Starting phenix.real_space_refine
on Sat Dec 28 08:18:48 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p6c_13225/12_2024/7p6c_13225.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p6c_13225/12_2024/7p6c_13225.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p6c_13225/12_2024/7p6c_13225.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p6c_13225/12_2024/7p6c_13225.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p6c_13225/12_2024/7p6c_13225.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p6c_13225/12_2024/7p6c_13225.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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      20      5.16       5
     C    5060      2.51       5
     N    1520      2.21       5
     O    1520      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 8120
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 812
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 4, 'TRANS': 103}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, J
  Time building chain proxies: 3.72, per 1000 atoms: 0.46
  Number of scatterers: 8120
  At special positions: 0
  Unit cell: (106.142, 114.139, 49.436, 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      20     16.00
     O    1520      8.00
     N    1520      7.00
     C    5060      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: 1.85
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1860

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 24 sheets defined
      0.0% alpha, 50.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.38
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 274 through 280
      removed outlier: 6.825A  pdb=" N   LYS B 274 " --> pdb=" O   VAL C 275 " (cutoff:3.500A)
      removed outlier: 7.708A  pdb=" N   ILE C 277 " --> pdb=" O   LYS B 274 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   GLN B 276 " --> pdb=" O   ILE C 277 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   ASN C 279 " --> pdb=" O   GLN B 276 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   ILE B 278 " --> pdb=" O   ASN C 279 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   LYS A 274 " --> pdb=" O   VAL B 275 " (cutoff:3.500A)
      removed outlier: 7.710A  pdb=" N   ILE B 277 " --> pdb=" O   LYS A 274 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   GLN A 276 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
      removed outlier: 7.618A  pdb=" N   ASN B 279 " --> pdb=" O   GLN A 276 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   ILE A 278 " --> pdb=" O   ASN B 279 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 283 through 284
      removed outlier: 6.209A  pdb=" N   ASP B 283 " --> pdb=" O   LEU C 284 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   ASP A 283 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 287 through 292
      removed outlier: 6.444A  pdb=" N   VAL A 287 " --> pdb=" O   GLN D 288 " (cutoff:3.500A)
      removed outlier: 7.938A  pdb=" N   LYS D 290 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   SER A 289 " --> pdb=" O   LYS D 290 " (cutoff:3.500A)
      removed outlier: 7.977A  pdb=" N   GLY D 292 " --> pdb=" O   SER A 289 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   CYS A 291 " --> pdb=" O   GLY D 292 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   VAL D 287 " --> pdb=" O   GLN E 288 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   LYS E 290 " --> pdb=" O   VAL D 287 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   SER D 289 " --> pdb=" O   LYS E 290 " (cutoff:3.500A)
      removed outlier: 7.974A  pdb=" N   GLY E 292 " --> pdb=" O   SER D 289 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   CYS D 291 " --> pdb=" O   GLY E 292 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 297 through 298
      removed outlier: 6.277A  pdb=" N   ILE A 297 " --> pdb=" O   LYS D 298 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   ILE D 297 " --> pdb=" O   LYS E 298 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 305 through 310
      removed outlier: 6.625A  pdb=" N   SER B 305 " --> pdb=" O   VAL C 306 " (cutoff:3.500A)
      removed outlier: 8.119A  pdb=" N   ILE C 308 " --> pdb=" O   SER B 305 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   GLN B 307 " --> pdb=" O   ILE C 308 " (cutoff:3.500A)
      removed outlier: 7.471A  pdb=" N   TYR C 310 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   VAL B 309 " --> pdb=" O   TYR C 310 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   SER A 305 " --> pdb=" O   VAL B 306 " (cutoff:3.500A)
      removed outlier: 8.112A  pdb=" N   ILE B 308 " --> pdb=" O   SER A 305 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   GLN A 307 " --> pdb=" O   ILE B 308 " (cutoff:3.500A)
      removed outlier: 7.467A  pdb=" N   TYR B 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   VAL A 309 " --> pdb=" O   TYR B 310 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 313 through 314
      removed outlier: 6.817A  pdb=" N   VAL B 313 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   VAL A 313 " --> pdb=" O   ASP B 314 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 317 through 322
      removed outlier: 6.274A  pdb=" N   VAL A 318 " --> pdb=" O   THR D 319 " (cutoff:3.500A)
      removed outlier: 7.953A  pdb=" N   LYS D 321 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   SER A 320 " --> pdb=" O   LYS D 321 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   VAL D 318 " --> pdb=" O   THR E 319 " (cutoff:3.500A)
      removed outlier: 7.961A  pdb=" N   LYS E 321 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   SER D 320 " --> pdb=" O   LYS E 321 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 328 through 330
      removed outlier: 6.698A  pdb=" N   ILE A 328 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   ILE D 328 " --> pdb=" O   HIS E 329 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 337 through 346
      removed outlier: 6.317A  pdb=" N   VAL A 337 " --> pdb=" O   GLU D 338 " (cutoff:3.500A)
      removed outlier: 7.694A  pdb=" N   LYS D 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   VAL A 339 " --> pdb=" O   LYS D 340 " (cutoff:3.500A)
      removed outlier: 7.900A  pdb=" N   GLU D 342 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   SER A 341 " --> pdb=" O   GLU D 342 " (cutoff:3.500A)
      removed outlier: 8.274A  pdb=" N   LEU D 344 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   LYS A 343 " --> pdb=" O   LEU D 344 " (cutoff:3.500A)
      removed outlier: 8.025A  pdb=" N   PHE D 346 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   ASP A 345 " --> pdb=" O   PHE D 346 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   VAL D 337 " --> pdb=" O   GLU E 338 " (cutoff:3.500A)
      removed outlier: 7.689A  pdb=" N   LYS E 340 " --> pdb=" O   VAL D 337 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   VAL D 339 " --> pdb=" O   LYS E 340 " (cutoff:3.500A)
      removed outlier: 7.892A  pdb=" N   GLU E 342 " --> pdb=" O   VAL D 339 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   SER D 341 " --> pdb=" O   GLU E 342 " (cutoff:3.500A)
      removed outlier: 8.265A  pdb=" N   LEU E 344 " --> pdb=" O   SER D 341 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   LYS D 343 " --> pdb=" O   LEU E 344 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   PHE E 346 " --> pdb=" O   LYS D 343 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   ASP D 345 " --> pdb=" O   PHE E 346 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 349 through 354
      removed outlier: 6.573A  pdb=" N   VAL B 350 " --> pdb=" O   GLN C 351 " (cutoff:3.500A)
      removed outlier: 7.812A  pdb=" N   LYS C 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   SER B 352 " --> pdb=" O   LYS C 353 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   VAL A 350 " --> pdb=" O   GLN B 351 " (cutoff:3.500A)
      removed outlier: 7.803A  pdb=" N   LYS B 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   SER A 352 " --> pdb=" O   LYS B 353 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 357 through 362
      removed outlier: 6.871A  pdb=" N   ASP B 358 " --> pdb=" O   LEU C 357 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   ASN C 359 " --> pdb=" O   ASP B 358 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   ASP A 358 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ASN B 359 " --> pdb=" O   ASP A 358 " (cutoff:3.500A)
      removed outlier: 8.897A  pdb=" N   LEU A 357 " --> pdb=" O   ASP D 358 " (cutoff:3.500A)
      removed outlier: 9.591A  pdb=" N   ILE D 360 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ASN A 359 " --> pdb=" O   ILE D 360 " (cutoff:3.500A)
      removed outlier: 7.920A  pdb=" N   HIS D 362 " --> pdb=" O   ASN A 359 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   THR A 361 " --> pdb=" O   HIS D 362 " (cutoff:3.500A)
      removed outlier: 8.889A  pdb=" N   LEU D 357 " --> pdb=" O   ASP E 358 " (cutoff:3.500A)
      removed outlier: 9.582A  pdb=" N   ILE E 360 " --> pdb=" O   LEU D 357 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   ASN D 359 " --> pdb=" O   ILE E 360 " (cutoff:3.500A)
      removed outlier: 7.915A  pdb=" N   HIS E 362 " --> pdb=" O   ASN D 359 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   THR D 361 " --> pdb=" O   HIS E 362 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 369 through 378
      removed outlier: 6.815A  pdb=" N   LYS B 370 " --> pdb=" O   LYS C 369 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   LYS A 370 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   LYS A 369 " --> pdb=" O   LYS D 370 " (cutoff:3.500A)
      removed outlier: 8.610A  pdb=" N   GLU D 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   ILE A 371 " --> pdb=" O   GLU D 372 " (cutoff:3.500A)
      removed outlier: 8.079A  pdb=" N   HIS D 374 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   THR A 373 " --> pdb=" O   HIS D 374 " (cutoff:3.500A)
      removed outlier: 8.017A  pdb=" N   LEU D 376 " --> pdb=" O   THR A 373 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   LYS A 375 " --> pdb=" O   LEU D 376 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   PHE D 378 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   THR A 377 " --> pdb=" O   PHE D 378 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   LYS D 369 " --> pdb=" O   LYS E 370 " (cutoff:3.500A)
      removed outlier: 8.619A  pdb=" N   GLU E 372 " --> pdb=" O   LYS D 369 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   ILE D 371 " --> pdb=" O   GLU E 372 " (cutoff:3.500A)
