 664 
 PHE   0.013   0.001   PHE F 167 
 TRP   0.029   0.001   TRP A 351 
 HIS   0.003   0.001   HIS F 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (39678)
  covalent geometry    : angle       0.61502 (53496)
  hydrogen bonds       : bond        0.03541 ( 2148)
  hydrogen bonds       : angle       3.59167 ( 6354)

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

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

  9960 Ramachandran restraints generated.
    4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  9960 Ramachandran restraints generated.
    4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  919 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 155
    poor density    : 764
  time to evaluate  : 1.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ASP cc_start: 0.7908 (m-30) cc_final: 0.7619 (m-30)
REVERT: A  149 VAL cc_start: 0.7879 (t) cc_final: 0.7611 (p)
REVERT: A  167 PHE cc_start: 0.7961 (t80) cc_final: 0.7653 (t80)
REVERT: A  188 GLN cc_start: 0.7511 (pp30) cc_final: 0.7269 (pp30)
REVERT: A  196 MET cc_start: 0.7061 (mtt) cc_final: 0.6860 (ttm)
REVERT: A  207 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7713 (tp-100)
REVERT: A  214 ARG cc_start: 0.8283 (mmm160) cc_final: 0.8013 (ttm-80)
REVERT: A  262 MET cc_start: 0.7920 (ttp) cc_final: 0.7669 (mtp)
REVERT: A  323 ARG cc_start: 0.7639 (mpp80) cc_final: 0.7273 (mpt-90)
REVERT: A  327 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6345 (tp30)
REVERT: A  363 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7352 (ttt)
REVERT: A  431 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7475 (tm-30)
REVERT: A  456 ASP cc_start: 0.8574 (t0) cc_final: 0.7863 (p0)
REVERT: A  519 ASP cc_start: 0.7496 (m-30) cc_final: 0.6958 (m-30)
REVERT: A  561 LYS cc_start: 0.9146 (pmtt) cc_final: 0.8700 (mmmt)
REVERT: A  573 ARG cc_start: 0.8027 (ttm-80) cc_final: 0.7806 (ttp80)
REVERT: A  592 MET cc_start: 0.6764 (tmm) cc_final: 0.6483 (tmm)
REVERT: A  625 MET cc_start: 0.8567 (mtt) cc_final: 0.8283 (mtm)
REVERT: A  664 TYR cc_start: 0.7429 (t80) cc_final: 0.7070 (t80)
REVERT: B  117 ASP cc_start: 0.8437 (t0) cc_final: 0.8025 (m-30)
REVERT: B  119 ASP cc_start: 0.8024 (m-30) cc_final: 0.7725 (m-30)
REVERT: B  149 VAL cc_start: 0.7762 (t) cc_final: 0.7359 (p)
REVERT: B  291 MET cc_start: 0.7936 (mmm) cc_final: 0.7677 (mtp)
REVERT: B  323 ARG cc_start: 0.7758 (mtt-85) cc_final: 0.7321 (mtt90)
REVERT: B  335 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7090 (mp0)
REVERT: B  363 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.6982 (ttt)
REVERT: B  378 MET cc_start: 0.8074 (ttp) cc_final: 0.7848 (ttt)
REVERT: B  388 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.8026 (t0)
REVERT: B  431 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7704 (tm-30)
REVERT: B  455 LYS cc_start: 0.9080 (ptmm) cc_final: 0.8524 (pmtt)
REVERT: B  550 ASP cc_start: 0.6936 (OUTLIER) cc_final: 0.6486 (t70)
REVERT: B  574 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7205 (mp0)
REVERT: B  581 ASP cc_start: 0.8415 (m-30) cc_final: 0.8116 (m-30)
REVERT: B  590 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6758 (pm20)
REVERT: B  592 MET cc_start: 0.6664 (tmm) cc_final: 0.5766 (tmt)
REVERT: B  594 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.6574 (tpp)
REVERT: B  602 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8340 (tptt)
REVERT: B  625 MET cc_start: 0.8703 (mtt) cc_final: 0.8341 (mtm)
REVERT: B  661 LEU cc_start: 0.8660 (mp) cc_final: 0.8416 (mt)
REVERT: B  684 ASP cc_start: 0.7997 (p0) cc_final: 0.7688 (p0)
REVERT: B  688 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6176 (mp)
REVERT: B  698 LYS cc_start: 0.7786 (mtmm) cc_final: 0.7561 (mttp)
REVERT: C   73 GLU cc_start: 0.8212 (tp30) cc_final: 0.7933 (tp30)
REVERT: C  117 ASP cc_start: 0.8297 (t0) cc_final: 0.7966 (m-30)
REVERT: C  149 VAL cc_start: 0.7929 (t) cc_final: 0.7630 (p)
REVERT: C  214 ARG cc_start: 0.8300 (ttm-80) cc_final: 0.7899 (mtp85)
REVERT: C  335 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7084 (mp0)
REVERT: C  405 LYS cc_start: 0.9123 (mtmp) cc_final: 0.8825 (ptpt)
REVERT: C  421 MET cc_start: 0.8502 (tpp) cc_final: 0.8102 (mmm)
REVERT: C  513 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7366 (mm-30)
REVERT: C  533 ASP cc_start: 0.8132 (m-30) cc_final: 0.7841 (m-30)
REVERT: C  543 LYS cc_start: 0.7327 (tppt) cc_final: 0.6812 (tppt)
REVERT: C  550 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6341 (t70)
REVERT: C  592 MET cc_start: 0.6651 (tmm) cc_final: 0.6228 (tmm)
REVERT: C  594 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.6771 (tpp)
REVERT: D  149 VAL cc_start: 0.7868 (t) cc_final: 0.7620 (p)
REVERT: D  167 PHE cc_start: 0.7961 (t80) cc_final: 0.7690 (t80)
REVERT: D  188 GLN cc_start: 0.7510 (pp30) cc_final: 0.7269 (pp30)
REVERT: D  207 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7704 (tp-100)
REVERT: D  262 MET cc_start: 0.7883 (ttp) cc_final: 0.7640 (mtp)
REVERT: D  363 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7359 (ttt)
REVERT: D  431 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7479 (tm-30)
REVERT: D  456 ASP cc_start: 0.8532 (t0) cc_final: 0.7745 (p0)
REVERT: D  519 ASP cc_start: 0.7483 (m-30) cc_final: 0.6930 (m-30)
REVERT: D  544 GLU cc_start: 0.8503 (mp0) cc_final: 0.8261 (pm20)
REVERT: D  574 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7565 (mm-30)
REVERT: D  625 MET cc_start: 0.8605 (mtt) cc_final: 0.8178 (mtm)
REVERT: D  664 TYR cc_start: 0.7284 (t80) cc_final: 0.6921 (t80)
