Starting phenix.real_space_refine
on Tue Jan 14 05:50:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ero_19928/01_2025/9ero_19928.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ero_19928/01_2025/9ero_19928.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ero_19928/01_2025/9ero_19928.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ero_19928/01_2025/9ero_19928.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ero_19928/01_2025/9ero_19928.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ero_19928/01_2025/9ero_19928.cif"
  }
  resolution = 2.9
  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=   0.001
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      10      5.16       5
     C    3625      2.51       5
     N    1070      2.21       5
     O    1070      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 5775
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 581
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
      Conformer: "B"
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
          bond proxies already assigned to first conformer: 574
    Chain: "B"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
  Restraints were copied for chains:
    C, E, G, I, D, F, H, J
  Time building chain proxies: 3.63, per 1000 atoms: 0.63
  Number of scatterers: 5775
  At special positions: 0
  Unit cell: (121.952, 131.84, 45.32, 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      10     16.00
     O    1070      8.00
     N    1070      7.00
     C    3625      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: 1.21
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1330

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 18 sheets defined
      0.0% alpha, 47.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'G' and resid 306 through 310
      removed outlier: 6.299A  pdb=" N   GLN E 307 " --> pdb=" O   ILE G 308 " (cutoff:3.500A)
      removed outlier: 7.979A  pdb=" N   TYR G 310 " --> pdb=" O   GLN E 307 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   VAL E 309 " --> pdb=" O   TYR G 310 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   GLN A 307 " --> pdb=" O   ILE E 308 " (cutoff:3.500A)
      removed outlier: 7.979A  pdb=" N   TYR E 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   VAL A 309 " --> pdb=" O   TYR E 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'G' and resid 313 through 314
      removed outlier: 6.725A  pdb=" N   VAL E 313 " --> pdb=" O   ASP G 314 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   VAL A 313 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'G' and resid 317 through 318
      removed outlier: 6.345A  pdb=" N   LYS E 317 " --> pdb=" O   VAL G 318 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   LYS A 317 " --> pdb=" O   VAL E 318 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'G' and resid 321 through 330
      removed outlier: 6.453A  pdb=" N   LYS E 321 " --> pdb=" O   CYS G 322 " (cutoff:3.500A)
      removed outlier: 7.171A  pdb=" N   SER G 324 " --> pdb=" O   LYS E 321 " (cutoff:3.500A)
      removed outlier: 7.291A  pdb=" N   GLY E 323 " --> pdb=" O   SER G 324 " (cutoff:3.500A)
      removed outlier: 10.047A  pdb=" N   GLY G 326 " --> pdb=" O   GLY E 323 " (cutoff:3.500A)
      removed outlier: 8.862A  pdb=" N   LEU E 325 " --> pdb=" O   GLY G 326 " (cutoff:3.500A)
      removed outlier: 9.392A  pdb=" N   ILE G 328 " --> pdb=" O   LEU E 325 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   ASN E 327 " --> pdb=" O   ILE G 328 " (cutoff:3.500A)
      removed outlier: 7.808A  pdb=" N   HIS G 330 " --> pdb=" O   ASN E 327 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   HIS E 329 " --> pdb=" O   HIS G 330 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   LYS A 321 " --> pdb=" O   CYS E 322 " (cutoff:3.500A)
      removed outlier: 7.171A  pdb=" N   SER E 324 " --> pdb=" O   LYS A 321 " (cutoff:3.500A)
      removed outlier: 7.291A  pdb=" N   GLY A 323 " --> pdb=" O   SER E 324 " (cutoff:3.500A)
      removed outlier: 10.047A  pdb=" N   GLY E 326 " --> pdb=" O   GLY A 323 " (cutoff:3.500A)
      removed outlier: 8.863A  pdb=" N   LEU A 325 " --> pdb=" O   GLY E 326 " (cutoff:3.500A)
      removed outlier: 9.392A  pdb=" N   ILE E 328 " --> pdb=" O   LEU A 325 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   ASN A 327 " --> pdb=" O   ILE E 328 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   HIS E 330 " --> pdb=" O   ASN A 327 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   HIS A 329 " --> pdb=" O   HIS E 330 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   SER A 324 " --> pdb=" O   GLY C 323 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   LEU C 325 " --> pdb=" O   SER A 324 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   GLY A 326 " --> pdb=" O   LEU C 325 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   ASN C 327 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   SER C 324 " --> pdb=" O   GLY I 323 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   LEU I 325 " --> pdb=" O   SER C 324 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   GLY C 326 " --> pdb=" O   LEU I 325 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   ASN I 327 " --> pdb=" O   GLY C 326 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'G' and resid 337 through 346
      removed outlier: 6.826A  pdb=" N   LEU E 344 " --> pdb=" O   LYS G 343 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   ASP G 345 " --> pdb=" O   LEU E 344 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   PHE E 346 " --> pdb=" O   ASP G 345 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   LEU A 344 " --> pdb=" O   LYS E 343 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   ASP E 345 " --> pdb=" O   LEU A 344 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   PHE A 346 " --> pdb=" O   ASP E 345 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   VAL A 337 " --> pdb=" O   GLU C 338 " (cutoff:3.500A)
      removed outlier: 8.112A  pdb=" N   LYS C 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   VAL A 339 " --> pdb=" O   LYS C 340 " (cutoff:3.500A)
      removed outlier: 8.097A  pdb=" N   GLU C 342 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   SER A 341 " --> pdb=" O   GLU C 342 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   LEU C 344 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
      removed outlier: 7.409A  pdb=" N   LYS A 343 " --> pdb=" O   LEU C 344 " (cutoff:3.500A)
      removed outlier: 9.995A  pdb=" N   PHE C 346 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 9.317A  pdb=" N   ASP A 345 " --> pdb=" O   PHE C 346 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   VAL C 337 " --> pdb=" O   GLU I 338 " (cutoff:3.500A)
      removed outlier: 8.112A  pdb=" N   LYS I 340 " --> pdb=" O   VAL C 337 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   VAL C 339 " --> pdb=" O   LYS I 340 " (cutoff:3.500A)
      removed outlier: 8.097A  pdb=" N   GLU I 342 " --> pdb=" O   VAL C 339 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   SER C 341 " --> pdb=" O   GLU I 342 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   LEU I 344 " --> pdb=" O   SER C 341 " (cutoff:3.500A)