      removed outlier: 8.089A  pdb=" N   HIS E 374 " --> pdb=" O   ILE D 371 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   THR D 373 " --> pdb=" O   HIS E 374 " (cutoff:3.500A)
      removed outlier: 8.024A  pdb=" N   LEU E 376 " --> pdb=" O   THR D 373 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   LYS D 375 " --> pdb=" O   LEU E 376 " (cutoff:3.500A)
      removed outlier: 7.914A  pdb=" N   PHE E 378 " --> pdb=" O   LYS D 375 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   THR D 377 " --> pdb=" O   PHE E 378 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 274 through 280
      removed outlier: 6.823A  pdb=" N   LYS G 274 " --> pdb=" O   VAL H 275 " (cutoff:3.500A)
      removed outlier: 7.709A  pdb=" N   ILE H 277 " --> pdb=" O   LYS G 274 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   GLN G 276 " --> pdb=" O   ILE H 277 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   ASN H 279 " --> pdb=" O   GLN G 276 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   ILE G 278 " --> pdb=" O   ASN H 279 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   LYS F 274 " --> pdb=" O   VAL G 275 " (cutoff:3.500A)
      removed outlier: 7.713A  pdb=" N   ILE G 277 " --> pdb=" O   LYS F 274 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   GLN F 276 " --> pdb=" O   ILE G 277 " (cutoff:3.500A)
      removed outlier: 7.620A  pdb=" N   ASN G 279 " --> pdb=" O   GLN F 276 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   ILE F 278 " --> pdb=" O   ASN G 279 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 283 through 284
      removed outlier: 6.206A  pdb=" N   ASP G 283 " --> pdb=" O   LEU H 284 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   ASP F 283 " --> pdb=" O   LEU G 284 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 287 through 292
      removed outlier: 6.440A  pdb=" N   VAL F 287 " --> pdb=" O   GLN I 288 " (cutoff:3.500A)
      removed outlier: 7.934A  pdb=" N   LYS I 290 " --> pdb=" O   VAL F 287 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   SER F 289 " --> pdb=" O   LYS I 290 " (cutoff:3.500A)
      removed outlier: 7.974A  pdb=" N   GLY I 292 " --> pdb=" O   SER F 289 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   CYS F 291 " --> pdb=" O   GLY I 292 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   VAL I 287 " --> pdb=" O   GLN J 288 " (cutoff:3.500A)
      removed outlier: 7.940A  pdb=" N   LYS J 290 " --> pdb=" O   VAL I 287 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   SER I 289 " --> pdb=" O   LYS J 290 " (cutoff:3.500A)
      removed outlier: 7.977A  pdb=" N   GLY J 292 " --> pdb=" O   SER I 289 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   CYS I 291 " --> pdb=" O   GLY J 292 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 297 through 298
      removed outlier: 6.270A  pdb=" N   ILE F 297 " --> pdb=" O   LYS I 298 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   ILE I 297 " --> pdb=" O   LYS J 298 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'H' and resid 305 through 310
      removed outlier: 6.627A  pdb=" N   SER G 305 " --> pdb=" O   VAL H 306 " (cutoff:3.500A)
      removed outlier: 8.121A  pdb=" N   ILE H 308 " --> pdb=" O   SER G 305 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   GLN G 307 " --> pdb=" O   ILE H 308 " (cutoff:3.500A)
      removed outlier: 7.475A  pdb=" N   TYR H 310 " --> pdb=" O   GLN G 307 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   VAL G 309 " --> pdb=" O   TYR H 310 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   SER F 305 " --> pdb=" O   VAL G 306 " (cutoff:3.500A)
      removed outlier: 8.111A  pdb=" N   ILE G 308 " --> pdb=" O   SER F 305 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   GLN F 307 " --> pdb=" O   ILE G 308 " (cutoff:3.500A)
      removed outlier: 7.463A  pdb=" N   TYR G 310 " --> pdb=" O   GLN F 307 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   VAL F 309 " --> pdb=" O   TYR G 310 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'H' and resid 313 through 314
      removed outlier: 6.819A  pdb=" N   VAL G 313 " --> pdb=" O   ASP H 314 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   VAL F 313 " --> pdb=" O   ASP G 314 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'H' and resid 317 through 322
      removed outlier: 6.278A  pdb=" N   VAL F 318 " --> pdb=" O   THR I 319 " (cutoff:3.500A)
      removed outlier: 7.957A  pdb=" N   LYS I 321 " --> pdb=" O   VAL F 318 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   SER F 320 " --> pdb=" O   LYS I 321 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   VAL I 318 " --> pdb=" O   THR J 319 " (cutoff:3.500A)
      removed outlier: 7.960A  pdb=" N   LYS J 321 " --> pdb=" O   VAL I 318 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   SER I 320 " --> pdb=" O   LYS J 321 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'H' and resid 328 through 330
      removed outlier: 6.696A  pdb=" N   ILE F 328 " --> pdb=" O   HIS I 329 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   ILE I 328 " --> pdb=" O   HIS J 329 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'H' and resid 337 through 346
      removed outlier: 6.311A  pdb=" N   VAL F 337 " --> pdb=" O   GLU I 338 " (cutoff:3.500A)
      removed outlier: 7.688A  pdb=" N   LYS I 340 " --> pdb=" O   VAL F 337 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   VAL F 339 " --> pdb=" O   LYS I 340 " (cutoff:3.500A)
      removed outlier: 7.891A  pdb=" N   GLU I 342 " --> pdb=" O   VAL F 339 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   SER F 341 " --> pdb=" O   GLU I 342 " (cutoff:3.500A)
      removed outlier: 8.265A  pdb=" N   LEU I 344 " --> pdb=" O   SER F 341 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   LYS F 343 " --> pdb=" O   LEU I 344 " (cutoff:3.500A)
      removed outlier: 8.017A  pdb=" N   PHE I 346 " --> pdb=" O   LYS F 343 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   ASP F 345 " --> pdb=" O   PHE I 346 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   VAL I 337 " --> pdb=" O   GLU J 338 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   LYS J 340 " --> pdb=" O   VAL I 337 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   VAL I 339 " --> pdb=" O   LYS J 340 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   GLU J 342 " --> pdb=" O   VAL I 339 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   SER I 341 " --> pdb=" O   GLU J 342 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   LEU J 344 " --> pdb=" O   SER I 341 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   LYS I 343 " --> pdb=" O   LEU J 344 " (cutoff:3.500A)
      removed outlier: 8.021A  pdb=" N   PHE J 346 " --> pdb=" O   LYS I 343 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   ASP I 345 " --> pdb=" O   PHE J 346 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'H' and resid 349 through 354
      removed outlier: 6.563A  pdb=" N   VAL G 350 " --> pdb=" O   GLN H 351 " (cutoff:3.500A)
      removed outlier: 7.802A  pdb=" N   LYS H 353 " --> pdb=" O   VAL G 350 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   SER G 352 " --> pdb=" O   LYS H 353 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   VAL F 350 " --> pdb=" O   GLN G 351 " (cutoff:3.500A)
      removed outlier: 7.811A  pdb=" N   LYS G 353 " --> pdb=" O   VAL F 350 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   SER F 352 " --> pdb=" O   LYS G 353 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'H' and resid 357 through 362
      removed outlier: 6.862A  pdb=" N   ASP G 358 " --> pdb=" O   LEU H 357 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   ASN H 359 " --> pdb=" O   ASP G 358 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   ASP F 358 " --> pdb=" O   LEU G 357 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   ASN G 359 " --> pdb=" O   ASP F 358 " (cutoff:3.500A)
      removed outlier: 8.888A  pdb=" N   LEU F 357 " --> pdb=" O   ASP I 358 " (cutoff:3.500A)
      removed outlier: 9.581A  pdb=" N   ILE I 360 " --> pdb=" O   LEU F 357 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   ASN F 359 " --> pdb=" O   ILE I 360 " (cutoff:3.500A)
      removed outlier: 7.914A  pdb=" N   HIS I 362 " --> pdb=" O   ASN F 359 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   THR F 361 " --> pdb=" O   HIS I 362 " (cutoff:3.500A)
      removed outlier: 8.890A  pdb=" N   LEU I 357 " --> pdb=" O   ASP J 358 " (cutoff:3.500A)
      removed outlier: 9.584A  pdb=" N   ILE J 360 " --> pdb=" O   LEU I 357 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   ASN I 359 " --> pdb=" O   ILE J 360 " (cutoff:3.500A)
      removed outlier: 7.917A  pdb=" N   HIS J 362 " --> pdb=" O   ASN I 359 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   THR I 361 " --> pdb=" O   HIS J 362 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'H' and resid 369 through 378
      removed outlier: 6.808A  pdb=" N   LYS G 370 " --> pdb=" O   LYS H 369 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   LYS F 370 " --> pdb=" O   LYS G 369 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   LYS F 369 " --> pdb=" O   LYS I 370 " (cutoff:3.500A)
      removed outlier: 8.618A  pdb=" N   GLU I 372 " --> pdb=" O   LYS F 369 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   ILE F 371 " --> pdb=" O   GLU I 372 " (cutoff:3.500A)
      removed outlier: 8.089A  pdb=" N   HIS I 374 " --> pdb=" O   ILE F 371 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   THR F 373 " --> pdb=" O   HIS I 374 " (cutoff:3.500A)
      removed outlier: 8.024A  pdb=" N   LEU I 376 " --> pdb=" O   THR F 373 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   LYS F 375 " --> pdb=" O   LEU I 376 " (cutoff:3.500A)
      removed outlier: 7.914A  pdb=" N   PHE I 378 " --> pdb=" O   LYS F 375 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   THR F 377 " --> pdb=" O   PHE I 378 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   LYS I 369 " --> pdb=" O   LYS J 370 " (cutoff:3.500A)
      removed outlier: 8.614A  pdb=" N   GLU J 372 " --> pdb=" O   LYS I 369 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   ILE I 371 " --> pdb=" O   GLU J 372 " (cutoff:3.500A)
      removed outlier: 8.083A  pdb=" N   HIS J 374 " --> pdb=" O   ILE I 371 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   THR I 373 " --> pdb=" O   HIS J 374 " (cutoff:3.500A)
      removed outlier: 8.018A  pdb=" N   LEU J 376 " --> pdb=" O   THR I 373 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   LYS I 375 " --> pdb=" O   LEU J 376 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   PHE J 378 " --> pdb=" O   LYS I 375 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   THR I 377 " --> pdb=" O   PHE J 378 " (cutoff:3.500A)

