Starting phenix.real_space_refine
on Thu May  1 00:58:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q7t_18233/05_2025/8q7t_18233.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q7t_18233/05_2025/8q7t_18233.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q7t_18233/05_2025/8q7t_18233.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q7t_18233/05_2025/8q7t_18233.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q7t_18233/05_2025/8q7t_18233.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q7t_18233/05_2025/8q7t_18233.cif"
  }
  resolution = 3.0
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S       9      5.16       5
     C    3102      2.51       5
     N     903      2.21       5
     O     933      1.98       5
     H    5136      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 10083
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "B"
      Number of atoms: 1155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1155
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "D"
      Number of atoms: 1155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1155
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "F"
      Number of atoms: 1155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1155
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "C"
      Number of atoms: 1051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 1051
          Classifications: {'peptide': 68}
          Link IDs: {'PTRANS': 3, 'TRANS': 64}
    Chain: "A"
      Number of atoms: 1155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1155
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "E"
      Number of atoms: 1051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 1051
          Classifications: {'peptide': 68}
          Link IDs: {'PTRANS': 3, 'TRANS': 64}
    Chain: "G"
      Number of atoms: 1155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1155
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
    Chain: "H"
      Number of atoms: 1051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 1051
          Classifications: {'peptide': 68}
          Link IDs: {'PTRANS': 3, 'TRANS': 64}
    Chain: "I"
      Number of atoms: 1155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1155
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
  Time building chain proxies: 6.47, per 1000 atoms: 0.64
  Number of scatterers: 10083
  At special positions: 0
  Unit cell: (161.394, 145.4, 47.982, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       9     16.00
     O     933      8.00
     N     903      7.00
     C    3102      6.00
     H    5136      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.59
  Conformation dependent library (CDL) restraints added in 706.2 milliseconds
  

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1134

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 25 sheets defined
      0.0% alpha, 54.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.05
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 306 through 310
      removed outlier: 6.488A  pdb=" N   GLN B 307 " --> pdb=" O   ILE D 308 " (cutoff:3.500A)
      removed outlier: 7.790A  pdb=" N   TYR D 310 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   VAL B 309 " --> pdb=" O   TYR D 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 313 through 314
      removed outlier: 6.859A  pdb=" N   VAL B 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 317 through 325
      removed outlier: 6.324A  pdb=" N   LYS B 317 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
      removed outlier: 8.002A  pdb=" N   SER D 320 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   THR B 319 " --> pdb=" O   SER D 320 " (cutoff:3.500A)
      removed outlier: 7.976A  pdb=" N   CYS D 322 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   LYS B 321 " --> pdb=" O   CYS D 322 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   SER D 324 " --> pdb=" O   LYS B 321 " (cutoff:3.500A)
      removed outlier: 5.981A  pdb=" N   GLY B 323 " --> pdb=" O   SER D 324 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 328 through 330
      removed outlier: 6.603A  pdb=" N   ILE B 328 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 337 through 346
      removed outlier: 6.569A  pdb=" N   GLU B 338 " --> pdb=" O   VAL D 339 " (cutoff:3.500A)
      removed outlier: 7.683A  pdb=" N   SER D 341 " --> pdb=" O   GLU B 338 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   LYS B 340 " --> pdb=" O   SER D 341 " (cutoff:3.500A)
      removed outlier: 8.266A  pdb=" N   LYS D 343 " --> pdb=" O   LYS B 340 " (cutoff:3.500A)
      removed outlier: 8.811A  pdb=" N   GLU B 342 " --> pdb=" O   LYS D 343 " (cutoff:3.500A)
      removed outlier: 8.200A  pdb=" N   ASP D 345 " --> pdb=" O   GLU B 342 " (cutoff:3.500A)
      removed outlier: 9.095A  pdb=" N   LEU B 344 " --> pdb=" O   ASP D 345 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   LEU F 344 " --> pdb=" O   LYS B 343 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   ASP B 345 " --> pdb=" O   LEU F 344 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   PHE F 346 " --> pdb=" O   ASP B 345 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 350 through 362