REVERT: E  119 ASP cc_start: 0.8148 (m-30) cc_final: 0.7879 (m-30)
REVERT: E  149 VAL cc_start: 0.7775 (t) cc_final: 0.7337 (p)
REVERT: E  327 GLU cc_start: 0.7407 (tp30) cc_final: 0.6963 (tp30)
REVERT: E  335 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7074 (mp0)
REVERT: E  363 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7369 (ttt)
REVERT: E  378 MET cc_start: 0.8133 (ttm) cc_final: 0.7809 (ttt)
REVERT: E  388 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.8028 (t0)
REVERT: E  431 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7654 (tm-30)
REVERT: E  455 LYS cc_start: 0.9082 (ptmm) cc_final: 0.8530 (pmtt)
REVERT: E  550 ASP cc_start: 0.6901 (OUTLIER) cc_final: 0.6422 (t70)
REVERT: E  574 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7270 (mp0)
REVERT: E  581 ASP cc_start: 0.8393 (m-30) cc_final: 0.8107 (m-30)
REVERT: E  590 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6822 (pm20)
REVERT: E  592 MET cc_start: 0.6668 (tmm) cc_final: 0.5798 (tmt)
REVERT: E  594 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.6526 (tpp)
REVERT: E  602 LYS cc_start: 0.8740 (ttmm) cc_final: 0.8398 (tptt)
REVERT: E  625 MET cc_start: 0.8718 (mtt) cc_final: 0.8361 (mtm)
REVERT: E  661 LEU cc_start: 0.8694 (mp) cc_final: 0.8469 (mt)
REVERT: E  684 ASP cc_start: 0.8013 (p0) cc_final: 0.7700 (p0)
REVERT: E  688 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6115 (mp)
REVERT: E  698 LYS cc_start: 0.7773 (mtmm) cc_final: 0.7517 (mttp)
REVERT: F   73 GLU cc_start: 0.8222 (tp30) cc_final: 0.7993 (tp30)
REVERT: F  117 ASP cc_start: 0.8335 (t0) cc_final: 0.7961 (m-30)
REVERT: F  214 ARG cc_start: 0.8308 (ttm-80) cc_final: 0.7903 (mtp85)
REVERT: F  335 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7026 (mp0)
REVERT: F  405 LYS cc_start: 0.9138 (mtmp) cc_final: 0.8839 (ptpt)
REVERT: F  421 MET cc_start: 0.8473 (tpp) cc_final: 0.8106 (mmm)
REVERT: F  482 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8334 (ptpt)
REVERT: F  513 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7478 (mm-30)
REVERT: F  543 LYS cc_start: 0.7519 (tppt) cc_final: 0.7144 (tppt)
REVERT: F  544 GLU cc_start: 0.8310 (mp0) cc_final: 0.8036 (pm20)
REVERT: F  550 ASP cc_start: 0.7062 (OUTLIER) cc_final: 0.6299 (t70)
REVERT: F  581 ASP cc_start: 0.8435 (m-30) cc_final: 0.8218 (m-30)
REVERT: F  592 MET cc_start: 0.6531 (tmm) cc_final: 0.5916 (tmm)
REVERT: F  594 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.6201 (tpt)
REVERT: G  112 GLU cc_start: 0.7949 (mp0) cc_final: 0.7393 (pp20)
REVERT: G  216 GLU cc_start: 0.8121 (pt0) cc_final: 0.7506 (pm20)
REVERT: H  163 LYS cc_start: 0.8865 (mtpp) cc_final: 0.8591 (mtmm)
REVERT: H  210 PHE cc_start: 0.8052 (t80) cc_final: 0.7745 (t80)
REVERT: H  216 GLU cc_start: 0.8104 (pt0) cc_final: 0.7470 (pm20)
REVERT: I  102 LEU cc_start: 0.8038 (mm) cc_final: 0.7743 (mm)
REVERT: I  112 GLU cc_start: 0.7905 (mp0) cc_final: 0.7011 (tm-30)
REVERT: I  127 ASP cc_start: 0.7148 (t0) cc_final: 0.6670 (t0)
REVERT: I  134 GLU cc_start: 0.7305 (mp0) cc_final: 0.7096 (mp0)
REVERT: I  208 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.7074 (tttp)
REVERT: I  216 GLU cc_start: 0.8244 (pt0) cc_final: 0.7757 (pm20)
REVERT: J  136 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.6485 (mtp180)
REVERT: J  163 LYS cc_start: 0.8881 (mtpp) cc_final: 0.8608 (mtmm)
REVERT: J  210 PHE cc_start: 0.8003 (t80) cc_final: 0.7760 (t80)
REVERT: J  216 GLU cc_start: 0.8091 (pt0) cc_final: 0.7535 (pm20)
REVERT: K  112 GLU cc_start: 0.7937 (mp0) cc_final: 0.7377 (pp20)
REVERT: K  180 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7818 (mt0)
REVERT: K  216 GLU cc_start: 0.8111 (pt0) cc_final: 0.7473 (pm20)
REVERT: L  102 LEU cc_start: 0.8031 (mm) cc_final: 0.7792 (mm)
REVERT: L  112 GLU cc_start: 0.8133 (mp0) cc_final: 0.7036 (tm-30)
REVERT: L  127 ASP cc_start: 0.7163 (t0) cc_final: 0.6580 (t0)
REVERT: L  200 GLU cc_start: 0.8069 (mp0) cc_final: 0.7859 (mp0)
REVERT: L  208 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.7052 (tttp)
REVERT: L  216 GLU cc_start: 0.8239 (pt0) cc_final: 0.7758 (pm20)
  outliers start: 155
  outliers final: 73
  residues processed: 842
  average time/residue: 0.7891
  time to fit residues: 794.5822
Evaluate side-chains
  840 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 105
    poor density    : 735
  time to evaluate  : 1.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  131 THR
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  207 GLN
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  327 GLU
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  454 SER
Chi-restraints excluded: chain A residue  490 MET
Chi-restraints excluded: chain A residue  594 MET
Chi-restraints excluded: chain A residue  661 LEU
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  335 GLU
Chi-restraints excluded: chain B residue  346 THR
Chi-restraints excluded: chain B residue  363 MET
Chi-restraints excluded: chain B residue  388 ASP
Chi-restraints excluded: chain B residue  454 SER
Chi-restraints excluded: chain B residue  482 LYS
Chi-restraints excluded: chain B residue  490 MET
Chi-restraints excluded: chain B residue  550 ASP
Chi-restraints excluded: chain B residue  574 GLU
Chi-restraints excluded: chain B residue  590 GLU
Chi-restraints excluded: chain B residue  594 MET
Chi-restraints excluded: chain B residue  688 LEU
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  335 GLU
Chi-restraints excluded: chain C residue  454 SER