    204 hydrogen bonds defined for protein.
    612 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.33

  Time building geometry restraints manager: 2.19 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2710
        1.34 -     1.46: 1245
        1.46 -     1.58: 4255
        1.58 -     1.69: 0
        1.69 -     1.81: 20
  Bond restraints: 8230
  Sorted by residual:
  bond pdb=" N   ILE F 371 "
       pdb=" CA  ILE F 371 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.034 1.24e-02 6.50e+03 7.73e+00
  bond pdb=" N   ILE D 371 "
       pdb=" CA  ILE D 371 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.24e-02 6.50e+03 7.56e+00
  bond pdb=" N   ILE E 371 "
       pdb=" CA  ILE E 371 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.24e-02 6.50e+03 7.42e+00
  bond pdb=" N   ILE B 371 "
       pdb=" CA  ILE B 371 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.24e-02 6.50e+03 7.37e+00
  bond pdb=" N   ILE C 371 "
       pdb=" CA  ILE C 371 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.24e-02 6.50e+03 7.34e+00
  ... (remaining 8225 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.99: 9229
        0.99 -     1.98: 1359
        1.98 -     2.98: 329
        2.98 -     3.97: 43
        3.97 -     4.96: 30
  Bond angle restraints: 10990
  Sorted by residual:
  angle pdb=" CA  ILE I 371 "
        pdb=" C   ILE I 371 "
        pdb=" O   ILE I 371 "
      ideal   model   delta    sigma   weight residual
     120.53  117.72    2.81 1.07e+00 8.73e-01 6.90e+00
  angle pdb=" CA  ILE G 371 "
        pdb=" C   ILE G 371 "
        pdb=" O   ILE G 371 "
      ideal   model   delta    sigma   weight residual
     120.53  117.74    2.79 1.07e+00 8.73e-01 6.81e+00
  angle pdb=" CA  ILE A 371 "
        pdb=" C   ILE A 371 "
        pdb=" O   ILE A 371 "
      ideal   model   delta    sigma   weight residual
     120.53  117.74    2.79 1.07e+00 8.73e-01 6.81e+00
  angle pdb=" CA  ILE B 371 "
        pdb=" C   ILE B 371 "
        pdb=" O   ILE B 371 "
      ideal   model   delta    sigma   weight residual
     120.53  117.74    2.79 1.07e+00 8.73e-01 6.80e+00
  angle pdb=" CA  ILE C 371 "
        pdb=" C   ILE C 371 "
        pdb=" O   ILE C 371 "
      ideal   model   delta    sigma   weight residual
     120.53  117.74    2.79 1.07e+00 8.73e-01 6.80e+00
  ... (remaining 10985 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.13: 4200
       13.13 -    26.25: 479
       26.25 -    39.38: 281
       39.38 -    52.51: 80
       52.51 -    65.63: 10
  Dihedral angle restraints: 5050
    sinusoidal: 2110
      harmonic: 2940
  Sorted by residual:
  dihedral pdb=" CG  LYS B 340 "
           pdb=" CD  LYS B 340 "
           pdb=" CE  LYS B 340 "
           pdb=" NZ  LYS B 340 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  132.86   47.14     3      1.50e+01 4.44e-03 8.45e+00
  dihedral pdb=" CG  LYS D 340 "
           pdb=" CD  LYS D 340 "
           pdb=" CE  LYS D 340 "
           pdb=" NZ  LYS D 340 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  132.89   47.11     3      1.50e+01 4.44e-03 8.44e+00
  dihedral pdb=" CG  LYS F 340 "
           pdb=" CD  LYS F 340 "
           pdb=" CE  LYS F 340 "
           pdb=" NZ  LYS F 340 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  132.89   47.11     3      1.50e+01 4.44e-03 8.44e+00
  ... (remaining 5047 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 752
       0.043 -    0.086: 184
       0.086 -    0.129: 284
       0.129 -    0.172: 0
       0.172 -    0.214: 10
  Chirality restraints: 1230
  Sorted by residual:
  chirality pdb=" CA  ILE H 371 "
            pdb=" N   ILE H 371 "
            pdb=" C   ILE H 371 "
            pdb=" CB  ILE H 371 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CA  ILE E 371 "
            pdb=" N   ILE E 371 "
            pdb=" C   ILE E 371 "
            pdb=" CB  ILE E 371 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CA  ILE I 371 "
            pdb=" N   ILE I 371 "
            pdb=" C   ILE I 371 "
            pdb=" CB  ILE I 371 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.21 2.00e-01 2.50e+01 1.14e+00
  ... (remaining 1227 not shown)

  Planarity restraints: 1410
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D 300 "   -0.014 5.00e-02 4.00e+02   2.09e-02 7.00e-01
        pdb=" N   PRO D 301 "    0.036 5.00e-02 4.00e+02
        pdb=" CA  PRO D 301 "   -0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO D 301 "   -0.012 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL J 300 "   -0.014 5.00e-02 4.00e+02   2.09e-02 6.99e-01
        pdb=" N   PRO J 301 "    0.036 5.00e-02 4.00e+02
        pdb=" CA  PRO J 301 "   -0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO J 301 "   -0.012 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 300 "   -0.014 5.00e-02 4.00e+02   2.08e-02 6.93e-01
        pdb=" N   PRO A 301 "    0.036 5.00e-02 4.00e+02
        pdb=" CA  PRO A 301 "   -0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO A 301 "   -0.012 5.00e-02 4.00e+02
  ... (remaining 1407 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 1669
        2.81 -     3.33: 6711
        3.33 -     3.85: 14379
        3.85 -     4.38: 16376
        4.38 -     4.90: 31438
  Nonbonded interactions: 70573
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 373 "
            pdb=" OG1 THR B 361 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OG1 THR I 361 "
            pdb=" OG1 THR J 373 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OG1 THR F 373 "
            pdb=" OG1 THR G 361 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" OG1 THR A 361 "
            pdb=" OG1 THR D 373 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" OG1 THR G 373 "
            pdb=" OG1 THR H 361 "
     model   vdw
     2.286 3.040
  ... (remaining 70568 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

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:             7.170
  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:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     20.200
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
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      :  0.005   0.040   8230  Z= 0.344
  Angle     :  0.803   4.959  10990  Z= 0.486
  Chirality :  0.061   0.214   1230
  Planarity :  0.003   0.021   1410
  Dihedral  : 15.343  65.635   3190
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 13.87 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.05 (0.18), residues: 1060
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.32 (0.13), residues: 1060

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS H 330 
 PHE   0.007   0.002   PHE G 346 
 TYR   0.008   0.002   TYR H 310 
 ARG   0.001   0.000   ARG I 379 