      removed outlier: 7.409A  pdb=" N   LYS C 343 " --> pdb=" O   LEU I 344 " (cutoff:3.500A)
      removed outlier: 9.995A  pdb=" N   PHE I 346 " --> pdb=" O   LYS C 343 " (cutoff:3.500A)
      removed outlier: 9.318A  pdb=" N   ASP C 345 " --> pdb=" O   PHE I 346 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'G' and resid 350 through 351
      removed outlier: 6.299A  pdb=" N   VAL A 350 " --> pdb=" O   GLN C 351 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   VAL C 350 " --> pdb=" O   GLN I 351 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'G' and resid 354 through 357
      removed outlier: 6.020A  pdb=" N   ILE A 354 " --> pdb=" O   GLY C 355 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   LEU C 357 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   SER A 356 " --> pdb=" O   LEU C 357 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   ILE C 354 " --> pdb=" O   GLY I 355 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   LEU I 357 " --> pdb=" O   ILE C 354 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   SER C 356 " --> pdb=" O   LEU I 357 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'G' and resid 360 through 362
      removed outlier: 6.421A  pdb=" N   THR A 361 " --> pdb=" O   HIS C 362 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   THR C 361 " --> pdb=" O   HIS I 362 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'G' and resid 371 through 378
      removed outlier: 6.568A  pdb=" N   GLU A 372 " --> pdb=" O   THR C 373 " (cutoff:3.500A)
      removed outlier: 8.305A  pdb=" N   LYS C 375 " --> pdb=" O   GLU A 372 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   HIS A 374 " --> pdb=" O   LYS C 375 " (cutoff:3.500A)
      removed outlier: 8.347A  pdb=" N   THR C 377 " --> pdb=" O   HIS A 374 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   LEU A 376 " --> pdb=" O   THR C 377 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   GLU C 372 " --> pdb=" O   THR I 373 " (cutoff:3.500A)
      removed outlier: 8.305A  pdb=" N   LYS I 375 " --> pdb=" O   GLU C 372 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   HIS C 374 " --> pdb=" O   LYS I 375 " (cutoff:3.500A)
      removed outlier: 8.347A  pdb=" N   THR I 377 " --> pdb=" O   HIS C 374 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   LEU C 376 " --> pdb=" O   THR I 377 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 306 through 310
      removed outlier: 6.392A  pdb=" N   GLN B 307 " --> pdb=" O   ILE D 308 " (cutoff:3.500A)
      removed outlier: 8.153A  pdb=" N   TYR D 310 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   VAL B 309 " --> pdb=" O   TYR D 310 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   GLN D 307 " --> pdb=" O   ILE J 308 " (cutoff:3.500A)
      removed outlier: 8.153A  pdb=" N   TYR J 310 " --> pdb=" O   GLN D 307 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   VAL D 309 " --> pdb=" O   TYR J 310 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 313 through 314
      removed outlier: 6.784A  pdb=" N   VAL B 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   VAL D 313 " --> pdb=" O   ASP J 314 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 317 through 325
      removed outlier: 6.858A  pdb=" N   VAL H 318 " --> pdb=" O   LYS F 317 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   THR F 319 " --> pdb=" O   VAL H 318 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   SER H 320 " --> pdb=" O   THR F 319 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   LYS F 321 " --> pdb=" O   SER H 320 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   CYS H 322 " --> pdb=" O   LYS F 321 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   GLY F 323 " --> pdb=" O   CYS H 322 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   VAL F 318 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   THR B 319 " --> pdb=" O   VAL F 318 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   SER F 320 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   LYS B 321 " --> pdb=" O   SER F 320 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   CYS F 322 " --> pdb=" O   LYS B 321 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   GLY B 323 " --> pdb=" O   CYS F 322 " (cutoff:3.500A)
      removed outlier: 8.805A  pdb=" N   VAL B 318 " --> pdb=" O   THR D 319 " (cutoff:3.500A)
      removed outlier: 10.692A  pdb=" N   LYS D 321 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 9.227A  pdb=" N   SER B 320 " --> pdb=" O   LYS D 321 " (cutoff:3.500A)
      removed outlier: 10.212A  pdb=" N   GLY D 323 " --> pdb=" O   SER B 320 " (cutoff:3.500A)
      removed outlier: 5.844A  pdb=" N   CYS B 322 " --> pdb=" O   GLY D 323 " (cutoff:3.500A)
      removed outlier: 7.472A  pdb=" N   LEU D 325 " --> pdb=" O   CYS B 322 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   SER B 324 " --> pdb=" O   LEU D 325 " (cutoff:3.500A)
      removed outlier: 8.805A  pdb=" N   VAL D 318 " --> pdb=" O   THR J 319 " (cutoff:3.500A)
      removed outlier: 10.692A  pdb=" N   LYS J 321 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
      removed outlier: 9.228A  pdb=" N   SER D 320 " --> pdb=" O   LYS J 321 " (cutoff:3.500A)
      removed outlier: 10.212A  pdb=" N   GLY J 323 " --> pdb=" O   SER D 320 " (cutoff:3.500A)
      removed outlier: 5.844A  pdb=" N   CYS D 322 " --> pdb=" O   GLY J 323 " (cutoff:3.500A)
      removed outlier: 7.472A  pdb=" N   LEU J 325 " --> pdb=" O   CYS D 322 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   SER D 324 " --> pdb=" O   LEU J 325 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 337 through 342
      removed outlier: 6.516A  pdb=" N   VAL F 337 " --> pdb=" O   GLU H 338 " (cutoff:3.500A)
      removed outlier: 8.254A  pdb=" N   LYS H 340 " --> pdb=" O   VAL F 337 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   VAL F 339 " --> pdb=" O   LYS H 340 " (cutoff:3.500A)
      removed outlier: 8.131A  pdb=" N   GLU H 342 " --> pdb=" O   VAL F 339 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   SER F 341 " --> pdb=" O   GLU H 342 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   VAL B 337 " --> pdb=" O   GLU F 338 " (cutoff:3.500A)
      removed outlier: 8.253A  pdb=" N   LYS F 340 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   VAL B 339 " --> pdb=" O   LYS F 340 " (cutoff:3.500A)
      removed outlier: 8.132A  pdb=" N   GLU F 342 " --> pdb=" O   VAL B 339 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   SER B 341 " --> pdb=" O   GLU F 342 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 345 through 346
      removed outlier: 6.405A  pdb=" N   ASP B 345 " --> pdb=" O   PHE D 346 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   ASP D 345 " --> pdb=" O   PHE J 346 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 350 through 351
      removed outlier: 6.368A  pdb=" N   VAL F 350 " --> pdb=" O   GLN H 351 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   VAL B 350 " --> pdb=" O   GLN F 351 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 354 through 357