Chi-restraints excluded: chain C residue  490 MET
Chi-restraints excluded: chain C residue  550 ASP
Chi-restraints excluded: chain C residue  574 GLU
Chi-restraints excluded: chain C residue  594 MET
Chi-restraints excluded: chain C residue  613 VAL
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  131 THR
Chi-restraints excluded: chain D residue  162 ASP
Chi-restraints excluded: chain D residue  207 GLN
Chi-restraints excluded: chain D residue  245 SER
Chi-restraints excluded: chain D residue  324 THR
Chi-restraints excluded: chain D residue  346 THR
Chi-restraints excluded: chain D residue  357 GLU
Chi-restraints excluded: chain D residue  363 MET
Chi-restraints excluded: chain D residue  421 MET
Chi-restraints excluded: chain D residue  454 SER
Chi-restraints excluded: chain D residue  688 LEU
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain E residue  161 VAL
Chi-restraints excluded: chain E residue  282 ILE
Chi-restraints excluded: chain E residue  335 GLU
Chi-restraints excluded: chain E residue  346 THR
Chi-restraints excluded: chain E residue  363 MET
Chi-restraints excluded: chain E residue  388 ASP
Chi-restraints excluded: chain E residue  411 GLU
Chi-restraints excluded: chain E residue  454 SER
Chi-restraints excluded: chain E residue  482 LYS
Chi-restraints excluded: chain E residue  490 MET
Chi-restraints excluded: chain E residue  550 ASP
Chi-restraints excluded: chain E residue  574 GLU
Chi-restraints excluded: chain E residue  590 GLU
Chi-restraints excluded: chain E residue  594 MET
Chi-restraints excluded: chain E residue  688 LEU
Chi-restraints excluded: chain F residue   91 THR
Chi-restraints excluded: chain F residue  245 SER
Chi-restraints excluded: chain F residue  335 GLU
Chi-restraints excluded: chain F residue  445 MET
Chi-restraints excluded: chain F residue  454 SER
Chi-restraints excluded: chain F residue  482 LYS
Chi-restraints excluded: chain F residue  490 MET
Chi-restraints excluded: chain F residue  550 ASP
Chi-restraints excluded: chain F residue  574 GLU
Chi-restraints excluded: chain F residue  594 MET
Chi-restraints excluded: chain F residue  613 VAL
Chi-restraints excluded: chain F residue  673 MET
Chi-restraints excluded: chain G residue  143 LEU
Chi-restraints excluded: chain G residue  148 SER
Chi-restraints excluded: chain G residue  180 GLN
Chi-restraints excluded: chain G residue  209 ASP
Chi-restraints excluded: chain H residue  115 LEU
Chi-restraints excluded: chain H residue  131 ILE
Chi-restraints excluded: chain H residue  143 LEU
Chi-restraints excluded: chain H residue  194 VAL
Chi-restraints excluded: chain I residue   30 LEU
Chi-restraints excluded: chain I residue  131 ILE
Chi-restraints excluded: chain I residue  143 LEU
Chi-restraints excluded: chain I residue  208 LYS
Chi-restraints excluded: chain J residue  115 LEU
Chi-restraints excluded: chain J residue  136 ARG
Chi-restraints excluded: chain J residue  194 VAL
Chi-restraints excluded: chain K residue  143 LEU
Chi-restraints excluded: chain K residue  180 GLN
Chi-restraints excluded: chain K residue  193 ASP
Chi-restraints excluded: chain K residue  194 VAL
Chi-restraints excluded: chain K residue  209 ASP
Chi-restraints excluded: chain L residue  131 ILE
Chi-restraints excluded: chain L residue  136 ARG
Chi-restraints excluded: chain L residue  143 LEU
Chi-restraints excluded: chain L residue  208 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 498
   random chunks:
   chunk 331 optimal weight:    0.7980
   chunk 192 optimal weight:   10.0000
   chunk 194 optimal weight:    0.6980
   chunk 215 optimal weight:    1.9990
   chunk 250 optimal weight:    0.9990
   chunk 223 optimal weight:    2.9990
   chunk 462 optimal weight:    5.9990
   chunk 24 optimal weight:    0.5980
   chunk 488 optimal weight:    1.9990
   chunk 233 optimal weight:    0.9990
   chunk 159 optimal weight:    0.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
B 660 GLN
** C 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 272 ASN
E 272 ASN
** E 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 180 GLN
H 180 GLN
J 180 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.142261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.116902 restraints weight = 57735.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3834 rms_B_bonded: 2.34
r_work: 0.3694 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.3117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  39678  Z= 0.138
  Angle     :  0.620  10.870  53496  Z= 0.311
  Chirality :  0.041   0.208   5754
  Planarity :  0.004   0.049   7182
  Dihedral  :  4.048  33.738   5445
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 26.32 %
    Favored  : 70.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.12), residues: 4980
  helix:  1.05 (0.09), residues: 3390
  sheet:  None (None), residues: 0
  loop : -0.92 (0.15), residues: 1590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG E 586 
 TYR   0.018   0.001   TYR F 664 
 PHE   0.012   0.001   PHE F 167 
 TRP   0.029   0.001   TRP A 351 
 HIS   0.002   0.001   HIS C 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (39678)
  covalent geometry    : angle       0.61961 (53496)
  hydrogen bonds       : bond        0.03411 ( 2148)
  hydrogen bonds       : angle       3.54088 ( 6354)

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

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

  9960 Ramachandran restraints generated.
    4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  9960 Ramachandran restraints generated.