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 260
  time to evaluate  : 1.067 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 LYS cc_start: 0.8149 (mtpt) cc_final: 0.7528 (mptp)
REVERT: B  281 LYS cc_start: 0.7364 (mttt) cc_final: 0.7070 (mttm)
REVERT: B  288 GLN cc_start: 0.8306 (tt0) cc_final: 0.8034 (tt0)
REVERT: B  347 LYS cc_start: 0.8128 (mtpt) cc_final: 0.7541 (mptp)
REVERT: C  288 GLN cc_start: 0.8392 (tt0) cc_final: 0.8186 (tt0)
REVERT: C  345 ASP cc_start: 0.7372 (t70) cc_final: 0.6985 (t70)
REVERT: C  347 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7588 (mptp)
REVERT: C  376 LEU cc_start: 0.8635 (mp) cc_final: 0.7928 (tp)
REVERT: D  288 GLN cc_start: 0.8322 (tt0) cc_final: 0.8070 (tt0)
REVERT: D  345 ASP cc_start: 0.7369 (t70) cc_final: 0.7029 (t70)
REVERT: D  347 LYS cc_start: 0.8249 (mtpt) cc_final: 0.7611 (mppt)
REVERT: E  340 LYS cc_start: 0.7583 (mtpt) cc_final: 0.6983 (mtpm)
REVERT: E  345 ASP cc_start: 0.7412 (t70) cc_final: 0.6871 (t70)
REVERT: E  347 LYS cc_start: 0.8200 (mtpt) cc_final: 0.7693 (mppt)
REVERT: F  340 LYS cc_start: 0.7410 (mtpt) cc_final: 0.6807 (mtpp)
REVERT: F  345 ASP cc_start: 0.7307 (t70) cc_final: 0.6633 (t70)
REVERT: F  347 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7501 (mppt)
REVERT: G  345 ASP cc_start: 0.7388 (t70) cc_final: 0.6827 (t70)
REVERT: G  347 LYS cc_start: 0.8153 (mtpt) cc_final: 0.7504 (mppt)
REVERT: H  345 ASP cc_start: 0.7378 (t70) cc_final: 0.7002 (t70)
REVERT: H  347 LYS cc_start: 0.8207 (mtpt) cc_final: 0.7651 (mppt)
REVERT: I  345 ASP cc_start: 0.7302 (t70) cc_final: 0.6841 (t70)
REVERT: I  347 LYS cc_start: 0.8182 (mtpt) cc_final: 0.7577 (mppt)
REVERT: I  351 GLN cc_start: 0.8121 (tt0) cc_final: 0.7914 (tt0)
REVERT: J  347 LYS cc_start: 0.8225 (mtpt) cc_final: 0.7632 (mptp)
  outliers start: 4
  outliers final: 3
  residues processed: 260
  average time/residue: 1.1982
  time to fit residues: 330.2108
Evaluate side-chains
  222 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 219
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain F residue  342 GLU
Chi-restraints excluded: chain I residue  342 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:   10.0000
   chunk 75 optimal weight:    8.9990
   chunk 42 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 51 optimal weight:   10.0000
   chunk 40 optimal weight:   10.0000
   chunk 78 optimal weight:    7.9990
   chunk 30 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   chunk 58 optimal weight:    8.9990
   chunk 90 optimal weight:    7.9990
   overall best weight:    6.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 296 ASN
E 296 ASN
F 296 ASN
G 296 ASN
H 288 GLN
I 296 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.1575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.043   8230  Z= 0.447
  Angle     :  0.690   5.231  10990  Z= 0.364
  Chirality :  0.053   0.138   1230
  Planarity :  0.004   0.025   1410
  Dihedral  :  6.302  30.575   1109
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 18.28 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.81 (0.17), residues: 1060
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.13 (0.13), residues: 1060

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS J 299 
 PHE   0.008   0.001   PHE B 378 
 TYR   0.009   0.003   TYR J 310 
 ARG   0.004   0.001   ARG E 379 

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 229
  time to evaluate  : 0.920 
Fit side-chains
REVERT: A  274 LYS cc_start: 0.7169 (mtmt) cc_final: 0.6796 (ttmm)
REVERT: A  347 LYS cc_start: 0.8294 (mtpt) cc_final: 0.7525 (mptp)
REVERT: B  274 LYS cc_start: 0.7127 (mtmt) cc_final: 0.6703 (ttmm)
REVERT: B  281 LYS cc_start: 0.7423 (mttt) cc_final: 0.7130 (mttm)
REVERT: B  288 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8129 (tt0)
REVERT: B  293 SER cc_start: 0.8337 (p) cc_final: 0.8018 (m)
REVERT: B  345 ASP cc_start: 0.7091 (t70) cc_final: 0.6858 (t70)
REVERT: B  347 LYS cc_start: 0.8294 (mtpt) cc_final: 0.7535 (mptp)
REVERT: C  274 LYS cc_start: 0.7496 (mtmt) cc_final: 0.7167 (ttmm)
REVERT: C  340 LYS cc_start: 0.7855 (mtpt) cc_final: 0.7214 (mtpp)
REVERT: C  345 ASP cc_start: 0.7494 (t70) cc_final: 0.7141 (t70)
REVERT: C  347 LYS cc_start: 0.8248 (mtpt) cc_final: 0.7531 (mptp)
REVERT: C  376 LEU cc_start: 0.8595 (mp) cc_final: 0.7926 (tp)
REVERT: D  274 LYS cc_start: 0.7010 (mtmt) cc_final: 0.6596 (ttmm)
REVERT: D  340 LYS cc_start: 0.7080 (mttt) cc_final: 0.6416 (mtpp)
REVERT: D  345 ASP cc_start: 0.7471 (t70) cc_final: 0.7179 (t70)
REVERT: D  347 LYS cc_start: 0.8307 (mtpt) cc_final: 0.7604 (mtmp)
REVERT: E  274 LYS cc_start: 0.6943 (mtmt) cc_final: 0.6569 (ttmm)
REVERT: E  347 LYS cc_start: 0.8348 (mtpt) cc_final: 0.7635 (mppt)
REVERT: F  345 ASP cc_start: 0.7463 (t70) cc_final: 0.7152 (t70)
REVERT: F  347 LYS cc_start: 0.8255 (mtpt) cc_final: 0.7555 (mptp)
REVERT: G  274 LYS cc_start: 0.7115 (mtmt) cc_final: 0.6462 (mttp)
REVERT: G  277 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7833 (mp)
REVERT: G  283 ASP cc_start: 0.7288 (t0) cc_final: 0.7079 (t0)
REVERT: G  347 LYS cc_start: 0.8342 (mtpt) cc_final: 0.7535 (mptp)
REVERT: H  293 SER cc_start: 0.8048 (p) cc_final: 0.7683 (m)
REVERT: H  345 ASP cc_start: 0.7410 (t70) cc_final: 0.6875 (t70)
REVERT: H  347 LYS cc_start: 0.8341 (mtpt) cc_final: 0.7689 (mptp)
REVERT: I  274 LYS cc_start: 0.7072 (mtmt) cc_final: 0.6700 (ttmm)
REVERT: I  345 ASP cc_start: 0.7437 (t70) cc_final: 0.7191 (t70)
REVERT: I  347 LYS cc_start: 0.8300 (mtpt) cc_final: 0.7647 (mtmp)
REVERT: J  293 SER cc_start: 0.8076 (p) cc_final: 0.7726 (m)
REVERT: J  347 LYS cc_start: 0.8390 (mtpt) cc_final: 0.7711 (mtmp)
REVERT: J  376 LEU cc_start: 0.8518 (mp) cc_final: 0.7750 (tp)
  outliers start: 14
  outliers final: 7
  residues processed: 235
  average time/residue: 1.3618
  time to fit residues: 337.0191
Evaluate side-chains
  224 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 215
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain B residue  288 GLN
Chi-restraints excluded: chain C residue  342 GLU
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain G residue  277 ILE
Chi-restraints excluded: chain G residue  342 GLU
Chi-restraints excluded: chain H residue  342 GLU
Chi-restraints excluded: chain J residue  342 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 28 optimal weight:    8.9990
   chunk 75 optimal weight:   10.0000
   chunk 61 optimal weight:    9.9990
   chunk 25 optimal weight:    7.9990
   chunk 90 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 81 optimal weight:    9.9990
   chunk 31 optimal weight:   20.0000
   chunk 72 optimal weight:    0.7980
   chunk 89 optimal weight:    0.8980
   overall best weight:    3.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 296 ASN
D 288 GLN
E 296 ASN
F 296 ASN
H 288 GLN
I 288 GLN
J 288 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.1568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8230  Z= 0.249
  Angle     :  0.574   5.202  10990  Z= 0.299
  Chirality :  0.050   0.135   1230
  Planarity :  0.003   0.025   1410
  Dihedral  :  5.815  14.267   1100
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 17.53 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.84 (0.18), residues: 1060
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.16 (0.13), residues: 1060

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS I 299 
 PHE   0.006   0.001   PHE B 378 
 TYR   0.010   0.002   TYR J 310 
 ARG   0.006   0.000   ARG E 379 