      removed outlier: 6.899A  pdb=" N   GLN D 351 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   SER B 352 " --> pdb=" O   GLN D 351 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   LYS D 353 " --> pdb=" O   SER B 352 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   ILE B 354 " --> pdb=" O   LYS D 353 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   GLY D 355 " --> pdb=" O   ILE B 354 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   SER B 356 " --> pdb=" O   GLY D 355 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   GLN B 351 " --> pdb=" O   VAL F 350 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   SER F 352 " --> pdb=" O   GLN B 351 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   LYS B 353 " --> pdb=" O   SER F 352 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   ILE F 354 " --> pdb=" O   LYS B 353 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   GLY B 355 " --> pdb=" O   ILE F 354 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   SER F 356 " --> pdb=" O   GLY B 355 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 368 through 377
      removed outlier: 6.462A  pdb=" N   LYS B 369 " --> pdb=" O   LYS D 370 " (cutoff:3.500A)
      removed outlier: 7.913A  pdb=" N   GLU D 372 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   ILE B 371 " --> pdb=" O   GLU D 372 " (cutoff:3.500A)
      removed outlier: 7.847A  pdb=" N   HIS D 374 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   THR B 373 " --> pdb=" O   HIS D 374 " (cutoff:3.500A)
      removed outlier: 7.994A  pdb=" N   LEU D 376 " --> pdb=" O   THR B 373 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   LYS B 375 " --> pdb=" O   LEU D 376 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 309 through 310
      removed outlier: 6.542A  pdb=" N   VAL E 309 " --> pdb=" O   TYR H 310 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 313 through 314
      removed outlier: 6.796A  pdb=" N   VAL E 313 " --> pdb=" O   ASP H 314 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 317 through 325
      removed outlier: 6.468A  pdb=" N   VAL C 318 " --> pdb=" O   THR H 319 " (cutoff:3.500A)
      removed outlier: 7.866A  pdb=" N   LYS H 321 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   SER C 320 " --> pdb=" O   LYS H 321 " (cutoff:3.500A)
      removed outlier: 7.980A  pdb=" N   GLY H 323 " --> pdb=" O   SER C 320 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   CYS C 322 " --> pdb=" O   GLY H 323 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   LEU H 325 " --> pdb=" O   CYS C 322 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   SER C 324 " --> pdb=" O   LEU H 325 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   LYS E 317 " --> pdb=" O   VAL H 318 " (cutoff:3.500A)
      removed outlier: 8.101A  pdb=" N   SER H 320 " --> pdb=" O   LYS E 317 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   THR E 319 " --> pdb=" O   SER H 320 " (cutoff:3.500A)
      removed outlier: 8.036A  pdb=" N   CYS H 322 " --> pdb=" O   THR E 319 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   LYS E 321 " --> pdb=" O   CYS H 322 " (cutoff:3.500A)
      removed outlier: 7.198A  pdb=" N   SER H 324 " --> pdb=" O   LYS E 321 " (cutoff:3.500A)
      removed outlier: 6.007A  pdb=" N   GLY E 323 " --> pdb=" O   SER H 324 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'C' and resid 328 through 330
      removed outlier: 6.461A  pdb=" N   ILE E 328 " --> pdb=" O   HIS H 329 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 337 through 342
      removed outlier: 6.576A  pdb=" N   GLU E 338 " --> pdb=" O   VAL H 339 " (cutoff:3.500A)
      removed outlier: 7.919A  pdb=" N   SER H 341 " --> pdb=" O   GLU E 338 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   LYS E 340 " --> pdb=" O   SER H 341 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 345 through 346
      removed outlier: 6.538A  pdb=" N   ASP E 345 " --> pdb=" O   PHE H 346 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 350 through 354
      removed outlier: 6.512A  pdb=" N   GLN E 351 " --> pdb=" O   SER H 352 " (cutoff:3.500A)
      removed outlier: 8.016A  pdb=" N   ILE H 354 " --> pdb=" O   GLN E 351 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   LYS E 353 " --> pdb=" O   ILE H 354 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 359 through 362
      removed outlier: 6.523A  pdb=" N   ASN C 359 " --> pdb=" O   ILE H 360 " (cutoff:3.500A)
      removed outlier: 8.154A  pdb=" N   HIS H 362 " --> pdb=" O   ASN C 359 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   THR C 361 " --> pdb=" O   HIS H 362 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 368 through 374
    Processing sheet with id=AB8, first strand: chain 'G' and resid 305 through 310
      removed outlier: 6.571A  pdb=" N   VAL A 306 " --> pdb=" O   GLN I 307 " (cutoff:3.500A)