    4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  888 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 131
    poor density    : 757
  time to evaluate  : 1.681 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ASP cc_start: 0.7607 (m-30) cc_final: 0.7357 (m-30)
REVERT: A  149 VAL cc_start: 0.7824 (t) cc_final: 0.7412 (p)
REVERT: A  167 PHE cc_start: 0.7830 (t80) cc_final: 0.7583 (t80)
REVERT: A  188 GLN cc_start: 0.7353 (pp30) cc_final: 0.7118 (pp30)
REVERT: A  196 MET cc_start: 0.6863 (mtt) cc_final: 0.6654 (ttm)
REVERT: A  262 MET cc_start: 0.7772 (ttp) cc_final: 0.7525 (mtp)
REVERT: A  323 ARG cc_start: 0.7410 (mpp80) cc_final: 0.7050 (mpt-90)
REVERT: A  431 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7289 (tm-30)
REVERT: A  456 ASP cc_start: 0.8342 (t0) cc_final: 0.7786 (p0)
REVERT: A  519 ASP cc_start: 0.7330 (m-30) cc_final: 0.6902 (m-30)
REVERT: A  561 LYS cc_start: 0.9076 (pmtt) cc_final: 0.8702 (mmmt)
REVERT: A  625 MET cc_start: 0.8487 (mtt) cc_final: 0.8197 (mtm)
REVERT: B  117 ASP cc_start: 0.8282 (t0) cc_final: 0.7895 (m-30)
REVERT: B  119 ASP cc_start: 0.7753 (m-30) cc_final: 0.7461 (m-30)
REVERT: B  149 VAL cc_start: 0.7733 (t) cc_final: 0.7330 (p)
REVERT: B  291 MET cc_start: 0.7712 (mmm) cc_final: 0.7434 (mtp)
REVERT: B  323 ARG cc_start: 0.7570 (mtt-85) cc_final: 0.7350 (mtt90)
REVERT: B  363 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.6649 (ttt)
REVERT: B  378 MET cc_start: 0.7861 (ttp) cc_final: 0.7642 (ttt)
REVERT: B  388 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7880 (t0)
REVERT: B  431 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7493 (tm-30)
REVERT: B  455 LYS cc_start: 0.9005 (ptmm) cc_final: 0.8487 (pmtt)
REVERT: B  543 LYS cc_start: 0.7396 (tppt) cc_final: 0.6878 (tppt)
REVERT: B  550 ASP cc_start: 0.6895 (OUTLIER) cc_final: 0.6441 (t70)
REVERT: B  574 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6886 (mp0)
REVERT: B  581 ASP cc_start: 0.8136 (m-30) cc_final: 0.7810 (m-30)
REVERT: B  592 MET cc_start: 0.6508 (tmm) cc_final: 0.5632 (tmt)
REVERT: B  594 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6364 (tpp)
REVERT: B  602 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8268 (tptt)
REVERT: B  625 MET cc_start: 0.8602 (mtt) cc_final: 0.8402 (mtt)
REVERT: B  647 LYS cc_start: 0.7083 (OUTLIER) cc_final: 0.6801 (mtpt)
REVERT: B  684 ASP cc_start: 0.7972 (p0) cc_final: 0.7685 (p0)
REVERT: B  688 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6222 (mp)
REVERT: B  698 LYS cc_start: 0.7832 (mtmm) cc_final: 0.7570 (mttp)
REVERT: C   73 GLU cc_start: 0.8127 (tp30) cc_final: 0.7839 (tp30)
REVERT: C  117 ASP cc_start: 0.8128 (t0) cc_final: 0.7806 (m-30)
REVERT: C  214 ARG cc_start: 0.8186 (ttm-80) cc_final: 0.7846 (mtp85)
REVERT: C  335 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6848 (mp0)
REVERT: C  405 LYS cc_start: 0.9057 (mtmp) cc_final: 0.8761 (ptpt)
REVERT: C  421 MET cc_start: 0.8348 (tpp) cc_final: 0.7937 (mmm)
REVERT: C  451 GLN cc_start: 0.7755 (tm-30) cc_final: 0.7451 (tm-30)
REVERT: C  513 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7138 (mm-30)
REVERT: C  533 ASP cc_start: 0.7943 (m-30) cc_final: 0.7648 (m-30)
REVERT: C  550 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.6383 (t70)
REVERT: C  592 MET cc_start: 0.6520 (tmm) cc_final: 0.6130 (tmm)
REVERT: C  594 MET cc_start: 0.7030 (OUTLIER) cc_final: 0.6530 (tpp)
REVERT: D  149 VAL cc_start: 0.7809 (t) cc_final: 0.7395 (p)
REVERT: D  167 PHE cc_start: 0.7802 (t80) cc_final: 0.7544 (t80)
REVERT: D  188 GLN cc_start: 0.7351 (pp30) cc_final: 0.7118 (pp30)
REVERT: D  214 ARG cc_start: 0.8277 (ttm-80) cc_final: 0.8055 (mtp85)
REVERT: D  262 MET cc_start: 0.7744 (ttp) cc_final: 0.7512 (mtp)
REVERT: D  286 GLN cc_start: 0.7528 (tp40) cc_final: 0.7308 (mm-40)
REVERT: D  363 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.7087 (ttt)
REVERT: D  403 ASP cc_start: 0.7232 (t0) cc_final: 0.7008 (t0)
REVERT: D  407 MET cc_start: 0.8215 (mmt) cc_final: 0.8004 (mmt)
REVERT: D  431 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7287 (tm-30)
REVERT: D  456 ASP cc_start: 0.8322 (t0) cc_final: 0.7703 (p0)
REVERT: D  519 ASP cc_start: 0.7340 (m-30) cc_final: 0.6843 (m-30)
REVERT: D  544 GLU cc_start: 0.8358 (mp0) cc_final: 0.8042 (pm20)
REVERT: D  561 LYS cc_start: 0.9117 (pmtt) cc_final: 0.8714 (mmmt)
REVERT: D  574 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7255 (mm-30)
REVERT: D  625 MET cc_start: 0.8512 (mtt) cc_final: 0.8081 (mtm)
REVERT: E  149 VAL cc_start: 0.7754 (t) cc_final: 0.7359 (p)
REVERT: E  327 GLU cc_start: 0.7066 (tp30) cc_final: 0.6582 (tp30)
REVERT: E  335 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6806 (mp0)
REVERT: E  363 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.6992 (ttt)
REVERT: E  378 MET cc_start: 0.7976 (ttm) cc_final: 0.7636 (ttt)
REVERT: E  388 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7874 (t0)
REVERT: E  431 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7497 (tm-30)
REVERT: E  455 LYS cc_start: 0.8997 (ptmm) cc_final: 0.8486 (pmtt)
REVERT: E  550 ASP cc_start: 0.6837 (OUTLIER) cc_final: 0.6347 (t70)
REVERT: E  574 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6977 (mp0)
REVERT: E  581 ASP cc_start: 0.8135 (m-30) cc_final: 0.7814 (m-30)
REVERT: E  592 MET cc_start: 0.6542 (tmm) cc_final: 0.5680 (tmt)
REVERT: E  594 MET cc_start: 0.7115 (OUTLIER) cc_final: 0.6311 (tpp)
REVERT: E  602 LYS cc_start: 0.8666 (ttmm) cc_final: 0.8321 (tptt)
REVERT: E  625 MET cc_start: 0.8615 (mtt) cc_final: 0.8405 (mtt)
REVERT: E  684 ASP cc_start: 0.7985 (p0) cc_final: 0.7691 (p0)
REVERT: E  688 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.6257 (mp)
REVERT: F   73 GLU cc_start: 0.8133 (tp30) cc_final: 0.7869 (tp30)