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 221
  time to evaluate  : 1.022 
Fit side-chains
REVERT: A  274 LYS cc_start: 0.7076 (mtmt) cc_final: 0.6791 (ttmm)
REVERT: A  347 LYS cc_start: 0.8211 (mtpt) cc_final: 0.7525 (mtmp)
REVERT: B  274 LYS cc_start: 0.7101 (mtmt) cc_final: 0.6731 (ttmm)
REVERT: B  281 LYS cc_start: 0.7377 (mttt) cc_final: 0.7101 (mttm)
REVERT: B  288 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8088 (tt0)
REVERT: B  293 SER cc_start: 0.8316 (p) cc_final: 0.7984 (m)
REVERT: B  347 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7574 (mtmp)
REVERT: B  351 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7814 (tt0)
REVERT: C  274 LYS cc_start: 0.7486 (mtmt) cc_final: 0.7186 (ttmm)
REVERT: C  340 LYS cc_start: 0.7847 (mtpt) cc_final: 0.7207 (mtpp)
REVERT: C  347 LYS cc_start: 0.8231 (mtpt) cc_final: 0.7582 (mtmp)
REVERT: C  376 LEU cc_start: 0.8584 (mp) cc_final: 0.7884 (tp)
REVERT: D  274 LYS cc_start: 0.6960 (mtmt) cc_final: 0.6637 (ttmm)
REVERT: D  340 LYS cc_start: 0.7089 (mttt) cc_final: 0.6406 (mtpp)
REVERT: D  345 ASP cc_start: 0.7364 (t70) cc_final: 0.7151 (t70)
REVERT: D  347 LYS cc_start: 0.8201 (mtpt) cc_final: 0.7562 (mtmp)
REVERT: E  274 LYS cc_start: 0.6924 (mtmt) cc_final: 0.6630 (ttmm)
REVERT: E  277 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8177 (mp)
REVERT: E  347 LYS cc_start: 0.8318 (mtpt) cc_final: 0.7661 (mptp)
REVERT: F  347 LYS cc_start: 0.8278 (mtpt) cc_final: 0.7566 (mtmp)
REVERT: G  274 LYS cc_start: 0.7087 (mtmt) cc_final: 0.6776 (ttmm)
REVERT: G  283 ASP cc_start: 0.7328 (t0) cc_final: 0.7102 (t0)
REVERT: G  347 LYS cc_start: 0.8314 (mtpt) cc_final: 0.7584 (mtmp)
REVERT: H  274 LYS cc_start: 0.7458 (mtmt) cc_final: 0.7139 (ttmm)
REVERT: H  347 LYS cc_start: 0.8340 (mtpt) cc_final: 0.7680 (mtmp)
REVERT: I  274 LYS cc_start: 0.7050 (mtmt) cc_final: 0.6733 (ttmm)
REVERT: I  345 ASP cc_start: 0.7470 (t70) cc_final: 0.7222 (t70)
REVERT: I  347 LYS cc_start: 0.8255 (mtpt) cc_final: 0.7561 (mtmp)
REVERT: J  347 LYS cc_start: 0.8348 (mtpt) cc_final: 0.7664 (mtmp)
REVERT: J  376 LEU cc_start: 0.8505 (mp) cc_final: 0.7714 (tp)
  outliers start: 21
  outliers final: 10
  residues processed: 231
  average time/residue: 1.3579
  time to fit residues: 330.2582
Evaluate side-chains
  231 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 218
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain B residue  288 GLN
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  351 GLN
Chi-restraints excluded: chain C residue  342 GLU
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain E residue  277 ILE
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain F residue  342 GLU
Chi-restraints excluded: chain G residue  342 GLU
Chi-restraints excluded: chain H residue  342 GLU
Chi-restraints excluded: chain J residue  284 LEU
Chi-restraints excluded: chain J residue  342 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 68 optimal weight:   10.0000
   chunk 47 optimal weight:    6.9990
   chunk 10 optimal weight:   10.0000
   chunk 43 optimal weight:    8.9990
   chunk 61 optimal weight:   20.0000
   chunk 91 optimal weight:    9.9990
   chunk 96 optimal weight:    8.9990
   chunk 86 optimal weight:    8.9990
   chunk 26 optimal weight:    7.9990
   chunk 80 optimal weight:   10.0000
   chunk 54 optimal weight:    8.9990
   overall best weight:    8.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 296 ASN
D 288 GLN
E 296 ASN
F 296 ASN
H 288 GLN
I 296 ASN
I 351 GLN
J 288 GLN
J 296 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.051   8230  Z= 0.569
  Angle     :  0.743   6.120  10990  Z= 0.391
  Chirality :  0.054   0.153   1230
  Planarity :  0.004   0.027   1410
  Dihedral  :  6.296  17.540   1100
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 15.81 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.73 (0.17), residues: 1060
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.07 (0.13), residues: 1060

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS J 299 
 PHE   0.010   0.001   PHE B 378 
 TYR   0.010   0.003   TYR J 310 
 ARG   0.004   0.001   ARG E 379 

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 219
  time to evaluate  : 1.028 
Fit side-chains
REVERT: A  274 LYS cc_start: 0.7208 (mtmt) cc_final: 0.6870 (ttmm)
REVERT: A  328 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.7880 (mp)
REVERT: A  347 LYS cc_start: 0.8340 (mtpt) cc_final: 0.7426 (mptp)
REVERT: B  274 LYS cc_start: 0.7173 (mtmt) cc_final: 0.6748 (ttmm)
REVERT: B  281 LYS cc_start: 0.7513 (mttt) cc_final: 0.7245 (mttm)
REVERT: B  288 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8136 (tt0)
REVERT: B  293 SER cc_start: 0.8368 (p) cc_final: 0.8079 (m)
REVERT: B  347 LYS cc_start: 0.8259 (mtpt) cc_final: 0.7495 (mttp)
REVERT: B  351 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7813 (tt0)
REVERT: C  274 LYS cc_start: 0.7592 (mtmt) cc_final: 0.7227 (ttmm)
REVERT: C  293 SER cc_start: 0.8002 (p) cc_final: 0.7663 (m)
REVERT: C  345 ASP cc_start: 0.7251 (t70) cc_final: 0.6802 (t70)
REVERT: C  347 LYS cc_start: 0.8285 (mtpt) cc_final: 0.7500 (mttp)
REVERT: D  274 LYS cc_start: 0.7047 (mtmt) cc_final: 0.6662 (ttmm)
REVERT: D  345 ASP cc_start: 0.7464 (t70) cc_final: 0.7218 (t70)
REVERT: D  347 LYS cc_start: 0.8350 (mtpt) cc_final: 0.7638 (mtmp)
REVERT: E  274 LYS cc_start: 0.6944 (mtmt) cc_final: 0.6657 (ttmm)
REVERT: E  277 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8231 (mp)
REVERT: E  347 LYS cc_start: 0.8383 (mtpt) cc_final: 0.7758 (mtmp)
REVERT: G  274 LYS cc_start: 0.7086 (mtmt) cc_final: 0.6872 (mtpm)
REVERT: G  277 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7855 (mp)
REVERT: G  283 ASP cc_start: 0.7393 (t0) cc_final: 0.7181 (t0)
REVERT: G  347 LYS cc_start: 0.8349 (mtpt) cc_final: 0.7620 (mtmp)
REVERT: H  293 SER cc_start: 0.8047 (p) cc_final: 0.7706 (m)
REVERT: H  347 LYS cc_start: 0.8418 (mtpt) cc_final: 0.7747 (mtmp)
REVERT: I  274 LYS cc_start: 0.6997 (mtmt) cc_final: 0.6612 (ttmm)
REVERT: I  345 ASP cc_start: 0.7497 (t70) cc_final: 0.7264 (t70)
REVERT: I  347 LYS cc_start: 0.8338 (mtpt) cc_final: 0.7646 (mtmp)
REVERT: J  293 SER cc_start: 0.8159 (p) cc_final: 0.7835 (m)
  outliers start: 29
  outliers final: 12
  residues processed: 233
  average time/residue: 1.3335
  time to fit residues: 327.6749
Evaluate side-chains
  223 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 206
  time to evaluate  : 1.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain B residue  288 GLN
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  351 GLN
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  342 GLU
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain E residue  277 ILE
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain G residue  277 ILE
Chi-restraints excluded: chain G residue  342 GLU
Chi-restraints excluded: chain H residue  284 LEU
Chi-restraints excluded: chain H residue  342 GLU
Chi-restraints excluded: chain J residue  284 LEU
Chi-restraints excluded: chain J residue  288 GLN
Chi-restraints excluded: chain J residue  342 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 71 optimal weight:    6.9990
   chunk 39 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    5.9990
   chunk 86 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 32 optimal weight:    8.9990
   chunk 87 optimal weight:    9.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 296 ASN
C 288 GLN
D 329 HIS
E 276 GLN
E 296 ASN
F 296 ASN
G 288 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.1787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8230  Z= 0.224
  Angle     :  0.567   5.840  10990  Z= 0.293
  Chirality :  0.050   0.131   1230
  Planarity :  0.003   0.028   1410
  Dihedral  :  5.844  14.088   1100
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.88 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.76 (0.18), residues: 1060
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.09 (0.13), residues: 1060