      removed outlier: 7.973A  pdb=" N   VAL I 309 " --> pdb=" O   VAL A 306 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   ILE A 308 " --> pdb=" O   VAL I 309 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'G' and resid 313 through 314
      removed outlier: 6.919A  pdb=" N   VAL A 313 " --> pdb=" O   ASP G 314 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'G' and resid 317 through 325
      removed outlier: 6.491A  pdb=" N   VAL A 318 " --> pdb=" O   THR I 319 " (cutoff:3.500A)
      removed outlier: 7.970A  pdb=" N   LYS I 321 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   SER A 320 " --> pdb=" O   LYS I 321 " (cutoff:3.500A)
      removed outlier: 8.002A  pdb=" N   GLY I 323 " --> pdb=" O   SER A 320 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   CYS A 322 " --> pdb=" O   GLY I 323 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   LEU I 325 " --> pdb=" O   CYS A 322 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   SER A 324 " --> pdb=" O   LEU I 325 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'G' and resid 328 through 330
      removed outlier: 6.696A  pdb=" N   ILE A 328 " --> pdb=" O   HIS G 329 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'G' and resid 333 through 334
      removed outlier: 6.854A  pdb=" N   GLY A 333 " --> pdb=" O   GLY G 334 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'G' and resid 337 through 346
      removed outlier: 6.403A  pdb=" N   GLU A 338 " --> pdb=" O   VAL G 339 " (cutoff:3.500A)
      removed outlier: 7.808A  pdb=" N   SER G 341 " --> pdb=" O   GLU A 338 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   LYS A 340 " --> pdb=" O   SER G 341 " (cutoff:3.500A)
      removed outlier: 8.624A  pdb=" N   LYS G 343 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
      removed outlier: 8.790A  pdb=" N   GLU A 342 " --> pdb=" O   LYS G 343 " (cutoff:3.500A)
      removed outlier: 8.543A  pdb=" N   ASP G 345 " --> pdb=" O   GLU A 342 " (cutoff:3.500A)
      removed outlier: 9.079A  pdb=" N   LEU A 344 " --> pdb=" O   ASP G 345 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   VAL A 337 " --> pdb=" O   GLU I 338 " (cutoff:3.500A)
      removed outlier: 7.863A  pdb=" N   LYS I 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   VAL A 339 " --> pdb=" O   LYS I 340 " (cutoff:3.500A)
      removed outlier: 8.040A  pdb=" N   GLU I 342 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   SER A 341 " --> pdb=" O   GLU I 342 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   LEU I 344 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
      removed outlier: 7.608A  pdb=" N   LYS A 343 " --> pdb=" O   LEU I 344 " (cutoff:3.500A)
      removed outlier: 10.382A  pdb=" N   PHE I 346 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 9.209A  pdb=" N   ASP A 345 " --> pdb=" O   PHE I 346 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC4
    Processing sheet with id=AC5, first strand: chain 'G' and resid 350 through 358
      removed outlier: 6.406A  pdb=" N   GLN A 351 " --> pdb=" O   SER G 352 " (cutoff:3.500A)
      removed outlier: 8.133A  pdb=" N   ILE G 354 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   LYS A 353 " --> pdb=" O   ILE G 354 " (cutoff:3.500A)
      removed outlier: 8.576A  pdb=" N   SER G 356 " --> pdb=" O   LYS A 353 " (cutoff:3.500A)
      removed outlier: 9.380A  pdb=" N   GLY A 355 " --> pdb=" O   SER G 356 " (cutoff:3.500A)
      removed outlier: 7.325A  pdb=" N   ASP G 358 " --> pdb=" O   GLY A 355 " (cutoff:3.500A)
      removed outlier: 8.771A  pdb=" N   LEU A 357 " --> pdb=" O   ASP G 358 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   VAL A 350 " --> pdb=" O   GLN I 351 " (cutoff:3.500A)
      removed outlier: 8.076A  pdb=" N   LYS I 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   SER A 352 " --> pdb=" O   LYS I 353 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC5
    Processing sheet with id=AC6, first strand: chain 'G' and resid 361 through 362
      removed outlier: 6.320A  pdb=" N   THR A 361 " --> pdb=" O   HIS I 362 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'G' and resid 368 through 377
      removed outlier: 6.478A  pdb=" N   LYS A 369 " --> pdb=" O   LYS G 370 " (cutoff:3.500A)
      removed outlier: 7.704A  pdb=" N   GLU G 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   ILE A 371 " --> pdb=" O   GLU G 372 " (cutoff:3.500A)
      removed outlier: 8.068A  pdb=" N   HIS G 374 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   THR A 373 " --> pdb=" O   HIS G 374 " (cutoff:3.500A)
      removed outlier: 7.990A  pdb=" N   LEU G 376 " --> pdb=" O   THR A 373 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   LYS A 375 " --> pdb=" O   LEU G 376 " (cutoff:3.500A)

    98 hydrogen bonds defined for protein.
    294 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: 3.53

  Time building geometry restraints manager: 3.20 seconds

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

  Histogram of bond lengths:
        0.95 -     1.12: 5127
        1.12 -     1.29: 834
        1.29 -     1.47: 1711
        1.47 -     1.64: 2480
        1.64 -     1.82: 9
  Bond restraints: 10161