      removed outlier: 6.014A  pdb=" N   ILE F 354 " --> pdb=" O   GLY H 355 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   LEU H 357 " --> pdb=" O   ILE F 354 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   SER F 356 " --> pdb=" O   LEU H 357 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   ILE B 354 " --> pdb=" O   GLY F 355 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   LEU F 357 " --> pdb=" O   ILE B 354 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   SER B 356 " --> pdb=" O   LEU F 357 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'H' and resid 360 through 362
      removed outlier: 6.451A  pdb=" N   THR F 361 " --> pdb=" O   HIS H 362 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   THR B 361 " --> pdb=" O   HIS F 362 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'H' and resid 369 through 378
      removed outlier: 6.373A  pdb=" N   LYS F 370 " --> pdb=" O   ILE H 371 " (cutoff:3.500A)
      removed outlier: 8.194A  pdb=" N   THR H 373 " --> pdb=" O   LYS F 370 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   GLU F 372 " --> pdb=" O   THR H 373 " (cutoff:3.500A)
      removed outlier: 8.338A  pdb=" N   LYS H 375 " --> pdb=" O   GLU F 372 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   HIS F 374 " --> pdb=" O   LYS H 375 " (cutoff:3.500A)
      removed outlier: 8.368A  pdb=" N   THR H 377 " --> pdb=" O   HIS F 374 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   LEU F 376 " --> pdb=" O   THR H 377 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   LYS B 370 " --> pdb=" O   ILE F 371 " (cutoff:3.500A)
      removed outlier: 8.194A  pdb=" N   THR F 373 " --> pdb=" O   LYS B 370 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   GLU B 372 " --> pdb=" O   THR F 373 " (cutoff:3.500A)
      removed outlier: 8.339A  pdb=" N   LYS F 375 " --> pdb=" O   GLU B 372 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   HIS B 374 " --> pdb=" O   LYS F 375 " (cutoff:3.500A)
      removed outlier: 8.367A  pdb=" N   THR F 377 " --> pdb=" O   HIS B 374 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   LEU B 376 " --> pdb=" O   THR F 377 " (cutoff:3.500A)

    116 hydrogen bonds defined for protein.
    346 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: 1.36

  Time building geometry restraints manager: 1.45 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1382
        1.33 -     1.45: 1330
        1.45 -     1.57: 3153
        1.57 -     1.70: 0
        1.70 -     1.82: 10
  Bond restraints: 5875
  Sorted by residual:
  bond pdb=" CG  HIS I 330 "
       pdb=" CD2 HIS I 330 "
    ideal  model  delta    sigma   weight residual
    1.354  1.296  0.058 1.10e-02 8.26e+03 2.75e+01
  bond pdb=" CG  HIS A 330 "
       pdb=" CD2 HIS A 330 "
    ideal  model  delta    sigma   weight residual
    1.354  1.297  0.057 1.10e-02 8.26e+03 2.72e+01
  bond pdb=" CG  HIS C 330 "
       pdb=" CD2 HIS C 330 "
    ideal  model  delta    sigma   weight residual
    1.354  1.297  0.057 1.10e-02 8.26e+03 2.72e+01
  bond pdb=" CG  HIS G 330 "
       pdb=" CD2 HIS G 330 "
    ideal  model  delta    sigma   weight residual
    1.354  1.297  0.057 1.10e-02 8.26e+03 2.70e+01
  bond pdb=" CG  HIS E 330 "
       pdb=" CD2 HIS E 330 "
    ideal  model  delta    sigma   weight residual
    1.354  1.297  0.057 1.10e-02 8.26e+03 2.68e+01
  ... (remaining 5870 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 5766
        1.65 -     3.31: 1613
        3.31 -     4.96: 387
        4.96 -     6.62: 89
        6.62 -     8.27: 15
  Bond angle restraints: 7870
  Sorted by residual:
  angle pdb=" CA  HIS H 330 "
        pdb=" CB  HIS H 330 "
        pdb=" CG  HIS H 330 "
      ideal   model   delta    sigma   weight residual
     113.80  120.13   -6.33 1.00e+00 1.00e+00 4.00e+01
  angle pdb=" CA  HIS B 330 "
        pdb=" CB  HIS B 330 "
        pdb=" CG  HIS B 330 "
      ideal   model   delta    sigma   weight residual
     113.80  120.12   -6.32 1.00e+00 1.00e+00 4.00e+01
  angle pdb=" CA  HIS F 330 "
        pdb=" CB  HIS F 330 "
        pdb=" CG  HIS F 330 "
      ideal   model   delta    sigma   weight residual
     113.80  120.12   -6.32 1.00e+00 1.00e+00 3.99e+01
  angle pdb=" CA  HIS J 330 "
        pdb=" CB  HIS J 330 "
        pdb=" CG  HIS J 330 "
      ideal   model   delta    sigma   weight residual
     113.80  120.11   -6.31 1.00e+00 1.00e+00 3.99e+01
  angle pdb=" CA  HIS D 330 "
        pdb=" CB  HIS D 330 "
        pdb=" CG  HIS D 330 "
      ideal   model   delta    sigma   weight residual
     113.80  120.09   -6.29 1.00e+00 1.00e+00 3.96e+01
  ... (remaining 7865 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.60: 2835
       10.60 -    21.20: 540
       21.20 -    31.80: 155
       31.80 -    42.40: 25
       42.40 -    53.00: 35
  Dihedral angle restraints: 3590
    sinusoidal: 1500
      harmonic: 2090
  Sorted by residual:
  dihedral pdb=" CA  PRO D 332 "
           pdb=" C   PRO D 332 "
           pdb=" N   GLY D 333 "
           pdb=" CA  GLY D 333 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -140.16  -39.84     0      5.00e+00 4.00e-02 6.35e+01
  dihedral pdb=" CA  PRO J 332 "
           pdb=" C   PRO J 332 "
           pdb=" N   GLY J 333 "
           pdb=" CA  GLY J 333 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -140.17  -39.83     0      5.00e+00 4.00e-02 6.34e+01
  dihedral pdb=" CA  PRO B 332 "
           pdb=" C   PRO B 332 "
           pdb=" N   GLY B 333 "
           pdb=" CA  GLY B 333 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -140.18  -39.82     0      5.00e+00 4.00e-02 6.34e+01
  ... (remaining 3587 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.054: 342
       0.054 -    0.107: 343
       0.107 -    0.159: 139
       0.159 -    0.212: 41
       0.212 -    0.264: 20
  Chirality restraints: 885
  Sorted by residual:
  chirality pdb=" CB  ILE C 328 "
            pdb=" CA  ILE C 328 "
            pdb=" CG1 ILE C 328 "
            pdb=" CG2 ILE C 328 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" CB  ILE A 328 "
            pdb=" CA  ILE A 328 "
            pdb=" CG1 ILE A 328 "
            pdb=" CG2 ILE A 328 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" CB  ILE E 328 "
            pdb=" CA  ILE E 328 "
            pdb=" CG1 ILE E 328 "
            pdb=" CG2 ILE E 328 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.74e+00
  ... (remaining 882 not shown)

  Planarity restraints: 1000
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS C 362 "   -0.027 2.00e-02 2.50e+03   2.16e-02 7.00e+00
        pdb=" CG  HIS C 362 "    0.041 2.00e-02 2.50e+03
        pdb=" ND1 HIS C 362 "   -0.000 2.00e-02 2.50e+03
        pdb=" CD2 HIS C 362 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 HIS C 362 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE2 HIS C 362 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A 362 "   -0.026 2.00e-02 2.50e+03   2.15e-02 6.93e+00
        pdb=" CG  HIS A 362 "    0.041 2.00e-02 2.50e+03