REVERT: F  117 ASP cc_start: 0.8150 (t0) cc_final: 0.7760 (m-30)
REVERT: F  214 ARG cc_start: 0.8193 (ttm-80) cc_final: 0.7848 (mtp85)
REVERT: F  335 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6794 (mp0)
REVERT: F  405 LYS cc_start: 0.9072 (mtmp) cc_final: 0.8769 (ptpt)
REVERT: F  421 MET cc_start: 0.8333 (tpp) cc_final: 0.7980 (mmm)
REVERT: F  451 GLN cc_start: 0.7774 (tm-30) cc_final: 0.7464 (tm-30)
REVERT: F  482 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8250 (ptpt)
REVERT: F  513 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7287 (mm-30)
REVERT: F  544 GLU cc_start: 0.8138 (mp0) cc_final: 0.7931 (pm20)
REVERT: F  550 ASP cc_start: 0.7048 (OUTLIER) cc_final: 0.6298 (t70)
REVERT: F  592 MET cc_start: 0.6329 (tmm) cc_final: 0.5768 (tmm)
REVERT: F  594 MET cc_start: 0.7057 (OUTLIER) cc_final: 0.6654 (tpp)
REVERT: G  112 GLU cc_start: 0.7898 (mp0) cc_final: 0.7318 (pp20)
REVERT: G  216 GLU cc_start: 0.7941 (pt0) cc_final: 0.7503 (pm20)
REVERT: H  163 LYS cc_start: 0.8718 (mtpp) cc_final: 0.8453 (mtmm)
REVERT: H  216 GLU cc_start: 0.7960 (pt0) cc_final: 0.7411 (pm20)
REVERT: I  102 LEU cc_start: 0.8025 (mm) cc_final: 0.7759 (mm)
REVERT: I  127 ASP cc_start: 0.7101 (t0) cc_final: 0.6499 (t0)
REVERT: I  163 LYS cc_start: 0.8738 (mtpp) cc_final: 0.8424 (mtmm)
REVERT: I  208 LYS cc_start: 0.7286 (OUTLIER) cc_final: 0.7046 (tttp)
REVERT: I  216 GLU cc_start: 0.8083 (pt0) cc_final: 0.7646 (pm20)
REVERT: J  136 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.6588 (mtp180)
REVERT: J  163 LYS cc_start: 0.8749 (mtpp) cc_final: 0.8483 (mtmm)
REVERT: J  210 PHE cc_start: 0.7995 (t80) cc_final: 0.7705 (t80)
REVERT: J  216 GLU cc_start: 0.7942 (pt0) cc_final: 0.7410 (pm20)
REVERT: K  112 GLU cc_start: 0.7912 (mp0) cc_final: 0.7297 (pp20)
REVERT: K  216 GLU cc_start: 0.7931 (pt0) cc_final: 0.7476 (pm20)
REVERT: L  102 LEU cc_start: 0.7996 (mm) cc_final: 0.7711 (mm)
REVERT: L  112 GLU cc_start: 0.8106 (mp0) cc_final: 0.7007 (tm-30)
REVERT: L  127 ASP cc_start: 0.7111 (t0) cc_final: 0.6536 (t0)
REVERT: L  208 LYS cc_start: 0.7283 (tttm) cc_final: 0.7045 (tttp)
REVERT: L  216 GLU cc_start: 0.8054 (pt0) cc_final: 0.7649 (pm20)
  outliers start: 131
  outliers final: 65
  residues processed: 828
  average time/residue: 0.7510
  time to fit residues: 745.8494
Evaluate side-chains
  822 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 89
    poor density    : 733
  time to evaluate  : 1.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  131 THR
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  454 SER
Chi-restraints excluded: chain A residue  490 MET
Chi-restraints excluded: chain A residue  594 MET
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  346 THR
Chi-restraints excluded: chain B residue  363 MET
Chi-restraints excluded: chain B residue  388 ASP
Chi-restraints excluded: chain B residue  411 GLU
Chi-restraints excluded: chain B residue  454 SER
Chi-restraints excluded: chain B residue  482 LYS
Chi-restraints excluded: chain B residue  550 ASP
Chi-restraints excluded: chain B residue  574 GLU
Chi-restraints excluded: chain B residue  594 MET
Chi-restraints excluded: chain B residue  647 LYS
Chi-restraints excluded: chain B residue  688 LEU
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  335 GLU
Chi-restraints excluded: chain C residue  454 SER
Chi-restraints excluded: chain C residue  490 MET
Chi-restraints excluded: chain C residue  550 ASP
Chi-restraints excluded: chain C residue  574 GLU
Chi-restraints excluded: chain C residue  594 MET
Chi-restraints excluded: chain C residue  613 VAL
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  131 THR
Chi-restraints excluded: chain D residue  162 ASP
Chi-restraints excluded: chain D residue  245 SER
Chi-restraints excluded: chain D residue  324 THR
Chi-restraints excluded: chain D residue  346 THR
Chi-restraints excluded: chain D residue  363 MET
Chi-restraints excluded: chain D residue  454 SER
Chi-restraints excluded: chain D residue  594 MET
Chi-restraints excluded: chain D residue  688 LEU
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  104 LEU
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain E residue  161 VAL
Chi-restraints excluded: chain E residue  282 ILE
Chi-restraints excluded: chain E residue  335 GLU
Chi-restraints excluded: chain E residue  346 THR
Chi-restraints excluded: chain E residue  363 MET
Chi-restraints excluded: chain E residue  388 ASP
Chi-restraints excluded: chain E residue  454 SER
Chi-restraints excluded: chain E residue  482 LYS
Chi-restraints excluded: chain E residue  550 ASP
Chi-restraints excluded: chain E residue  574 GLU
Chi-restraints excluded: chain E residue  594 MET
Chi-restraints excluded: chain E residue  688 LEU
Chi-restraints excluded: chain F residue   91 THR
Chi-restraints excluded: chain F residue  245 SER
Chi-restraints excluded: chain F residue  335 GLU
Chi-restraints excluded: chain F residue  454 SER
Chi-restraints excluded: chain F residue  482 LYS
Chi-restraints excluded: chain F residue  490 MET
Chi-restraints excluded: chain F residue  550 ASP
Chi-restraints excluded: chain F residue  574 GLU
Chi-restraints excluded: chain F residue  594 MET
Chi-restraints excluded: chain F residue  613 VAL
Chi-restraints excluded: chain F residue  679 VAL
Chi-restraints excluded: chain G residue  143 LEU
Chi-restraints excluded: chain G residue  180 GLN
Chi-restraints excluded: chain G residue  209 ASP
Chi-restraints excluded: chain H residue  115 LEU
Chi-restraints excluded: chain H residue  131 ILE
Chi-restraints excluded: chain H residue  143 LEU
Chi-restraints excluded: chain H residue  194 VAL
Chi-restraints excluded: chain I residue   30 LEU
Chi-restraints excluded: chain I residue  131 ILE
Chi-restraints excluded: chain I residue  143 LEU
Chi-restraints excluded: chain I residue  208 LYS