  Sorted by residual:
  bond pdb=" NE2 HIS F 329 "
       pdb=" HE2 HIS F 329 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.69e+01
  bond pdb=" ND2 ASN F 327 "
       pdb="HD22 ASN F 327 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.69e+01
  bond pdb=" N   LYS D 353 "
       pdb=" H   LYS D 353 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.69e+01
  bond pdb=" NE2 HIS D 362 "
       pdb=" HE2 HIS D 362 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.69e+01
  bond pdb=" N   ASP E 345 "
       pdb=" H   ASP E 345 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.69e+01
  ... (remaining 10156 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.57: 15834
        2.57 -     5.15: 2071
        5.15 -     7.72: 613
        7.72 -    10.29: 10
       10.29 -    12.87: 6
  Bond angle restraints: 18534
  Sorted by residual:
  angle pdb=" CA  GLY I 355 "
        pdb=" C   GLY I 355 "
        pdb=" N   SER I 356 "
      ideal   model   delta    sigma   weight residual
     114.58  119.53   -4.95 8.60e-01 1.35e+00 3.31e+01
  angle pdb=" OE1 GLN I 336 "
        pdb=" CD  GLN I 336 "
        pdb=" NE2 GLN I 336 "
      ideal   model   delta    sigma   weight residual
     122.60  117.08    5.52 1.00e+00 1.00e+00 3.05e+01
  angle pdb=" OE1 GLN B 336 "
        pdb=" CD  GLN B 336 "
        pdb=" NE2 GLN B 336 "
      ideal   model   delta    sigma   weight residual
     122.60  117.08    5.52 1.00e+00 1.00e+00 3.04e+01
  angle pdb=" CA  ASP C 358 "
        pdb=" CB  ASP C 358 "
        pdb=" CG  ASP C 358 "
      ideal   model   delta    sigma   weight residual
     112.60  117.95   -5.35 1.00e+00 1.00e+00 2.86e+01
  angle pdb=" OE1 GLN G 336 "
        pdb=" CD  GLN G 336 "
        pdb=" NE2 GLN G 336 "
      ideal   model   delta    sigma   weight residual
     122.60  117.32    5.28 1.00e+00 1.00e+00 2.79e+01
  ... (remaining 18529 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.79: 4147
       16.79 -    33.58: 266
       33.58 -    50.38: 119
       50.38 -    67.17: 145
       67.17 -    83.96: 6
  Dihedral angle restraints: 4683
    sinusoidal: 2676
      harmonic: 2007
  Sorted by residual:
  dihedral pdb=" CA  PRO C 332 "
           pdb=" C   PRO C 332 "
           pdb=" N   GLY C 333 "
           pdb=" CA  GLY C 333 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.19   25.81     0      5.00e+00 4.00e-02 2.66e+01
  dihedral pdb=" CA  GLY C 334 "
           pdb=" C   GLY C 334 "
           pdb=" N   GLY C 335 "
           pdb=" CA  GLY C 335 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.38   20.62     0      5.00e+00 4.00e-02 1.70e+01
  dihedral pdb=" CA  GLY A 367 "
           pdb=" C   GLY A 367 "
           pdb=" N   ASN A 368 "
           pdb=" CA  ASN A 368 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.83  -20.17     0      5.00e+00 4.00e-02 1.63e+01
  ... (remaining 4680 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 508
       0.081 -    0.161: 213
       0.161 -    0.242: 27
       0.242 -    0.322: 6
       0.322 -    0.402: 2
  Chirality restraints: 756
  Sorted by residual:
  chirality pdb=" CA  PRO H 332 "
            pdb=" N   PRO H 332 "
            pdb=" C   PRO H 332 "
            pdb=" CB  PRO H 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.32    0.40 2.00e-01 2.50e+01 4.05e+00
  chirality pdb=" CA  PRO C 332 "
            pdb=" N   PRO C 332 "
            pdb=" C   PRO C 332 "
            pdb=" CB  PRO C 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.39    0.33 2.00e-01 2.50e+01 2.67e+00
  chirality pdb=" CA  LYS F 347 "
            pdb=" N   LYS F 347 "
            pdb=" C   LYS F 347 "
            pdb=" CB  LYS F 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.19e+00
  ... (remaining 753 not shown)

  Planarity restraints: 1473
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 368 "    0.110 2.00e-02 2.50e+03   1.01e-01 1.53e+02
        pdb=" CG  ASN A 368 "   -0.027 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 368 "   -0.085 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 368 "   -0.044 2.00e-02 2.50e+03
        pdb="HD21 ASN A 368 "   -0.115 2.00e-02 2.50e+03
        pdb="HD22 ASN A 368 "    0.161 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 310 "    0.099 2.00e-02 2.50e+03   5.55e-02 9.25e+01
        pdb=" CG  TYR E 310 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 310 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 310 "   -0.033 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 310 "   -0.047 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 310 "   -0.040 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 310 "   -0.018 2.00e-02 2.50e+03
        pdb=" OH  TYR E 310 "    0.139 2.00e-02 2.50e+03
        pdb=" HD1 TYR E 310 "    0.006 2.00e-02 2.50e+03
        pdb=" HD2 TYR E 310 "   -0.010 2.00e-02 2.50e+03
        pdb=" HE1 TYR E 310 "   -0.033 2.00e-02 2.50e+03
        pdb=" HE2 TYR E 310 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN G 368 "    0.082 2.00e-02 2.50e+03   7.83e-02 9.19e+01
        pdb=" CG  ASN G 368 "   -0.010 2.00e-02 2.50e+03