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS I 299 
 PHE   0.007   0.001   PHE I 378 
 TYR   0.011   0.002   TYR J 310 
 ARG   0.007   0.000   ARG E 379 

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 214
  time to evaluate  : 1.006 
Fit side-chains
REVERT: A  274 LYS cc_start: 0.7069 (mtmt) cc_final: 0.6828 (ttmm)
REVERT: A  277 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7646 (mt)
REVERT: A  347 LYS cc_start: 0.8275 (mtpt) cc_final: 0.7508 (mtmp)
REVERT: B  274 LYS cc_start: 0.7123 (mtmt) cc_final: 0.6776 (ttmm)
REVERT: B  288 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8114 (tt0)
REVERT: B  347 LYS cc_start: 0.8246 (mtpt) cc_final: 0.7576 (mtmp)
REVERT: B  351 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7822 (tt0)
REVERT: C  274 LYS cc_start: 0.7534 (mtmt) cc_final: 0.7211 (ttmm)
REVERT: C  347 LYS cc_start: 0.8230 (mtpt) cc_final: 0.7586 (mtmp)
REVERT: D  274 LYS cc_start: 0.6998 (mtmt) cc_final: 0.6672 (ttmm)
REVERT: D  345 ASP cc_start: 0.7404 (t70) cc_final: 0.7150 (t70)
REVERT: D  347 LYS cc_start: 0.8296 (mtpt) cc_final: 0.7577 (mtmp)
REVERT: E  274 LYS cc_start: 0.6862 (mtmt) cc_final: 0.6647 (ttmm)
REVERT: E  277 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8163 (mp)
REVERT: E  347 LYS cc_start: 0.8368 (mtpt) cc_final: 0.7630 (mtmm)
REVERT: F  347 LYS cc_start: 0.8294 (mtpt) cc_final: 0.7552 (mtmp)
REVERT: G  274 LYS cc_start: 0.7093 (mtmt) cc_final: 0.6826 (ttmm)
REVERT: G  277 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7822 (mp)
REVERT: G  283 ASP cc_start: 0.7401 (t0) cc_final: 0.7172 (t0)
REVERT: G  347 LYS cc_start: 0.8300 (mtpt) cc_final: 0.7562 (mtmp)
REVERT: H  345 ASP cc_start: 0.7233 (t70) cc_final: 0.7006 (t70)
REVERT: H  347 LYS cc_start: 0.8366 (mtpt) cc_final: 0.7734 (mtmp)
REVERT: I  274 LYS cc_start: 0.7040 (mtmt) cc_final: 0.6739 (ttmm)
REVERT: I  345 ASP cc_start: 0.7501 (t70) cc_final: 0.7201 (t70)
REVERT: I  347 LYS cc_start: 0.8347 (mtpt) cc_final: 0.7609 (mtmp)
REVERT: J  347 LYS cc_start: 0.8377 (mtpt) cc_final: 0.7638 (mtmp)
  outliers start: 23
  outliers final: 12
  residues processed: 222
  average time/residue: 1.4761
  time to fit residues: 344.7774
Evaluate side-chains
  229 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 212
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 ILE
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain B residue  288 GLN
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  351 GLN
Chi-restraints excluded: chain C residue  342 GLU
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain E residue  277 ILE
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain F residue  342 GLU
Chi-restraints excluded: chain G residue  277 ILE
Chi-restraints excluded: chain G residue  342 GLU
Chi-restraints excluded: chain H residue  342 GLU
Chi-restraints excluded: chain I residue  342 GLU
Chi-restraints excluded: chain J residue  284 LEU
Chi-restraints excluded: chain J residue  288 GLN
Chi-restraints excluded: chain J residue  342 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:   10.0000
   chunk 56 optimal weight:    2.9990
   chunk 23 optimal weight:    8.9990
   chunk 96 optimal weight:    2.9990
   chunk 80 optimal weight:    8.9990
   chunk 44 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 32 optimal weight:   20.0000
   chunk 50 optimal weight:    9.9990
   chunk 93 optimal weight:    7.9990
   chunk 10 optimal weight:    9.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 296 ASN
E 276 GLN
E 296 ASN
F 296 ASN
H 288 GLN
I 296 ASN
I 351 GLN
J 288 GLN
J 296 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.1925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.046   8230  Z= 0.449
  Angle     :  0.680   6.606  10990  Z= 0.356
  Chirality :  0.052   0.132   1230
  Planarity :  0.003   0.025   1410
  Dihedral  :  6.181  17.088   1100
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 16.45 %
    Favored  : 80.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.69 (0.18), residues: 1060
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.04 (0.14), residues: 1060

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS J 299 
 PHE   0.009   0.001   PHE B 378 
 TYR   0.010   0.003   TYR D 310 
 ARG   0.006   0.001   ARG E 379 

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 218
  time to evaluate  : 1.088 
Fit side-chains
REVERT: A  274 LYS cc_start: 0.7129 (mtmt) cc_final: 0.6858 (ttmm)
REVERT: A  277 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7719 (mt)
REVERT: A  347 LYS cc_start: 0.8339 (mtpt) cc_final: 0.7352 (mtmm)
REVERT: B  274 LYS cc_start: 0.7150 (mtmt) cc_final: 0.6753 (ttmm)
REVERT: B  281 LYS cc_start: 0.7463 (mttt) cc_final: 0.7163 (mttm)
REVERT: B  293 SER cc_start: 0.8381 (p) cc_final: 0.8030 (m)
REVERT: B  347 LYS cc_start: 0.8290 (mtpt) cc_final: 0.7601 (mtmp)
REVERT: B  351 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7818 (tt0)
REVERT: C  274 LYS cc_start: 0.7602 (mtmt) cc_final: 0.7209 (ttmm)
REVERT: C  347 LYS cc_start: 0.8256 (mtpt) cc_final: 0.7463 (mttm)
REVERT: D  274 LYS cc_start: 0.7049 (mtmt) cc_final: 0.6666 (ttmm)
REVERT: D  284 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8403 (mt)
REVERT: D  345 ASP cc_start: 0.7451 (t70) cc_final: 0.7144 (t70)
REVERT: D  347 LYS cc_start: 0.8296 (mtpt) cc_final: 0.7555 (mtmp)
REVERT: E  274 LYS cc_start: 0.6923 (mtmt) cc_final: 0.6662 (ttmm)
REVERT: E  277 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8185 (mp)
REVERT: E  347 LYS cc_start: 0.8381 (mtpt) cc_final: 0.7741 (mtmp)
REVERT: F  347 LYS cc_start: 0.8306 (mtpt) cc_final: 0.7532 (mtmp)
REVERT: G  274 LYS cc_start: 0.7147 (mtmt) cc_final: 0.6469 (mttp)
REVERT: G  277 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7870 (mp)
REVERT: G  283 ASP cc_start: 0.7448 (t0) cc_final: 0.7222 (t0)
REVERT: G  347 LYS cc_start: 0.8373 (mtpt) cc_final: 0.7565 (mtmp)
REVERT: H  293 SER cc_start: 0.8044 (p) cc_final: 0.7674 (m)
REVERT: H  345 ASP cc_start: 0.7235 (t70) cc_final: 0.6889 (t70)
REVERT: H  347 LYS cc_start: 0.8402 (mtpt) cc_final: 0.7701 (mttp)
REVERT: I  274 LYS cc_start: 0.7035 (mtmt) cc_final: 0.6668 (ttmm)
REVERT: I  345 ASP cc_start: 0.7508 (t70) cc_final: 0.7233 (t70)
REVERT: I  347 LYS cc_start: 0.8349 (mtpt) cc_final: 0.7603 (mtmp)
  outliers start: 25
  outliers final: 11
  residues processed: 226
  average time/residue: 1.3679
  time to fit residues: 325.4562
Evaluate side-chains
  227 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 211
  time to evaluate  : 1.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 ILE
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  351 GLN
Chi-restraints excluded: chain C residue  342 GLU
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain E residue  277 ILE
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain G residue  277 ILE
Chi-restraints excluded: chain G residue  342 GLU
Chi-restraints excluded: chain H residue  284 LEU
Chi-restraints excluded: chain H residue  342 GLU
Chi-restraints excluded: chain I residue  342 GLU
Chi-restraints excluded: chain J residue  284 LEU
Chi-restraints excluded: chain J residue  342 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 55 optimal weight:   10.0000
   chunk 70 optimal weight:    3.9990
   chunk 54 optimal weight:    6.9990
   chunk 81 optimal weight:   10.0000
   chunk 96 optimal weight:    8.9990
   chunk 60 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 44 optimal weight:    7.9990
   chunk 59 optimal weight:    1.9990
   chunk 38 optimal weight:   10.0000
   chunk 57 optimal weight:    9.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 296 ASN
D 288 GLN
E 296 ASN
F 296 ASN
H 288 GLN
J 288 GLN
J 296 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.1871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   8230  Z= 0.316
  Angle     :  0.615   7.228  10990  Z= 0.319
  Chirality :  0.051   0.133   1230
  Planarity :  0.003   0.028   1410
  Dihedral  :  6.033  15.874   1100
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 16.99 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.67 (0.18), residues: 1060
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.03 (0.14), residues: 1060