        pdb=" ND1 HIS A 362 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 HIS A 362 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 HIS A 362 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE2 HIS A 362 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS G 362 "   -0.026 2.00e-02 2.50e+03   2.15e-02 6.93e+00
        pdb=" CG  HIS G 362 "    0.041 2.00e-02 2.50e+03
        pdb=" ND1 HIS G 362 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 HIS G 362 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 HIS G 362 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE2 HIS G 362 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 997 not shown)

  Histogram of nonbonded interaction distances:
        2.43 -     2.92: 2165
        2.92 -     3.42: 5189
        3.42 -     3.91: 9284
        3.91 -     4.41: 9861
        4.41 -     4.90: 20275
  Nonbonded interactions: 46774
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP I 314 "
            pdb=" OG  SER I 316 "
     model   vdw
     2.427 3.040
  nonbonded pdb=" OD1 ASP G 314 "
            pdb=" OG  SER G 316 "
     model   vdw
     2.427 3.040
  nonbonded pdb=" OD1 ASP C 314 "
            pdb=" OG  SER C 316 "
     model   vdw
     2.427 3.040
  nonbonded pdb=" OD1 ASP A 314 "
            pdb=" OG  SER A 316 "
     model   vdw
     2.427 3.040
  nonbonded pdb=" OD1 ASP E 314 "
            pdb=" OG  SER E 316 "
     model   vdw
     2.428 3.040
  ... (remaining 46769 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
  selection = chain 'G'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'H'
  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=0.50 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.690
  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:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     17.100
  Find NCS groups from input model:        0.110
  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:             0.000
  Load rotamer database and sin/cos tables:12.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.069   5875  Z= 0.643
  Angle     :  1.675   8.271   7870  Z= 1.070
  Chirality :  0.091   0.264    885
  Planarity :  0.011   0.046   1000
  Dihedral  : 13.222  53.002   2260
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  :  6.02 %
    Favored  : 88.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 1.39 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.12 (0.17), residues: 735
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.13 (0.13), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.015   0.007   HIS C 374 
 PHE   0.026   0.006   PHE G 346 
 TYR   0.021   0.007   TYR H 310 
 ARG   0.009   0.002   ARG J 349 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 123
  time to evaluate  : 0.649 
Fit side-chains
   revert: symmetry clash
REVERT: B  317 LYS cc_start: 0.7966 (pttt) cc_final: 0.7500 (ptpt)
REVERT: B  338 GLU cc_start: 0.8554 (tt0) cc_final: 0.8222 (tm-30)
REVERT: B  340 LYS cc_start: 0.8127 (mttt) cc_final: 0.7402 (tppp)
REVERT: D  338 GLU cc_start: 0.8491 (tt0) cc_final: 0.8059 (tm-30)
REVERT: D  340 LYS cc_start: 0.8215 (mttt) cc_final: 0.7386 (tppp)
REVERT: F  317 LYS cc_start: 0.8005 (pttt) cc_final: 0.7742 (ptmm)
REVERT: F  338 GLU cc_start: 0.8522 (tt0) cc_final: 0.8209 (tm-30)
REVERT: F  340 LYS cc_start: 0.8083 (mttt) cc_final: 0.7378 (tppp)
REVERT: G  340 LYS cc_start: 0.8769 (mttt) cc_final: 0.8470 (mmtp)
REVERT: G  378 PHE cc_start: 0.7443 (t80) cc_final: 0.7233 (t80)
REVERT: H  329 HIS cc_start: 0.7875 (OUTLIER) cc_final: 0.7649 (t-90)
REVERT: H  338 GLU cc_start: 0.8643 (tt0) cc_final: 0.8401 (tm-30)
REVERT: H  349 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.5542 (mmm160)
REVERT: I  349 ARG cc_start: 0.8401 (mtt180) cc_final: 0.7063 (mmp-170)
REVERT: J  317 LYS cc_start: 0.8516 (pttt) cc_final: 0.8248 (ptmt)
REVERT: J  338 GLU cc_start: 0.8659 (tt0) cc_final: 0.8449 (tm-30)
REVERT: J  340 LYS cc_start: 0.8468 (mttt) cc_final: 0.7789 (tppp)
REVERT: J  349 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7491 (ptp-170)
REVERT: J  375 LYS cc_start: 0.8597 (tttt) cc_final: 0.8293 (tttm)
  outliers start: 35
  outliers final: 8
  residues processed: 157
  average time/residue: 1.4440
  time to fit residues: 234.8403
Evaluate side-chains
  110 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain D residue  331 LYS
Chi-restraints excluded: chain D residue  350 VAL
Chi-restraints excluded: chain F residue  350 VAL
Chi-restraints excluded: chain H residue  329 HIS
Chi-restraints excluded: chain H residue  349 ARG
Chi-restraints excluded: chain H residue  350 VAL
Chi-restraints excluded: chain J residue  325 LEU
Chi-restraints excluded: chain J residue  349 ARG
Chi-restraints excluded: chain J residue  350 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:    9.9990
   chunk 53 optimal weight:    6.9990
   chunk 29 optimal weight:    9.9990
   chunk 18 optimal weight:    2.9990
   chunk 35 optimal weight:    8.9990
   chunk 28 optimal weight:    6.9990
   chunk 54 optimal weight:    0.4980
   chunk 21 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   overall best weight:    2.2988

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
J 368 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.137143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.106916 restraints weight = 20776.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.3989 rms_B_bonded: 4.12
r_work: 0.3837 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3821
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3821 r_free = 0.3821    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3821 r_free = 0.3821    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3821
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5875  Z= 0.246
  Angle     :  0.692   7.460   7870  Z= 0.343
  Chirality :  0.051   0.136    885
  Planarity :  0.003   0.024   1000
  Dihedral  :  7.798  56.160    803
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 15.34 %
    Favored  : 80.90 %
  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: -2.51 (0.24), residues: 735
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.90 (0.18), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS I 330 
 PHE   0.013   0.002   PHE A 378 
 TYR   0.017   0.003   TYR F 310 
 ARG   0.001   0.000   ARG E 379 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 74
  time to evaluate  : 0.716 
Fit side-chains
REVERT: B  379 ARG cc_start: 0.6876 (mmt90) cc_final: 0.6600 (mmt90)
REVERT: C  340 LYS cc_start: 0.8240 (mttt) cc_final: 0.7817 (mttp)
REVERT: G  340 LYS cc_start: 0.8642 (mttt) cc_final: 0.8249 (mtpp)
REVERT: G  342 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8338 (mp0)
REVERT: H  317 LYS cc_start: 0.8167 (pttt) cc_final: 0.7713 (ptmt)
REVERT: H  340 LYS cc_start: 0.7601 (mttt) cc_final: 0.7400 (mttp)
REVERT: I  349 ARG cc_start: 0.7827 (mtt180) cc_final: 0.6156 (mmm160)
  outliers start: 25
  outliers final: 7
  residues processed: 95
  average time/residue: 1.1684
  time to fit residues: 116.4360
Evaluate side-chains
  65 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain D residue  350 VAL
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain F residue  350 VAL
Chi-restraints excluded: chain H residue  350 VAL