        pdb=" OD1 ASN G 368 "   -0.073 2.00e-02 2.50e+03
        pdb=" ND2 ASN G 368 "   -0.029 2.00e-02 2.50e+03
        pdb="HD21 ASN G 368 "   -0.094 2.00e-02 2.50e+03
        pdb="HD22 ASN G 368 "    0.123 2.00e-02 2.50e+03
  ... (remaining 1470 not shown)

  Histogram of nonbonded interaction distances:
        1.52 -     2.14: 599
        2.14 -     2.75: 15950
        2.75 -     3.37: 26764
        3.37 -     3.98: 35994
        3.98 -     4.60: 49732
  Nonbonded interactions: 129039
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP E 314 "
            pdb=" HG  SER E 316 "
     model   vdw
     1.520 2.450
  nonbonded pdb=" OD1 ASP H 314 "
            pdb=" HG  SER H 316 "
     model   vdw
     1.527 2.450
  nonbonded pdb=" OD1 ASP F 314 "
            pdb=" HG  SER F 316 "
     model   vdw
     1.559 2.450
  nonbonded pdb=" OD1 ASP A 314 "
            pdb=" HG  SER A 316 "
     model   vdw
     1.581 2.450
  nonbonded pdb=" OD1 ASP I 314 "
            pdb=" HG  SER I 316 "
     model   vdw
     1.582 2.450
  ... (remaining 129034 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: 0.01
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 308 through 375)
  selection = (chain 'B' and resid 308 through 375)
  selection = chain 'C'
  selection = (chain 'D' and resid 308 through 375)
  selection = chain 'E'
  selection = (chain 'F' and resid 308 through 375)
  selection = (chain 'G' and resid 308 through 375)
  selection = chain 'H'
  selection = (chain 'I' and resid 308 through 375)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.870
  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:             0.190
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     27.430
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.030
  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:13.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6409
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      :  0.011   0.040   5025  Z= 0.674
  Angle     :  1.800   6.507   6723  Z= 1.186
  Chirality :  0.085   0.402    756
  Planarity :  0.009   0.066    855
  Dihedral  : 12.353  83.957   1920
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 0.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.17 %
    Favored  : 96.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.27), residues: 636
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.25 (0.21), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.012   0.003   HIS E 374 
 PHE   0.071   0.019   PHE C 346 
 TYR   0.123   0.015   TYR E 310 
 ARG   0.009   0.002   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07534 (   98)
  hydrogen bonds       : angle       7.90665 (  294)
  covalent geometry    : bond        0.01086 ( 5025)
  covalent geometry    : angle       1.80017 ( 6723)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 166
  time to evaluate  : 0.873 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  368 ASN cc_start: 0.5745 (m-40) cc_final: 0.5432 (m110)
REVERT: D  368 ASN cc_start: 0.4983 (m-40) cc_final: 0.4758 (m110)
REVERT: C  317 LYS cc_start: 0.8151 (mttt) cc_final: 0.7898 (mttm)
REVERT: C  338 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7812 (tt0)
REVERT: C  347 LYS cc_start: 0.8162 (mttt) cc_final: 0.7478 (pmtt)
REVERT: C  369 LYS cc_start: 0.8165 (ttmt) cc_final: 0.7439 (mtmt)
REVERT: A  311 LYS cc_start: 0.7844 (mttt) cc_final: 0.7414 (tttm)
REVERT: E  311 LYS cc_start: 0.7720 (mtmt) cc_final: 0.6994 (mmtm)
REVERT: E  347 LYS cc_start: 0.8054 (mttt) cc_final: 0.7608 (tttt)
REVERT: E  369 LYS cc_start: 0.7681 (ttmt) cc_final: 0.7048 (ttpm)
REVERT: G  311 LYS cc_start: 0.8106 (mttt) cc_final: 0.7610 (tttm)
REVERT: G  360 ILE cc_start: 0.8454 (mt) cc_final: 0.8228 (mp)
REVERT: H  340 LYS cc_start: 0.7485 (mttt) cc_final: 0.7134 (mtmp)
REVERT: H  347 LYS cc_start: 0.8031 (mttt) cc_final: 0.7218 (tttp)
REVERT: H  369 LYS cc_start: 0.7528 (ttmt) cc_final: 0.6759 (mtmt)
REVERT: H  372 GLU cc_start: 0.7438 (tt0) cc_final: 0.7180 (tt0)
REVERT: I  311 LYS cc_start: 0.7744 (mttt) cc_final: 0.6975 (mmtm)
REVERT: I  360 ILE cc_start: 0.8178 (mt) cc_final: 0.7751 (mm)
REVERT: I  375 LYS cc_start: 0.7171 (tttt) cc_final: 0.6581 (ttmm)
  outliers start: 1
  outliers final: 2
  residues processed: 167
  average time/residue: 2.4785
  time to fit residues: 429.8584
Evaluate side-chains
  97 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  328 ILE
Chi-restraints excluded: chain A residue  348 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 45 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 15 optimal weight:    7.9990
   chunk 30 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 28 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
D 336 GLN
F 368 ASN
A 327 ASN
G 327 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4675 r_free = 0.4675 target = 0.203112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.150665 restraints weight = 17060.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.4138 rms_B_bonded: 2.44
r_work: 0.3995 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3909 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.4025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   5025  Z= 0.240