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS I 299 
 PHE   0.008   0.001   PHE B 378 
 TYR   0.011   0.003   TYR J 310 
 ARG   0.007   0.001   ARG E 379 

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 215
  time to evaluate  : 0.917 
Fit side-chains
REVERT: A  274 LYS cc_start: 0.7091 (mtmt) cc_final: 0.6827 (ttmm)
REVERT: A  277 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7701 (mt)
REVERT: A  347 LYS cc_start: 0.8331 (mtpt) cc_final: 0.7415 (mptp)
REVERT: B  274 LYS cc_start: 0.7122 (mtmt) cc_final: 0.6780 (ttmm)
REVERT: B  281 LYS cc_start: 0.7445 (mttt) cc_final: 0.7170 (mttm)
REVERT: B  293 SER cc_start: 0.8337 (p) cc_final: 0.8008 (m)
REVERT: B  347 LYS cc_start: 0.8254 (mtpt) cc_final: 0.7499 (mttm)
REVERT: B  351 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7803 (tt0)
REVERT: C  274 LYS cc_start: 0.7574 (mtmt) cc_final: 0.7214 (ttmm)
REVERT: C  347 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7605 (mtmp)
REVERT: D  274 LYS cc_start: 0.7037 (mtmt) cc_final: 0.6689 (ttmm)
REVERT: D  345 ASP cc_start: 0.7407 (t70) cc_final: 0.7150 (t70)
REVERT: D  347 LYS cc_start: 0.8292 (mtpt) cc_final: 0.7602 (mtmp)
REVERT: E  274 LYS cc_start: 0.6867 (mtmt) cc_final: 0.6640 (ttmm)
REVERT: E  277 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8178 (mp)
REVERT: E  347 LYS cc_start: 0.8387 (mtpt) cc_final: 0.7656 (mtmm)
REVERT: G  274 LYS cc_start: 0.7141 (mtmt) cc_final: 0.6816 (ttmm)
REVERT: G  277 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7877 (mp)
REVERT: G  281 LYS cc_start: 0.7453 (mttt) cc_final: 0.7190 (mttm)
REVERT: G  283 ASP cc_start: 0.7482 (t0) cc_final: 0.7273 (t0)
REVERT: G  347 LYS cc_start: 0.8341 (mtpt) cc_final: 0.7566 (mtmp)
REVERT: H  293 SER cc_start: 0.7992 (p) cc_final: 0.7679 (m)
REVERT: H  345 ASP cc_start: 0.7160 (t70) cc_final: 0.6948 (t70)
REVERT: H  347 LYS cc_start: 0.8401 (mtpt) cc_final: 0.7749 (mtmp)
REVERT: I  274 LYS cc_start: 0.7040 (mtmt) cc_final: 0.6698 (ttmm)
REVERT: I  345 ASP cc_start: 0.7515 (t70) cc_final: 0.7249 (t70)
REVERT: I  347 LYS cc_start: 0.8341 (mtpt) cc_final: 0.7645 (mtmp)
  outliers start: 22
  outliers final: 11
  residues processed: 224
  average time/residue: 1.4082
  time to fit residues: 332.0338
Evaluate side-chains
  226 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 211
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 ILE
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  351 GLN
Chi-restraints excluded: chain C residue  342 GLU
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain E residue  277 ILE
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain F residue  342 GLU
Chi-restraints excluded: chain G residue  277 ILE
Chi-restraints excluded: chain G residue  342 GLU
Chi-restraints excluded: chain H residue  342 GLU
Chi-restraints excluded: chain I residue  342 GLU
Chi-restraints excluded: chain J residue  284 LEU
Chi-restraints excluded: chain J residue  342 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:   10.0000
   chunk 18 optimal weight:    9.9990
   chunk 61 optimal weight:   20.0000
   chunk 65 optimal weight:    9.9990
   chunk 47 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 87 optimal weight:    8.9990
   chunk 92 optimal weight:    4.9990
   chunk 84 optimal weight:    1.9990
   chunk 89 optimal weight:    9.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 296 ASN
E 296 ASN
F 296 ASN
G 288 GLN
H 288 GLN
J 288 GLN
J 296 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   8230  Z= 0.316
  Angle     :  0.617   7.292  10990  Z= 0.320
  Chirality :  0.051   0.134   1230
  Planarity :  0.003   0.041   1410
  Dihedral  :  6.036  15.935   1100
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 17.20 %
    Favored  : 80.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.66 (0.18), residues: 1060
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.02 (0.14), residues: 1060

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS G 299 
 PHE   0.008   0.001   PHE B 378 
 TYR   0.011   0.003   TYR J 310 
 ARG   0.008   0.001   ARG E 379 

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 215
  time to evaluate  : 1.616 
Fit side-chains
REVERT: A  274 LYS cc_start: 0.7067 (mtmt) cc_final: 0.6806 (ttmm)
REVERT: A  277 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7699 (mt)
REVERT: A  347 LYS cc_start: 0.8328 (mtpt) cc_final: 0.7385 (mtmm)
REVERT: B  274 LYS cc_start: 0.7126 (mtmt) cc_final: 0.6773 (ttmm)
REVERT: B  281 LYS cc_start: 0.7414 (mttt) cc_final: 0.7145 (mttm)
REVERT: B  293 SER cc_start: 0.8323 (p) cc_final: 0.7992 (m)
REVERT: B  347 LYS cc_start: 0.8246 (mtpt) cc_final: 0.7553 (mtmp)
REVERT: B  351 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7797 (tt0)
REVERT: C  274 LYS cc_start: 0.7580 (mtmt) cc_final: 0.7217 (ttmm)
REVERT: C  347 LYS cc_start: 0.8246 (mtpt) cc_final: 0.7595 (mtmp)
REVERT: D  274 LYS cc_start: 0.7041 (mtmt) cc_final: 0.6692 (ttmm)
REVERT: D  345 ASP cc_start: 0.7409 (t70) cc_final: 0.7126 (t70)
REVERT: D  347 LYS cc_start: 0.8291 (mtpt) cc_final: 0.7551 (mtmp)
REVERT: E  274 LYS cc_start: 0.6869 (mtmt) cc_final: 0.6641 (ttmm)
REVERT: E  277 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8175 (mp)
REVERT: E  347 LYS cc_start: 0.8378 (mtpt) cc_final: 0.7639 (mtmm)
REVERT: G  274 LYS cc_start: 0.7128 (mtmt) cc_final: 0.6813 (ttmm)
REVERT: G  277 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7887 (mp)
REVERT: G  283 ASP cc_start: 0.7491 (t0) cc_final: 0.7279 (t0)
REVERT: G  347 LYS cc_start: 0.8348 (mtpt) cc_final: 0.7563 (mtmp)
REVERT: H  293 SER cc_start: 0.7982 (p) cc_final: 0.7672 (m)
REVERT: H  345 ASP cc_start: 0.7157 (t70) cc_final: 0.6937 (t70)
REVERT: H  347 LYS cc_start: 0.8395 (mtpt) cc_final: 0.7748 (mtmp)
REVERT: I  274 LYS cc_start: 0.7040 (mtmt) cc_final: 0.6694 (ttmm)
REVERT: I  345 ASP cc_start: 0.7508 (t70) cc_final: 0.7240 (t70)
REVERT: I  347 LYS cc_start: 0.8358 (mtpt) cc_final: 0.7654 (mtmp)
  outliers start: 19
  outliers final: 12
  residues processed: 221
  average time/residue: 1.3971
  time to fit residues: 325.6391
Evaluate side-chains
  227 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 211
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 ILE
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  351 GLN
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  342 GLU
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain E residue  277 ILE
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain F residue  342 GLU
Chi-restraints excluded: chain G residue  277 ILE
Chi-restraints excluded: chain G residue  342 GLU
Chi-restraints excluded: chain H residue  342 GLU
Chi-restraints excluded: chain I residue  342 GLU
Chi-restraints excluded: chain J residue  284 LEU
Chi-restraints excluded: chain J residue  342 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 92 optimal weight:    0.5980
   chunk 54 optimal weight:    6.9990
   chunk 39 optimal weight:    9.9990
   chunk 70 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 81 optimal weight:   20.0000
   chunk 84 optimal weight:    2.9990
   chunk 89 optimal weight:    9.9990
   chunk 58 optimal weight:    7.9990
   chunk 94 optimal weight:    2.9990
   chunk 57 optimal weight:    9.9990
   overall best weight:    2.3188