Chi-restraints excluded: chain J residue  320 SER
Chi-restraints excluded: chain J residue  350 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 35 optimal weight:   10.0000
   chunk 30 optimal weight:    6.9990
   chunk 56 optimal weight:    0.3980
   chunk 32 optimal weight:    0.5980
   chunk 50 optimal weight:    9.9990
   chunk 43 optimal weight:    9.9990
   chunk 52 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    2.3986

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.164465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.132831 restraints weight = 18145.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.4065 rms_B_bonded: 4.14
r_work: 0.3889 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3889
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3873
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3873 r_free = 0.3873    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3873 r_free = 0.3873    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3873
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5875  Z= 0.248
  Angle     :  0.669   7.458   7870  Z= 0.328
  Chirality :  0.050   0.134    885
  Planarity :  0.003   0.022   1000
  Dihedral  :  5.894  36.848    785
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 17.74 %
    Favored  : 78.65 %
  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: -2.00 (0.25), residues: 735
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.52 (0.19), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS I 330 
 PHE   0.014   0.002   PHE A 378 
 TYR   0.018   0.004   TYR F 310 
 ARG   0.001   0.000   ARG C 349 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 63
  time to evaluate  : 0.668 
Fit side-chains
REVERT: B  379 ARG cc_start: 0.6634 (mmt90) cc_final: 0.6382 (mmt90)
REVERT: C  347 LYS cc_start: 0.8164 (mmtp) cc_final: 0.7886 (mmtp)
REVERT: D  348 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7505 (t0)
REVERT: E  340 LYS cc_start: 0.7817 (mttt) cc_final: 0.7304 (mtpp)
REVERT: F  349 ARG cc_start: 0.6166 (ptp-170) cc_final: 0.5936 (ptp-170)
REVERT: G  318 VAL cc_start: 0.7927 (OUTLIER) cc_final: 0.7659 (m)
REVERT: G  340 LYS cc_start: 0.8565 (mttt) cc_final: 0.8025 (mtpp)
REVERT: G  342 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8203 (mp0)
REVERT: H  349 ARG cc_start: 0.6832 (ptp-170) cc_final: 0.6490 (ptp-170)
REVERT: I  349 ARG cc_start: 0.7524 (mtt180) cc_final: 0.5798 (mmm160)
REVERT: J  338 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8387 (tm-30)
  outliers start: 24
  outliers final: 9
  residues processed: 80
  average time/residue: 1.2805
  time to fit residues: 107.2949
Evaluate side-chains
  70 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain D residue  350 VAL
Chi-restraints excluded: chain F residue  325 LEU
Chi-restraints excluded: chain F residue  350 VAL
Chi-restraints excluded: chain G residue  318 VAL
Chi-restraints excluded: chain H residue  348 ASP
Chi-restraints excluded: chain H residue  350 VAL
Chi-restraints excluded: chain J residue  350 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 2 optimal weight:    8.9990
   chunk 19 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 63 optimal weight:    9.9990
   chunk 8 optimal weight:    2.9990
   chunk 4 optimal weight:    9.9990
   chunk 12 optimal weight:   10.0000
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4578 r_free = 0.4578 target = 0.165729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.133730 restraints weight = 21358.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.4077 rms_B_bonded: 4.44
r_work: 0.3894 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3878
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3878 r_free = 0.3878    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3878 r_free = 0.3878    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3878
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5875  Z= 0.210
  Angle     :  0.641   8.104   7870  Z= 0.309
  Chirality :  0.049   0.130    885
  Planarity :  0.003   0.019   1000
  Dihedral  :  5.523  34.263    785
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 18.20 %
    Favored  : 78.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.26), residues: 735
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.35 (0.19), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS I 330 
 PHE   0.015   0.001   PHE A 378 
 TYR   0.016   0.003   TYR F 310 
 ARG   0.001   0.000   ARG C 349 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 74
  time to evaluate  : 0.639 
Fit side-chains
   revert: symmetry clash
REVERT: B  379 ARG cc_start: 0.6687 (mmt90) cc_final: 0.6395 (mmt90)
REVERT: C  347 LYS cc_start: 0.8127 (mmtp) cc_final: 0.7800 (mmtp)
REVERT: D  317 LYS cc_start: 0.7829 (ptmt) cc_final: 0.7135 (ptpt)
REVERT: E  340 LYS cc_start: 0.7847 (mttt) cc_final: 0.7281 (mtpp)
REVERT: G  318 VAL cc_start: 0.7983 (OUTLIER) cc_final: 0.7710 (m)
REVERT: G  342 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8260 (mp0)
REVERT: H  317 LYS cc_start: 0.8149 (pttt) cc_final: 0.7714 (ptmt)
REVERT: H  338 GLU cc_start: 0.7816 (tt0) cc_final: 0.7440 (tm-30)
REVERT: H  369 LYS cc_start: 0.8114 (mttp) cc_final: 0.7399 (mtpt)
REVERT: I  349 ARG cc_start: 0.7542 (mtt180) cc_final: 0.5760 (mmm160)
REVERT: J  338 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8326 (tm-30)
REVERT: J  348 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7741 (t0)
  outliers start: 22
  outliers final: 10
  residues processed: 88
  average time/residue: 1.4103
  time to fit residues: 129.7561
Evaluate side-chains
  71 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain D residue  350 VAL
Chi-restraints excluded: chain E residue  311 LYS
Chi-restraints excluded: chain F residue  350 VAL
Chi-restraints excluded: chain G residue  311 LYS
Chi-restraints excluded: chain G residue  318 VAL
Chi-restraints excluded: chain H residue  348 ASP
Chi-restraints excluded: chain H residue  350 VAL
Chi-restraints excluded: chain I residue  311 LYS
Chi-restraints excluded: chain J residue  320 SER
Chi-restraints excluded: chain J residue  348 ASP
Chi-restraints excluded: chain J residue  350 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 44 optimal weight:    8.9990
   chunk 63 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 8 optimal weight:    4.9990
   chunk 23 optimal weight:   10.0000
   chunk 3 optimal weight:   10.0000
   chunk 43 optimal weight:    0.8980
   chunk 65 optimal weight:    8.9990
   chunk 19 optimal weight:    9.9990
   chunk 36 optimal weight:   10.0000
   overall best weight:    3.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.160316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.129337 restraints weight = 15843.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.4035 rms_B_bonded: 3.90
r_work: 0.3871 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3871
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3841
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3841 r_free = 0.3841    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3841 r_free = 0.3841    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3841