Chi-restraints excluded: chain J residue  115 LEU
Chi-restraints excluded: chain J residue  131 ILE
Chi-restraints excluded: chain J residue  136 ARG
Chi-restraints excluded: chain J residue  143 LEU
Chi-restraints excluded: chain J residue  194 VAL
Chi-restraints excluded: chain K residue  143 LEU
Chi-restraints excluded: chain K residue  194 VAL
Chi-restraints excluded: chain K residue  209 ASP
Chi-restraints excluded: chain L residue  131 ILE
Chi-restraints excluded: chain L residue  143 LEU
Chi-restraints excluded: chain L residue  194 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 498
   random chunks:
   chunk 219 optimal weight:    1.9990
   chunk 292 optimal weight:    0.7980
   chunk 225 optimal weight:    5.9990
   chunk 156 optimal weight:    2.9990
   chunk 432 optimal weight:    6.9990
   chunk 170 optimal weight:    0.9980
   chunk 248 optimal weight:    0.8980
   chunk 412 optimal weight:    3.9990
   chunk 260 optimal weight:    0.9980
   chunk 314 optimal weight:    0.9980
   chunk 267 optimal weight:    0.6980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 330 GLN
** C 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 330 GLN
** E 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 180 GLN
H 141 ASN
H 180 GLN
J 180 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.142576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.117049 restraints weight = 57856.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3832 rms_B_bonded: 2.37
r_work: 0.3691 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.3169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  39678  Z= 0.144
  Angle     :  0.644  13.649  53496  Z= 0.322
  Chirality :  0.041   0.239   5754
  Planarity :  0.004   0.051   7182
  Dihedral  :  4.063  33.049   5445
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 27.22 %
    Favored  : 69.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.12), residues: 4980
  helix:  1.09 (0.09), residues: 3420
  sheet: -2.29 (0.67), residues: 60
  loop : -0.86 (0.15), residues: 1500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG E 586 
 TYR   0.018   0.001   TYR F 664 
 PHE   0.012   0.001   PHE F 167 
 TRP   0.034   0.001   TRP A 351 
 HIS   0.003   0.001   HIS G 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (39678)
  covalent geometry    : angle       0.64429 (53496)
  hydrogen bonds       : bond        0.03446 ( 2148)
  hydrogen bonds       : angle       3.55968 ( 6354)

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

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

  9960 Ramachandran restraints generated.
    4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  9960 Ramachandran restraints generated.
    4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  857 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 113
    poor density    : 744
  time to evaluate  : 1.547 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ASP cc_start: 0.7589 (m-30) cc_final: 0.7330 (m-30)
REVERT: A  167 PHE cc_start: 0.7780 (t80) cc_final: 0.7539 (t80)
REVERT: A  188 GLN cc_start: 0.7329 (pp30) cc_final: 0.7084 (pp30)
REVERT: A  262 MET cc_start: 0.7781 (ttp) cc_final: 0.7522 (mtp)
REVERT: A  323 ARG cc_start: 0.7398 (mpp80) cc_final: 0.7056 (mpt-90)
REVERT: A  431 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7253 (tm-30)
REVERT: A  456 ASP cc_start: 0.8360 (t0) cc_final: 0.7803 (p0)
REVERT: A  519 ASP cc_start: 0.7322 (m-30) cc_final: 0.6880 (m-30)
REVERT: A  561 LYS cc_start: 0.9143 (pmtt) cc_final: 0.8714 (mmmt)
REVERT: A  592 MET cc_start: 0.6492 (tmm) cc_final: 0.6248 (tmm)
REVERT: A  625 MET cc_start: 0.8488 (mtt) cc_final: 0.8196 (mtm)
REVERT: B  117 ASP cc_start: 0.8295 (t0) cc_final: 0.7888 (m-30)
REVERT: B  119 ASP cc_start: 0.7762 (m-30) cc_final: 0.7480 (m-30)
REVERT: B  149 VAL cc_start: 0.7672 (t) cc_final: 0.7306 (p)
REVERT: B  291 MET cc_start: 0.7684 (mmm) cc_final: 0.7393 (mtp)
REVERT: B  327 GLU cc_start: 0.7183 (tp30) cc_final: 0.6535 (tp30)
REVERT: B  363 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.6629 (ttt)
REVERT: B  378 MET cc_start: 0.7885 (ttp) cc_final: 0.7672 (ttt)
REVERT: B  431 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7572 (tp30)
REVERT: B  455 LYS cc_start: 0.9030 (ptmm) cc_final: 0.8490 (pmtt)
REVERT: B  543 LYS cc_start: 0.7333 (tppt) cc_final: 0.6830 (tppt)
REVERT: B  550 ASP cc_start: 0.6830 (OUTLIER) cc_final: 0.6415 (t70)
REVERT: B  574 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6876 (mp0)
REVERT: B  581 ASP cc_start: 0.8138 (m-30) cc_final: 0.7807 (m-30)
REVERT: B  592 MET cc_start: 0.6457 (tmm) cc_final: 0.5593 (tmt)
REVERT: B  594 MET cc_start: 0.7090 (OUTLIER) cc_final: 0.6321 (tpp)
REVERT: B  623 LYS cc_start: 0.7932 (mtpt) cc_final: 0.7302 (mttm)
REVERT: B  625 MET cc_start: 0.8629 (mtt) cc_final: 0.8419 (mtt)
REVERT: B  647 LYS cc_start: 0.7040 (OUTLIER) cc_final: 0.6767 (mtpt)
REVERT: B  684 ASP cc_start: 0.7962 (p0) cc_final: 0.7666 (p0)
REVERT: B  688 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6206 (mp)
REVERT: C   73 GLU cc_start: 0.8127 (tp30) cc_final: 0.7830 (tp30)
REVERT: C  117 ASP cc_start: 0.8135 (t0) cc_final: 0.7792 (m-30)
REVERT: C  214 ARG cc_start: 0.8163 (ttm-80) cc_final: 0.7820 (mtp85)
REVERT: C  335 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6851 (mp0)
REVERT: C  405 LYS cc_start: 0.9068 (mtmp) cc_final: 0.8765 (ptpt)
REVERT: C  421 MET cc_start: 0.8335 (tpp) cc_final: 0.7982 (mmm)
REVERT: C  451 GLN cc_start: 0.7743 (tm-30) cc_final: 0.7430 (tm-30)
REVERT: C  513 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7092 (mm-30)
REVERT: C  543 LYS cc_start: 0.7225 (tppt) cc_final: 0.6736 (tppt)
REVERT: C  550 ASP cc_start: 0.7071 (OUTLIER) cc_final: 0.6353 (t70)