  Angle     :  0.641   4.691   6723  Z= 0.329
  Chirality :  0.050   0.147    756
  Planarity :  0.004   0.024    855
  Dihedral  :  6.786  37.158    667
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 13.23 %
    Favored  : 83.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.28 (0.29), residues: 636
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.97 (0.22), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS E 374 
 PHE   0.007   0.001   PHE A 346 
 TYR   0.011   0.002   TYR A 310 
 ARG   0.004   0.001   ARG F 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02904 (   98)
  hydrogen bonds       : angle       5.24443 (  294)
  covalent geometry    : bond        0.00553 ( 5025)
  covalent geometry    : angle       0.64117 ( 6723)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.928 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  314 ASP cc_start: 0.4156 (t0) cc_final: 0.3940 (t70)
REVERT: B  353 LYS cc_start: 0.5972 (tttt) cc_final: 0.5750 (tmtm)
REVERT: B  368 ASN cc_start: 0.5877 (m-40) cc_final: 0.5583 (m110)
REVERT: D  321 LYS cc_start: 0.3248 (pptt) cc_final: 0.2581 (pmtt)
REVERT: D  368 ASN cc_start: 0.5095 (m-40) cc_final: 0.4752 (m110)
REVERT: F  325 LEU cc_start: 0.3878 (mt) cc_final: 0.3464 (mt)
REVERT: F  358 ASP cc_start: 0.6957 (p0) cc_final: 0.6498 (t0)
REVERT: F  368 ASN cc_start: 0.4783 (OUTLIER) cc_final: 0.4568 (m110)
REVERT: C  338 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8282 (tt0)
REVERT: C  347 LYS cc_start: 0.8354 (mttt) cc_final: 0.8092 (pmtt)
REVERT: C  369 LYS cc_start: 0.8512 (ttmt) cc_final: 0.8043 (mtmt)
REVERT: A  360 ILE cc_start: 0.8979 (mt) cc_final: 0.8706 (mm)
REVERT: E  311 LYS cc_start: 0.7969 (mtmt) cc_final: 0.7174 (mmtm)
REVERT: E  347 LYS cc_start: 0.8344 (mttt) cc_final: 0.8096 (tttt)
REVERT: E  369 LYS cc_start: 0.8411 (ttmt) cc_final: 0.8060 (tttm)
REVERT: H  369 LYS cc_start: 0.8413 (ttmt) cc_final: 0.7861 (mtmt)
REVERT: I  311 LYS cc_start: 0.8104 (mttt) cc_final: 0.7647 (mmtm)
REVERT: I  360 ILE cc_start: 0.8962 (mt) cc_final: 0.8678 (mm)
REVERT: I  375 LYS cc_start: 0.8143 (tttt) cc_final: 0.7819 (ttmm)
  outliers start: 18
  outliers final: 11
  residues processed: 119
  average time/residue: 2.3982
  time to fit residues: 297.2494
Evaluate side-chains
  99 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  336 GLN
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain D residue  353 LYS
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain F residue  328 ILE
Chi-restraints excluded: chain F residue  356 SER
Chi-restraints excluded: chain F residue  368 ASN
Chi-restraints excluded: chain C residue  340 LYS
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain G residue  320 SER
Chi-restraints excluded: chain I residue  315 LEU
Chi-restraints excluded: chain I residue  320 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 39 optimal weight:    0.0000
   chunk 36 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   chunk 13 optimal weight:    8.9990
   chunk 57 optimal weight:    0.3980
   chunk 9 optimal weight:    0.0050
   chunk 46 optimal weight:    5.9990
   chunk 14 optimal weight:   10.0000
   chunk 25 optimal weight:    9.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    1.2600

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4720 r_free = 0.4720 target = 0.206831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.153298 restraints weight = 17094.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.4190 rms_B_bonded: 2.27
r_work: 0.4069 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3986 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.4758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5025  Z= 0.107
  Angle     :  0.558   8.277   6723  Z= 0.281
  Chirality :  0.053   0.144    756
  Planarity :  0.003   0.028    855
  Dihedral  :  5.783  29.556    665
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 16.58 %
    Favored  : 80.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.28), residues: 636
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.98 (0.22), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E 374 
 PHE   0.005   0.001   PHE B 346 
 TYR   0.009   0.001   TYR A 310 
 ARG   0.001   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02418 (   98)
  hydrogen bonds       : angle       4.80526 (  294)
  covalent geometry    : bond        0.00255 ( 5025)
  covalent geometry    : angle       0.55799 ( 6723)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  314 ASP cc_start: 0.4225 (t0) cc_final: 0.3773 (t70)
REVERT: B  353 LYS cc_start: 0.5993 (tttt) cc_final: 0.5710 (tmtm)
REVERT: B  358 ASP cc_start: 0.7657 (p0) cc_final: 0.7428 (p0)
REVERT: D  368 ASN cc_start: 0.5042 (m-40) cc_final: 0.4711 (m110)
REVERT: D  372 GLU cc_start: 0.5486 (mm-30) cc_final: 0.4740 (mm-30)
REVERT: F  327 ASN cc_start: 0.3329 (m-40) cc_final: 0.2940 (m110)
REVERT: F  358 ASP cc_start: 0.6912 (p0) cc_final: 0.6635 (t0)
REVERT: C  338 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8237 (tt0)