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.2821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   5875  Z= 0.320
  Angle     :  0.693   8.214   7870  Z= 0.342
  Chirality :  0.050   0.128    885
  Planarity :  0.003   0.018   1000
  Dihedral  :  6.005  41.491    785
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 17.59 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.26), residues: 735
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.35 (0.20), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS D 362 
 PHE   0.018   0.002   PHE A 378 
 TYR   0.022   0.005   TYR F 310 
 ARG   0.002   0.000   ARG F 349 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 72
  time to evaluate  : 0.670 
Fit side-chains
REVERT: B  348 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.7822 (t0)
REVERT: C  342 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7691 (mp0)
REVERT: D  348 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.7463 (t0)
REVERT: E  340 LYS cc_start: 0.7875 (mttt) cc_final: 0.7359 (mtpp)
REVERT: E  342 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7599 (mp0)
REVERT: E  378 PHE cc_start: 0.7280 (t80) cc_final: 0.6605 (t80)
REVERT: G  318 VAL cc_start: 0.8020 (OUTLIER) cc_final: 0.7747 (m)
REVERT: G  340 LYS cc_start: 0.8586 (mttt) cc_final: 0.8194 (mtpm)
REVERT: G  342 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8190 (mp0)
REVERT: G  378 PHE cc_start: 0.7349 (t80) cc_final: 0.6930 (t80)
REVERT: H  338 GLU cc_start: 0.7806 (tt0) cc_final: 0.7392 (tm-30)
REVERT: I  342 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7598 (mp0)
REVERT: I  349 ARG cc_start: 0.7536 (mtt180) cc_final: 0.5779 (mmm160)
REVERT: J  338 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8319 (tm-30)
REVERT: J  348 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7737 (t0)
  outliers start: 27
  outliers final: 12
  residues processed: 92
  average time/residue: 1.2820
  time to fit residues: 123.3110
Evaluate side-chains
  84 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  348 ASP
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain D residue  350 VAL
Chi-restraints excluded: chain E residue  311 LYS
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain F residue  350 VAL
Chi-restraints excluded: chain G residue  311 LYS
Chi-restraints excluded: chain G residue  318 VAL
Chi-restraints excluded: chain H residue  348 ASP
Chi-restraints excluded: chain H residue  350 VAL
Chi-restraints excluded: chain I residue  311 LYS
Chi-restraints excluded: chain J residue  348 ASP
Chi-restraints excluded: chain J residue  350 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 16 optimal weight:    8.9990
   chunk 49 optimal weight:    5.9990
   chunk 30 optimal weight:    9.9990
   chunk 15 optimal weight:   10.0000
   chunk 63 optimal weight:    8.9990
   chunk 46 optimal weight:    8.9990
   chunk 54 optimal weight:    7.9990
   chunk 53 optimal weight:    4.9990
   chunk 69 optimal weight:    0.3980
   chunk 10 optimal weight:    9.9990
   chunk 14 optimal weight:    7.9990
   overall best weight:    5.4788

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.128915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.096933 restraints weight = 21174.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3961 rms_B_bonded: 4.44
r_work: 0.3792 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3771
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3771 r_free = 0.3771    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3771 r_free = 0.3771    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3771
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.2888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050   5875  Z= 0.490
  Angle     :  0.792   8.007   7870  Z= 0.403
  Chirality :  0.053   0.129    885
  Planarity :  0.004   0.018   1000
  Dihedral  :  6.584  46.460    785
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 18.20 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.96 (0.25), residues: 735
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.48 (0.19), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS D 362 
 PHE   0.015   0.002   PHE I 378 
 TYR   0.030   0.007   TYR F 310 
 ARG   0.003   0.000   ARG F 349 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 71
  time to evaluate  : 0.708 
Fit side-chains
REVERT: B  348 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.7835 (t0)
REVERT: C  342 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7768 (mp0)
REVERT: D  348 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7309 (t0)
REVERT: E  340 LYS cc_start: 0.7921 (mttt) cc_final: 0.7408 (mtpp)
REVERT: E  342 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7657 (mp0)
REVERT: E  378 PHE cc_start: 0.7314 (t80) cc_final: 0.6632 (t80)
REVERT: G  340 LYS cc_start: 0.8609 (mttt) cc_final: 0.8224 (mtpm)
REVERT: G  342 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8175 (mp0)
REVERT: G  378 PHE cc_start: 0.7448 (t80) cc_final: 0.6942 (t80)
REVERT: H  338 GLU cc_start: 0.7839 (tt0) cc_final: 0.7427 (tm-30)
REVERT: I  342 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7672 (mp0)
REVERT: I  349 ARG cc_start: 0.7564 (mtt180) cc_final: 0.5887 (mmm160)
REVERT: J  338 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8460 (tm-30)
REVERT: J  348 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7783 (t0)
  outliers start: 31
  outliers final: 13
  residues processed: 96
  average time/residue: 1.2220
  time to fit residues: 123.0950
Evaluate side-chains
  91 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain B residue  348 ASP
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain D residue  350 VAL
Chi-restraints excluded: chain D residue  369 LYS
Chi-restraints excluded: chain E residue  311 LYS
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain F residue  350 VAL
Chi-restraints excluded: chain H residue  348 ASP
Chi-restraints excluded: chain H residue  350 VAL
Chi-restraints excluded: chain I residue  311 LYS
Chi-restraints excluded: chain J residue  338 GLU
Chi-restraints excluded: chain J residue  348 ASP
Chi-restraints excluded: chain J residue  350 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 7 optimal weight:   10.0000
   chunk 48 optimal weight:    2.9990
   chunk 22 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   chunk 20 optimal weight:    0.2980
   chunk 10 optimal weight:    9.9990
   chunk 16 optimal weight:    0.0980
   chunk 53 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4580 r_free = 0.4580 target = 0.165535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.133809 restraints weight = 21783.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.4089 rms_B_bonded: 4.47
r_work: 0.3906 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3867
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3867 r_free = 0.3867    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3867 r_free = 0.3867    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3867
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.3101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   5875  Z= 0.180