REVERT: C  592 MET cc_start: 0.6479 (tmm) cc_final: 0.6076 (tmm)
REVERT: C  594 MET cc_start: 0.7049 (OUTLIER) cc_final: 0.6551 (tpp)
REVERT: D  188 GLN cc_start: 0.7321 (pp30) cc_final: 0.7078 (pp30)
REVERT: D  214 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7945 (mtp85)
REVERT: D  262 MET cc_start: 0.7758 (ttp) cc_final: 0.7513 (mtp)
REVERT: D  286 GLN cc_start: 0.7501 (tp40) cc_final: 0.7273 (mm-40)
REVERT: D  363 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.7050 (ttt)
REVERT: D  403 ASP cc_start: 0.7217 (t0) cc_final: 0.6987 (t0)
REVERT: D  431 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7262 (tm-30)
REVERT: D  456 ASP cc_start: 0.8376 (t0) cc_final: 0.7713 (p0)
REVERT: D  519 ASP cc_start: 0.7319 (m-30) cc_final: 0.6897 (m-30)
REVERT: D  544 GLU cc_start: 0.8360 (mp0) cc_final: 0.8068 (pm20)
REVERT: D  561 LYS cc_start: 0.9140 (pmtt) cc_final: 0.8692 (mmmt)
REVERT: D  574 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7147 (mm-30)
REVERT: D  625 MET cc_start: 0.8520 (mtt) cc_final: 0.8228 (mtm)
REVERT: E  131 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.8065 (t)
REVERT: E  149 VAL cc_start: 0.7677 (t) cc_final: 0.7313 (p)
REVERT: E  363 MET cc_start: 0.7195 (OUTLIER) cc_final: 0.6954 (ttt)
REVERT: E  378 MET cc_start: 0.7960 (ttm) cc_final: 0.7632 (ttt)
REVERT: E  388 ASP cc_start: 0.8069 (OUTLIER) cc_final: 0.7863 (t0)
REVERT: E  403 ASP cc_start: 0.7343 (t0) cc_final: 0.7090 (t0)
REVERT: E  431 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7457 (tm-30)
REVERT: E  455 LYS cc_start: 0.9016 (ptmm) cc_final: 0.8490 (pmtt)
REVERT: E  543 LYS cc_start: 0.7368 (tppt) cc_final: 0.6872 (tppt)
REVERT: E  550 ASP cc_start: 0.6814 (OUTLIER) cc_final: 0.6321 (t70)
REVERT: E  574 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6997 (mp0)
REVERT: E  581 ASP cc_start: 0.8136 (m-30) cc_final: 0.7822 (m-30)
REVERT: E  592 MET cc_start: 0.6456 (tmm) cc_final: 0.5653 (tmt)
REVERT: E  594 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6332 (tpp)
REVERT: E  602 LYS cc_start: 0.8666 (ttmm) cc_final: 0.8334 (tptt)
REVERT: E  623 LYS cc_start: 0.7940 (mtpt) cc_final: 0.7308 (mttm)
REVERT: E  625 MET cc_start: 0.8621 (mtt) cc_final: 0.8406 (mtt)
REVERT: E  684 ASP cc_start: 0.7965 (p0) cc_final: 0.7658 (p0)
REVERT: E  688 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6153 (mp)
REVERT: E  698 LYS cc_start: 0.7897 (mtmm) cc_final: 0.7596 (mttp)
REVERT: F   73 GLU cc_start: 0.8133 (tp30) cc_final: 0.7845 (tp30)
REVERT: F  117 ASP cc_start: 0.8166 (t0) cc_final: 0.7756 (m-30)
REVERT: F  214 ARG cc_start: 0.8163 (ttm-80) cc_final: 0.7781 (mtp85)
REVERT: F  335 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6765 (mp0)
REVERT: F  405 LYS cc_start: 0.9078 (mtmp) cc_final: 0.8772 (ptpt)
REVERT: F  421 MET cc_start: 0.8318 (tpp) cc_final: 0.7949 (mmm)
REVERT: F  451 GLN cc_start: 0.7764 (tm-30) cc_final: 0.7443 (tm-30)
REVERT: F  482 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8196 (ptpt)
REVERT: F  513 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7280 (mm-30)
REVERT: F  544 GLU cc_start: 0.8154 (mp0) cc_final: 0.7932 (pm20)
REVERT: F  550 ASP cc_start: 0.6974 (OUTLIER) cc_final: 0.6241 (t70)
REVERT: F  592 MET cc_start: 0.6290 (tmm) cc_final: 0.5724 (tmm)
REVERT: F  594 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.6633 (tpp)
REVERT: F  664 TYR cc_start: 0.6978 (t80) cc_final: 0.6545 (t80)
REVERT: F  673 MET cc_start: 0.7997 (mtp) cc_final: 0.7789 (ttt)
REVERT: G  112 GLU cc_start: 0.7918 (mp0) cc_final: 0.7299 (pp20)
REVERT: G  216 GLU cc_start: 0.7886 (pt0) cc_final: 0.7405 (pm20)
REVERT: H  163 LYS cc_start: 0.8748 (mtpp) cc_final: 0.8463 (mtmm)
REVERT: H  210 PHE cc_start: 0.7890 (t80) cc_final: 0.7627 (t80)
REVERT: H  216 GLU cc_start: 0.7947 (pt0) cc_final: 0.7410 (pm20)
REVERT: I  102 LEU cc_start: 0.7972 (mm) cc_final: 0.7738 (mm)
REVERT: I  127 ASP cc_start: 0.7066 (t0) cc_final: 0.6502 (t0)
REVERT: I  163 LYS cc_start: 0.8756 (mtpp) cc_final: 0.8428 (mtmm)
REVERT: I  208 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.7003 (tttp)
REVERT: I  216 GLU cc_start: 0.8094 (pt0) cc_final: 0.7551 (pm20)
REVERT: J  136 ARG cc_start: 0.6861 (OUTLIER) cc_final: 0.6529 (mtp180)
REVERT: J  163 LYS cc_start: 0.8778 (mtpp) cc_final: 0.8491 (mtmm)
REVERT: J  216 GLU cc_start: 0.7956 (pt0) cc_final: 0.7371 (pm20)
REVERT: K  112 GLU cc_start: 0.7913 (mp0) cc_final: 0.7286 (pp20)
REVERT: K  216 GLU cc_start: 0.7889 (pt0) cc_final: 0.7439 (pm20)
REVERT: L  102 LEU cc_start: 0.7958 (mm) cc_final: 0.7707 (mm)
REVERT: L  112 GLU cc_start: 0.8116 (mp0) cc_final: 0.6990 (tm-30)
REVERT: L  127 ASP cc_start: 0.7080 (t0) cc_final: 0.6498 (t0)
REVERT: L  163 LYS cc_start: 0.8728 (mtpp) cc_final: 0.8394 (mtmm)
REVERT: L  208 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6989 (tttp)
REVERT: L  216 GLU cc_start: 0.8091 (pt0) cc_final: 0.7550 (pm20)
  outliers start: 113
  outliers final: 72
  residues processed: 805
  average time/residue: 0.7527
  time to fit residues: 725.3799
Evaluate side-chains
  820 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 96
    poor density    : 724
  time to evaluate  : 1.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  131 THR
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  454 SER
Chi-restraints excluded: chain A residue  490 MET
Chi-restraints excluded: chain A residue  594 MET
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  346 THR
Chi-restraints excluded: chain B residue  363 MET
Chi-restraints excluded: chain B residue  454 SER
Chi-restraints excluded: chain B residue  482 LYS
Chi-restraints excluded: chain B residue  490 MET
Chi-restraints excluded: chain B residue  514 LEU
Chi-restraints excluded: chain B residue  550 ASP
Chi-restraints excluded: chain B residue  574 GLU
Chi-restraints excluded: chain B residue  594 MET