REVERT: C  347 LYS cc_start: 0.8317 (mttt) cc_final: 0.8057 (pmtt)
REVERT: C  369 LYS cc_start: 0.8485 (ttmt) cc_final: 0.8033 (mtmt)
REVERT: A  360 ILE cc_start: 0.8960 (mt) cc_final: 0.8670 (mm)
REVERT: E  311 LYS cc_start: 0.7858 (mtmt) cc_final: 0.7036 (mmtt)
REVERT: E  347 LYS cc_start: 0.8313 (mttt) cc_final: 0.8050 (tttt)
REVERT: E  369 LYS cc_start: 0.8401 (ttmt) cc_final: 0.8049 (tttm)
REVERT: G  311 LYS cc_start: 0.8107 (tttm) cc_final: 0.7569 (tmmt)
REVERT: H  338 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8134 (tt0)
REVERT: H  369 LYS cc_start: 0.8381 (ttmt) cc_final: 0.7829 (mtmt)
REVERT: I  311 LYS cc_start: 0.8016 (mttt) cc_final: 0.7549 (mmtm)
REVERT: I  375 LYS cc_start: 0.8146 (tttt) cc_final: 0.7784 (ttmm)
  outliers start: 15
  outliers final: 11
  residues processed: 107
  average time/residue: 2.2886
  time to fit residues: 255.5893
Evaluate side-chains
  100 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain D residue  328 ILE
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain D residue  353 LYS
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain F residue  328 ILE
Chi-restraints excluded: chain F residue  339 VAL
Chi-restraints excluded: chain F residue  368 ASN
Chi-restraints excluded: chain G residue  320 SER
Chi-restraints excluded: chain I residue  315 LEU
Chi-restraints excluded: chain I residue  320 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 55 optimal weight:    0.4980
   chunk 12 optimal weight:   20.0000
   chunk 44 optimal weight:    5.9990
   chunk 25 optimal weight:    9.9990
   chunk 28 optimal weight:   10.0000
   chunk 32 optimal weight:    7.9990
   chunk 45 optimal weight:    0.7980
   chunk 59 optimal weight:    7.9990
   chunk 8 optimal weight:    0.5980
   chunk 38 optimal weight:    9.9990
   chunk 40 optimal weight:    0.0970
   overall best weight:    1.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 327 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4720 r_free = 0.4720 target = 0.207260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.155064 restraints weight = 16867.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.4201 rms_B_bonded: 2.47
r_work: 0.4065 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3980 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.5090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5025  Z= 0.111
  Angle     :  0.515   4.740   6723  Z= 0.258
  Chirality :  0.051   0.141    756
  Planarity :  0.003   0.031    855
  Dihedral  :  5.430  29.210    665
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 17.46 %
    Favored  : 79.72 %
  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: -1.26 (0.29), residues: 636
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.95 (0.22), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 374 
 PHE   0.004   0.001   PHE A 346 
 TYR   0.012   0.002   TYR C 310 
 ARG   0.001   0.000   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02253 (   98)
  hydrogen bonds       : angle       4.53083 (  294)
  covalent geometry    : bond        0.00257 ( 5025)
  covalent geometry    : angle       0.51535 ( 6723)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.874 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  314 ASP cc_start: 0.4293 (t0) cc_final: 0.3770 (t70)
REVERT: B  353 LYS cc_start: 0.6028 (tttt) cc_final: 0.5783 (tmtm)
REVERT: D  321 LYS cc_start: 0.3250 (pptt) cc_final: 0.2884 (pmtt)
REVERT: D  331 LYS cc_start: 0.5902 (mttt) cc_final: 0.4999 (pptt)
REVERT: D  368 ASN cc_start: 0.5067 (m-40) cc_final: 0.4785 (m110)
REVERT: D  372 GLU cc_start: 0.5409 (mm-30) cc_final: 0.4668 (mm-30)
REVERT: F  321 LYS cc_start: 0.6054 (OUTLIER) cc_final: 0.5568 (mtpp)
REVERT: F  325 LEU cc_start: 0.3696 (mt) cc_final: 0.3043 (mt)
REVERT: F  327 ASN cc_start: 0.3399 (m-40) cc_final: 0.3060 (m110)
REVERT: F  368 ASN cc_start: 0.5229 (OUTLIER) cc_final: 0.4983 (m110)
REVERT: C  311 LYS cc_start: 0.8075 (mtmt) cc_final: 0.7779 (mttt)
REVERT: C  338 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8294 (tt0)
REVERT: C  347 LYS cc_start: 0.8326 (mttt) cc_final: 0.8064 (pmtt)
REVERT: C  369 LYS cc_start: 0.8504 (ttmt) cc_final: 0.8242 (ttpm)
REVERT: A  360 ILE cc_start: 0.9006 (mt) cc_final: 0.8700 (mm)
REVERT: E  311 LYS cc_start: 0.7858 (mtmt) cc_final: 0.7029 (mmtt)
REVERT: E  347 LYS cc_start: 0.8338 (mttt) cc_final: 0.8046 (tttt)
REVERT: E  369 LYS cc_start: 0.8355 (ttmt) cc_final: 0.8070 (tttm)
REVERT: G  311 LYS cc_start: 0.8093 (tttm) cc_final: 0.7534 (tmmt)
REVERT: H  338 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8130 (tt0)
REVERT: H  369 LYS cc_start: 0.8412 (ttmt) cc_final: 0.7864 (mtmt)
REVERT: I  311 LYS cc_start: 0.8013 (mttt) cc_final: 0.7556 (mmtm)
REVERT: I  375 LYS cc_start: 0.8160 (tttt) cc_final: 0.7794 (ttmm)
  outliers start: 16
  outliers final: 11
  residues processed: 106
  average time/residue: 2.3675
  time to fit residues: 261.3959
Evaluate side-chains
  102 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain D residue  328 ILE
Chi-restraints excluded: chain D residue  339 VAL