  Angle     :  0.640   8.911   7870  Z= 0.307
  Chirality :  0.049   0.123    885
  Planarity :  0.002   0.015   1000
  Dihedral  :  5.404  32.973    785
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 20.60 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.26), residues: 735
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.31 (0.20), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 330 
 PHE   0.016   0.001   PHE C 378 
 TYR   0.014   0.003   TYR F 310 
 ARG   0.002   0.000   ARG F 349 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 0.548 
Fit side-chains
REVERT: C  342 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7709 (mp0)
REVERT: E  342 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7548 (mp0)
REVERT: E  378 PHE cc_start: 0.7123 (t80) cc_final: 0.6468 (t80)
REVERT: F  338 GLU cc_start: 0.7905 (tt0) cc_final: 0.7437 (tm-30)
REVERT: G  342 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8121 (mp0)
REVERT: G  347 LYS cc_start: 0.8564 (mmtp) cc_final: 0.7003 (pptt)
REVERT: G  378 PHE cc_start: 0.7264 (t80) cc_final: 0.6787 (t80)
REVERT: H  338 GLU cc_start: 0.7759 (tt0) cc_final: 0.7392 (tm-30)
REVERT: I  342 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7592 (mp0)
REVERT: I  349 ARG cc_start: 0.7530 (mtt180) cc_final: 0.5747 (mmm160)
REVERT: J  338 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8395 (tm-30)
REVERT: J  348 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7746 (t0)
  outliers start: 18
  outliers final: 9
  residues processed: 86
  average time/residue: 1.2071
  time to fit residues: 108.6437
Evaluate side-chains
  81 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain D residue  350 VAL
Chi-restraints excluded: chain E residue  311 LYS
Chi-restraints excluded: chain F residue  350 VAL
Chi-restraints excluded: chain H residue  348 ASP
Chi-restraints excluded: chain H residue  350 VAL
Chi-restraints excluded: chain J residue  338 GLU
Chi-restraints excluded: chain J residue  348 ASP
Chi-restraints excluded: chain J residue  350 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 51 optimal weight:    0.0670
   chunk 60 optimal weight:    3.9990
   chunk 32 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 56 optimal weight:    6.9990
   chunk 52 optimal weight:   10.0000
   chunk 59 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 36 optimal weight:    9.9990
   chunk 38 optimal weight:    8.9990
   chunk 39 optimal weight:   10.0000
   overall best weight:    4.0126

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.130786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.098382 restraints weight = 23324.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.3995 rms_B_bonded: 4.64
r_work: 0.3819 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3776
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3776 r_free = 0.3776    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3776 r_free = 0.3776    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3776
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.3043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   5875  Z= 0.372
  Angle     :  0.734   8.682   7870  Z= 0.365
  Chirality :  0.051   0.130    885
  Planarity :  0.003   0.019   1000
  Dihedral  :  6.140  42.332    785
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 20.30 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.81 (0.26), residues: 735
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.37 (0.20), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS D 362 
 PHE   0.012   0.001   PHE I 378 
 TYR   0.024   0.005   TYR F 310 
 ARG   0.002   0.000   ARG F 349 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.721 
Fit side-chains
REVERT: C  342 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7785 (mp0)
REVERT: D  348 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.7437 (t0)
REVERT: E  340 LYS cc_start: 0.7886 (mttt) cc_final: 0.7379 (mtpp)
REVERT: E  342 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7648 (mp0)
REVERT: E  378 PHE cc_start: 0.7306 (t80) cc_final: 0.6650 (t80)
REVERT: F  338 GLU cc_start: 0.7938 (tt0) cc_final: 0.7429 (tm-30)
REVERT: G  340 LYS cc_start: 0.8599 (mttt) cc_final: 0.8227 (mtpm)
REVERT: G  342 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8187 (mp0)
REVERT: G  347 LYS cc_start: 0.8563 (mmtp) cc_final: 0.7041 (pptt)
REVERT: G  378 PHE cc_start: 0.7402 (t80) cc_final: 0.6911 (t80)
REVERT: H  338 GLU cc_start: 0.7801 (tt0) cc_final: 0.7350 (tm-30)
REVERT: H  349 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6707 (ptp-170)
REVERT: I  342 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7676 (mp0)
REVERT: I  349 ARG cc_start: 0.7579 (mtt180) cc_final: 0.5862 (mmm160)
REVERT: J  338 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8394 (tm-30)
REVERT: J  348 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7725 (t0)
  outliers start: 20
  outliers final: 10
  residues processed: 87
  average time/residue: 1.2794
  time to fit residues: 116.4255
Evaluate side-chains
  84 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain D residue  350 VAL
Chi-restraints excluded: chain E residue  311 LYS
Chi-restraints excluded: chain F residue  350 VAL
Chi-restraints excluded: chain H residue  348 ASP
Chi-restraints excluded: chain H residue  349 ARG
Chi-restraints excluded: chain H residue  350 VAL
Chi-restraints excluded: chain I residue  311 LYS
Chi-restraints excluded: chain J residue  338 GLU
Chi-restraints excluded: chain J residue  348 ASP
Chi-restraints excluded: chain J residue  350 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 49 optimal weight:    0.2980
   chunk 60 optimal weight:    6.9990
   chunk 22 optimal weight:    9.9990
   chunk 57 optimal weight:   10.0000
   chunk 56 optimal weight:    1.9990
   chunk 41 optimal weight:    7.9990
   chunk 16 optimal weight:    0.2980
   chunk 55 optimal weight:    0.2980
   chunk 51 optimal weight:    8.9990
   chunk 23 optimal weight:    9.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4591 r_free = 0.4591 target = 0.166248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.135157 restraints weight = 17389.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.4102 rms_B_bonded: 4.07
r_work: 0.3933 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3933
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3914
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3914 r_free = 0.3914    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3914 r_free = 0.3914    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3914
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.3228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   5875  Z= 0.168
  Angle     :  0.647   9.157   7870  Z= 0.306
  Chirality :  0.049   0.122    885
  Planarity :  0.002   0.016   1000
  Dihedral  :  5.223  30.095    785
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 20.45 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.26), residues: 735
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.25 (0.20), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C 330 