Chi-restraints excluded: chain B residue  647 LYS
Chi-restraints excluded: chain B residue  688 LEU
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  282 ILE
Chi-restraints excluded: chain C residue  335 GLU
Chi-restraints excluded: chain C residue  454 SER
Chi-restraints excluded: chain C residue  550 ASP
Chi-restraints excluded: chain C residue  574 GLU
Chi-restraints excluded: chain C residue  594 MET
Chi-restraints excluded: chain C residue  613 VAL
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  131 THR
Chi-restraints excluded: chain D residue  162 ASP
Chi-restraints excluded: chain D residue  245 SER
Chi-restraints excluded: chain D residue  324 THR
Chi-restraints excluded: chain D residue  346 THR
Chi-restraints excluded: chain D residue  363 MET
Chi-restraints excluded: chain D residue  421 MET
Chi-restraints excluded: chain D residue  454 SER
Chi-restraints excluded: chain D residue  594 MET
Chi-restraints excluded: chain D residue  688 LEU
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  104 LEU
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain E residue  282 ILE
Chi-restraints excluded: chain E residue  346 THR
Chi-restraints excluded: chain E residue  363 MET
Chi-restraints excluded: chain E residue  388 ASP
Chi-restraints excluded: chain E residue  454 SER
Chi-restraints excluded: chain E residue  482 LYS
Chi-restraints excluded: chain E residue  514 LEU
Chi-restraints excluded: chain E residue  550 ASP
Chi-restraints excluded: chain E residue  574 GLU
Chi-restraints excluded: chain E residue  594 MET
Chi-restraints excluded: chain E residue  688 LEU
Chi-restraints excluded: chain F residue   91 THR
Chi-restraints excluded: chain F residue  245 SER
Chi-restraints excluded: chain F residue  282 ILE
Chi-restraints excluded: chain F residue  335 GLU
Chi-restraints excluded: chain F residue  411 GLU
Chi-restraints excluded: chain F residue  454 SER
Chi-restraints excluded: chain F residue  482 LYS
Chi-restraints excluded: chain F residue  490 MET
Chi-restraints excluded: chain F residue  550 ASP
Chi-restraints excluded: chain F residue  574 GLU
Chi-restraints excluded: chain F residue  594 MET
Chi-restraints excluded: chain F residue  613 VAL
Chi-restraints excluded: chain F residue  679 VAL
Chi-restraints excluded: chain G residue  143 LEU
Chi-restraints excluded: chain G residue  180 GLN
Chi-restraints excluded: chain G residue  209 ASP
Chi-restraints excluded: chain H residue  115 LEU
Chi-restraints excluded: chain H residue  131 ILE
Chi-restraints excluded: chain H residue  143 LEU
Chi-restraints excluded: chain H residue  194 VAL
Chi-restraints excluded: chain I residue   30 LEU
Chi-restraints excluded: chain I residue  131 ILE
Chi-restraints excluded: chain I residue  143 LEU
Chi-restraints excluded: chain I residue  194 VAL
Chi-restraints excluded: chain I residue  208 LYS
Chi-restraints excluded: chain I residue  218 LEU
Chi-restraints excluded: chain J residue  115 LEU
Chi-restraints excluded: chain J residue  131 ILE
Chi-restraints excluded: chain J residue  136 ARG
Chi-restraints excluded: chain J residue  143 LEU
Chi-restraints excluded: chain J residue  194 VAL
Chi-restraints excluded: chain K residue  143 LEU
Chi-restraints excluded: chain K residue  194 VAL
Chi-restraints excluded: chain K residue  209 ASP
Chi-restraints excluded: chain L residue  131 ILE
Chi-restraints excluded: chain L residue  194 VAL
Chi-restraints excluded: chain L residue  208 LYS
Chi-restraints excluded: chain L residue  218 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 498
   random chunks:
   chunk 276 optimal weight:    0.6980
   chunk 289 optimal weight:    0.6980
   chunk 136 optimal weight:    0.9990
   chunk 188 optimal weight:    5.9990
   chunk 394 optimal weight:    7.9990
   chunk 88 optimal weight:    0.9990
   chunk 204 optimal weight:    0.9980
   chunk 441 optimal weight:    0.0000
   chunk 227 optimal weight:    0.0980
   chunk 167 optimal weight:    1.9990
   chunk 336 optimal weight:    0.9980
   overall best weight:    0.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 242 GLN
B 272 ASN
B 330 GLN
** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 318 ASN
C 498 ASN
** C 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 188 GLN
E 242 GLN
** E 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 318 ASN
** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 180 GLN
H 180 GLN
I 109 ASN
J 180 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.144467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.118933 restraints weight = 57781.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3860 rms_B_bonded: 2.37
r_work: 0.3720 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.3350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  39678  Z= 0.126
  Angle     :  0.633  12.196  53496  Z= 0.316
  Chirality :  0.040   0.257   5754
  Planarity :  0.004   0.063   7182
  Dihedral  :  3.994  32.407   5445
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 27.72 %
    Favored  : 69.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.89 (0.12), residues: 4980
  helix:  1.29 (0.09), residues: 3402
  sheet: -2.25 (0.67), residues: 60
  loop : -0.82 (0.15), residues: 1518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG F 573 
 TYR   0.020   0.001   TYR D 664 
 PHE   0.012   0.001   PHE E 220 
 TRP   0.031   0.001   TRP A 351 
 HIS   0.002   0.001   HIS G 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (39678)
  covalent geometry    : angle       0.63298 (53496)
  hydrogen bonds       : bond        0.03246 ( 2148)
  hydrogen bonds       : angle       3.51894 ( 6354)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 16228.41 seconds
wall clock time: 276 minutes 17.76 seconds (16577.76 seconds total)