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

Flipped N/Q/H residues before XYZ refinement:
A 296 ASN
B 288 GLN
C 288 GLN
D 288 GLN
E 296 ASN
F 296 ASN
G 288 GLN
I 296 ASN
J 296 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8230  Z= 0.203
  Angle     :  0.560   7.395  10990  Z= 0.287
  Chirality :  0.050   0.132   1230
  Planarity :  0.003   0.037   1410
  Dihedral  :  5.748  15.398   1100
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 17.63 %
    Favored  : 80.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.68 (0.18), residues: 1060
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.04 (0.14), residues: 1060

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS I 299 
 PHE   0.006   0.001   PHE B 378 
 TYR   0.012   0.002   TYR E 310 
 ARG   0.009   0.001   ARG E 379 

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 213
  time to evaluate  : 0.907 
Fit side-chains
REVERT: A  274 LYS cc_start: 0.7095 (mtmt) cc_final: 0.6847 (ttmm)
REVERT: A  277 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7638 (mt)
REVERT: A  347 LYS cc_start: 0.8285 (mtpt) cc_final: 0.7389 (mptp)
REVERT: B  274 LYS cc_start: 0.7026 (mtmt) cc_final: 0.6720 (ttmm)
REVERT: B  347 LYS cc_start: 0.8251 (mtpt) cc_final: 0.7486 (mttm)
REVERT: B  351 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7816 (tt0)
REVERT: C  274 LYS cc_start: 0.7531 (mtmt) cc_final: 0.7215 (ttmm)
REVERT: C  347 LYS cc_start: 0.8209 (mtpt) cc_final: 0.7464 (mttm)
REVERT: D  274 LYS cc_start: 0.6981 (mtmt) cc_final: 0.6699 (ttmm)
REVERT: D  345 ASP cc_start: 0.7404 (t70) cc_final: 0.7113 (t70)
REVERT: D  347 LYS cc_start: 0.8291 (mtpt) cc_final: 0.7607 (mtmp)
REVERT: E  277 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8170 (mp)
REVERT: E  347 LYS cc_start: 0.8359 (mtpt) cc_final: 0.7598 (mppt)
REVERT: G  274 LYS cc_start: 0.7099 (mtmt) cc_final: 0.6829 (ttmm)
REVERT: G  277 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7872 (mp)
REVERT: G  281 LYS cc_start: 0.7431 (mttt) cc_final: 0.7170 (mttm)
REVERT: G  283 ASP cc_start: 0.7515 (t0) cc_final: 0.7306 (t0)
REVERT: G  347 LYS cc_start: 0.8310 (mtpt) cc_final: 0.7542 (mtmp)
REVERT: H  345 ASP cc_start: 0.7142 (t70) cc_final: 0.6479 (t70)
REVERT: H  347 LYS cc_start: 0.8366 (mtpt) cc_final: 0.7688 (mtmt)
REVERT: I  274 LYS cc_start: 0.7045 (mtmt) cc_final: 0.6762 (ttmm)
REVERT: I  345 ASP cc_start: 0.7506 (t70) cc_final: 0.7243 (t70)
REVERT: I  347 LYS cc_start: 0.8361 (mtpt) cc_final: 0.7648 (mtmp)
  outliers start: 14
  outliers final: 9
  residues processed: 216
  average time/residue: 1.3850
  time to fit residues: 314.6260
Evaluate side-chains
  223 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 210
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 ILE
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  351 GLN
Chi-restraints excluded: chain C residue  342 GLU
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain E residue  277 ILE
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain F residue  342 GLU
Chi-restraints excluded: chain G residue  277 ILE
Chi-restraints excluded: chain G residue  342 GLU
Chi-restraints excluded: chain H residue  342 GLU
Chi-restraints excluded: chain J residue  342 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 66 optimal weight:    9.9990
   chunk 99 optimal weight:   10.0000
   chunk 91 optimal weight:    9.9990
   chunk 79 optimal weight:    0.9990
   chunk 8 optimal weight:    9.9990
   chunk 61 optimal weight:   20.0000
   chunk 48 optimal weight:   10.0000
   chunk 63 optimal weight:   10.0000
   chunk 84 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   overall best weight:    6.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 296 ASN
E 296 ASN
F 296 ASN
H 288 GLN
I 296 ASN
J 288 GLN
J 296 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.1985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.045   8230  Z= 0.448
  Angle     :  0.685   7.756  10990  Z= 0.357
  Chirality :  0.053   0.137   1230
  Planarity :  0.003   0.042   1410
  Dihedral  :  6.163  16.842   1100
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 17.53 %
    Favored  : 80.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.63 (0.18), residues: 1060
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.99 (0.14), residues: 1060

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E 299 
 PHE   0.008   0.001   PHE B 378 
 TYR   0.010   0.003   TYR I 310 
 ARG   0.008   0.001   ARG E 379 

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 206
  time to evaluate  : 0.997 
Fit side-chains
REVERT: A  274 LYS cc_start: 0.7084 (mtmt) cc_final: 0.6848 (ttmm)
REVERT: A  277 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7725 (mt)
REVERT: A  347 LYS cc_start: 0.8288 (mtpt) cc_final: 0.7345 (mtmm)
REVERT: B  274 LYS cc_start: 0.7124 (mtmt) cc_final: 0.6737 (ttmm)
REVERT: B  281 LYS cc_start: 0.7455 (mttt) cc_final: 0.7185 (mttm)
REVERT: B  293 SER cc_start: 0.8360 (p) cc_final: 0.8024 (m)
REVERT: B  347 LYS cc_start: 0.8271 (mtpt) cc_final: 0.7565 (mtmp)
REVERT: B  351 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7803 (tt0)
REVERT: C  274 LYS cc_start: 0.7595 (mtmt) cc_final: 0.7204 (ttmm)
REVERT: C  347 LYS cc_start: 0.8276 (mtpt) cc_final: 0.7471 (mttm)
REVERT: D  274 LYS cc_start: 0.7045 (mtmt) cc_final: 0.6658 (ttmm)
REVERT: D  345 ASP cc_start: 0.7452 (t70) cc_final: 0.7139 (t70)
REVERT: D  347 LYS cc_start: 0.8297 (mtpt) cc_final: 0.7557 (mtmp)
REVERT: E  277 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8226 (mp)
REVERT: E  347 LYS cc_start: 0.8385 (mtpt) cc_final: 0.7665 (mtmm)
REVERT: G  274 LYS cc_start: 0.7114 (mtmt) cc_final: 0.6424 (mttp)
REVERT: G  277 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7915 (mp)
REVERT: G  283 ASP cc_start: 0.7511 (t0) cc_final: 0.7293 (t0)
REVERT: G  347 LYS cc_start: 0.8354 (mtpt) cc_final: 0.7572 (mtmp)
REVERT: H  293 SER cc_start: 0.8032 (p) cc_final: 0.7703 (m)
REVERT: H  347 LYS cc_start: 0.8393 (mtpt) cc_final: 0.7739 (mtmp)
REVERT: I  274 LYS cc_start: 0.7047 (mtmt) cc_final: 0.6678 (ttmm)
REVERT: I  345 ASP cc_start: 0.7517 (t70) cc_final: 0.7258 (t70)
REVERT: I  347 LYS cc_start: 0.8349 (mtpt) cc_final: 0.7649 (mtmp)
  outliers start: 16
  outliers final: 10
  residues processed: 210
  average time/residue: 1.4389
  time to fit residues: 317.2794
Evaluate side-chains
  219 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 205
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 ILE
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  351 GLN
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  342 GLU
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain E residue  277 ILE
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain G residue  277 ILE
Chi-restraints excluded: chain G residue  342 GLU
Chi-restraints excluded: chain H residue  342 GLU
Chi-restraints excluded: chain I residue  342 GLU
Chi-restraints excluded: chain J residue  342 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    6.9990
   chunk 11 optimal weight:    9.9990
   chunk 22 optimal weight:    0.5980
   chunk 79 optimal weight:    1.9990
   chunk 33 optimal weight:    9.9990
   chunk 81 optimal weight:   10.0000
   chunk 10 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 4 optimal weight:    7.9990
   chunk 57 optimal weight:    7.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 296 ASN
B 288 GLN
D 288 GLN
E 296 ASN
F 296 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.135607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.116852 restraints weight = 8817.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3756 rms_B_bonded: 1.46
r_work: 0.3641 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3533 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8575
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8230  Z= 0.194
  Angle     :  0.562   7.574  10990  Z= 0.287
  Chirality :  0.050   0.134   1230
  Planarity :  0.003   0.037   1410
  Dihedral  :  5.739  15.343   1100
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 17.85 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.65 (0.18), residues: 1060
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.01 (0.14), residues: 1060

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS I 299 
 PHE   0.006   0.001   PHE B 378 
 TYR   0.012   0.002   TYR E 310 
 ARG   0.009   0.001   ARG E 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4803.52 seconds
wall clock time: 86 minutes 59.16 seconds (5219.16 seconds total)