 PHE   0.006   0.001   PHE I 378 
 TYR   0.012   0.002   TYR F 310 
 ARG   0.001   0.000   ARG F 349 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.678 
Fit side-chains
REVERT: C  342 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7722 (mp0)
REVERT: D  348 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.7465 (t0)
REVERT: E  342 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7533 (mp0)
REVERT: E  378 PHE cc_start: 0.7071 (t80) cc_final: 0.6408 (t80)
REVERT: F  338 GLU cc_start: 0.7861 (tt0) cc_final: 0.7404 (tm-30)
REVERT: G  342 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8123 (mp0)
REVERT: G  378 PHE cc_start: 0.7213 (t80) cc_final: 0.6740 (t80)
REVERT: H  338 GLU cc_start: 0.7764 (tt0) cc_final: 0.7366 (tm-30)
REVERT: H  349 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.6542 (ptp-170)
REVERT: I  342 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7615 (mp0)
REVERT: I  349 ARG cc_start: 0.7578 (mtt180) cc_final: 0.5742 (mmm160)
REVERT: J  338 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8475 (tm-30)
REVERT: J  348 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7715 (t0)
  outliers start: 19
  outliers final: 10
  residues processed: 82
  average time/residue: 1.1958
  time to fit residues: 102.9393
Evaluate side-chains
  79 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain D residue  350 VAL
Chi-restraints excluded: chain F residue  350 VAL
Chi-restraints excluded: chain H residue  325 LEU
Chi-restraints excluded: chain H residue  348 ASP
Chi-restraints excluded: chain H residue  349 ARG
Chi-restraints excluded: chain H residue  350 VAL
Chi-restraints excluded: chain I residue  311 LYS
Chi-restraints excluded: chain J residue  348 ASP
Chi-restraints excluded: chain J residue  350 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 19 optimal weight:    7.9990
   chunk 10 optimal weight:   10.0000
   chunk 26 optimal weight:    9.9990
   chunk 60 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 22 optimal weight:    8.9990
   chunk 46 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 21 optimal weight:    6.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4549 r_free = 0.4549 target = 0.160653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.128745 restraints weight = 22678.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.4015 rms_B_bonded: 4.49
r_work: 0.3831 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3814
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3814 r_free = 0.3814    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3814 r_free = 0.3814    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3814
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.3164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5875  Z= 0.307
  Angle     :  0.712   9.060   7870  Z= 0.349
  Chirality :  0.050   0.123    885
  Planarity :  0.003   0.018   1000
  Dihedral  :  5.741  37.015    785
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 20.60 %
    Favored  : 76.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.69 (0.26), residues: 735
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.28 (0.20), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B 362 
 PHE   0.007   0.001   PHE I 378 
 TYR   0.022   0.005   TYR F 310 
 ARG   0.002   0.000   ARG J 379 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 0.679 
Fit side-chains
REVERT: B  348 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.7743 (t0)
REVERT: C  342 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7668 (mp0)
REVERT: D  348 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7440 (t0)
REVERT: E  340 LYS cc_start: 0.7818 (mttt) cc_final: 0.7306 (mtpp)
REVERT: E  342 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7569 (mp0)
REVERT: E  378 PHE cc_start: 0.7195 (t80) cc_final: 0.6550 (t80)
REVERT: F  338 GLU cc_start: 0.7917 (tt0) cc_final: 0.7422 (tm-30)
REVERT: G  342 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8139 (mp0)
REVERT: G  378 PHE cc_start: 0.7320 (t80) cc_final: 0.6819 (t80)
REVERT: H  338 GLU cc_start: 0.7774 (tt0) cc_final: 0.7338 (tm-30)
REVERT: H  349 ARG cc_start: 0.6861 (OUTLIER) cc_final: 0.6649 (ptp-170)
REVERT: I  342 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7573 (mp0)
REVERT: I  349 ARG cc_start: 0.7496 (mtt180) cc_final: 0.5762 (mmm160)
REVERT: J  338 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8469 (tm-30)
REVERT: J  348 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7686 (t0)
  outliers start: 19
  outliers final: 10
  residues processed: 79
  average time/residue: 1.2652
  time to fit residues: 105.5063
Evaluate side-chains
  82 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  348 ASP
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain D residue  350 VAL
Chi-restraints excluded: chain F residue  350 VAL
Chi-restraints excluded: chain G residue  311 LYS
Chi-restraints excluded: chain H residue  348 ASP
Chi-restraints excluded: chain H residue  349 ARG
Chi-restraints excluded: chain H residue  350 VAL
Chi-restraints excluded: chain I residue  311 LYS
Chi-restraints excluded: chain J residue  338 GLU
Chi-restraints excluded: chain J residue  348 ASP
Chi-restraints excluded: chain J residue  350 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 42 optimal weight:    0.7980
   chunk 20 optimal weight:    6.9990
   chunk 9 optimal weight:    6.9990
   chunk 67 optimal weight:    0.2980
   chunk 18 optimal weight:   10.0000
   chunk 57 optimal weight:    9.9990
   chunk 15 optimal weight:    3.9990
   chunk 7 optimal weight:    9.9990
   chunk 6 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0670
   overall best weight:    1.4322

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 329 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4595 r_free = 0.4595 target = 0.165964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.134926 restraints weight = 16877.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.4096 rms_B_bonded: 4.02
r_work: 0.3933 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3933
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3910
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3910 r_free = 0.3910    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3910 r_free = 0.3910    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3910
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.3274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   5875  Z= 0.174
  Angle     :  0.658   9.305   7870  Z= 0.312
  Chirality :  0.049   0.124    885
  Planarity :  0.002   0.019   1000
  Dihedral  :  5.274  30.523    785
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 21.35 %
    Favored  : 76.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.27), residues: 735
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.23 (0.20), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 330 
 PHE   0.005   0.001   PHE F 378 
 TYR   0.015   0.003   TYR H 310 
 ARG   0.002   0.000   ARG J 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5833.46 seconds
wall clock time: 104 minutes 14.37 seconds (6254.37 seconds total)