Chi-restraints excluded: chain D residue  353 LYS
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain F residue  321 LYS
Chi-restraints excluded: chain F residue  328 ILE
Chi-restraints excluded: chain F residue  339 VAL
Chi-restraints excluded: chain F residue  368 ASN
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain G residue  320 SER
Chi-restraints excluded: chain I residue  315 LEU
Chi-restraints excluded: chain I residue  320 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 3 optimal weight:   30.0000
   chunk 10 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   chunk 26 optimal weight:    6.9990
   chunk 12 optimal weight:   20.0000
   chunk 11 optimal weight:    6.9990
   chunk 51 optimal weight:   10.0000
   chunk 44 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
D 336 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4691 r_free = 0.4691 target = 0.203948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.149603 restraints weight = 16941.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.4123 rms_B_bonded: 2.18
r_work: 0.4013 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3933 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.5331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   5025  Z= 0.144
  Angle     :  0.532   5.535   6723  Z= 0.268
  Chirality :  0.050   0.155    756
  Planarity :  0.003   0.034    855
  Dihedral  :  5.361  29.989    665
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 14.81 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.37 (0.28), residues: 636
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.03 (0.21), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 374 
 PHE   0.005   0.001   PHE A 346 
 TYR   0.011   0.002   TYR C 310 
 ARG   0.003   0.000   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02284 (   98)
  hydrogen bonds       : angle       4.46282 (  294)
  covalent geometry    : bond        0.00326 ( 5025)
  covalent geometry    : angle       0.53235 ( 6723)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 90
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  314 ASP cc_start: 0.4444 (t0) cc_final: 0.4152 (t70)
REVERT: B  353 LYS cc_start: 0.6085 (tttt) cc_final: 0.5859 (tmtp)
REVERT: D  321 LYS cc_start: 0.3054 (OUTLIER) cc_final: 0.2678 (pmtt)
REVERT: D  331 LYS cc_start: 0.6147 (mttt) cc_final: 0.5238 (pptt)
REVERT: D  368 ASN cc_start: 0.5215 (m-40) cc_final: 0.4952 (m110)
REVERT: D  372 GLU cc_start: 0.5288 (mm-30) cc_final: 0.4697 (mm-30)
REVERT: F  321 LYS cc_start: 0.6160 (OUTLIER) cc_final: 0.5633 (mtpp)
REVERT: F  325 LEU cc_start: 0.3747 (mt) cc_final: 0.3078 (mt)
REVERT: F  327 ASN cc_start: 0.3674 (m-40) cc_final: 0.3290 (m110)
REVERT: F  345 ASP cc_start: 0.4673 (m-30) cc_final: 0.4311 (m-30)
REVERT: F  358 ASP cc_start: 0.7006 (p0) cc_final: 0.6551 (t0)
REVERT: F  368 ASN cc_start: 0.5159 (OUTLIER) cc_final: 0.4936 (m110)
REVERT: C  311 LYS cc_start: 0.8095 (mtmt) cc_final: 0.7815 (mttt)
REVERT: C  338 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8247 (tt0)
REVERT: C  347 LYS cc_start: 0.8334 (mttt) cc_final: 0.8106 (pmtt)
REVERT: A  360 ILE cc_start: 0.9022 (mt) cc_final: 0.8702 (mm)
REVERT: E  311 LYS cc_start: 0.7877 (mtmt) cc_final: 0.7088 (mmtm)
REVERT: E  347 LYS cc_start: 0.8339 (mttt) cc_final: 0.8071 (tttt)
REVERT: E  369 LYS cc_start: 0.8354 (ttmt) cc_final: 0.8082 (tttm)
REVERT: H  369 LYS cc_start: 0.8416 (ttmt) cc_final: 0.7872 (ttmt)
REVERT: I  311 LYS cc_start: 0.8044 (mttt) cc_final: 0.7570 (mmtm)
REVERT: I  375 LYS cc_start: 0.8163 (tttt) cc_final: 0.7822 (ttmm)
  outliers start: 26
  outliers final: 14
  residues processed: 110
  average time/residue: 2.3445
  time to fit residues: 268.9278
Evaluate side-chains
  103 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain D residue  321 LYS
Chi-restraints excluded: chain D residue  339 VAL
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain D residue  353 LYS
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain F residue  321 LYS
Chi-restraints excluded: chain F residue  328 ILE
Chi-restraints excluded: chain F residue  339 VAL
Chi-restraints excluded: chain F residue  356 SER
Chi-restraints excluded: chain F residue  368 ASN
Chi-restraints excluded: chain C residue  340 LYS
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain G residue  320 SER
Chi-restraints excluded: chain I residue  315 LEU
Chi-restraints excluded: chain I residue  320 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 19 optimal weight:   20.0000
   chunk 15 optimal weight:   20.0000
   chunk 23 optimal weight:    5.9990
   chunk 40 optimal weight:    5.9990
   chunk 6 optimal weight:   20.0000
   chunk 52 optimal weight:    7.9990
   chunk 24 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 9 optimal weight:   20.0000
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
D 336 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4681 r_free = 0.4681 target = 0.203232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.150273 restraints weight = 17109.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.4145 rms_B_bonded: 2.11
r_work: 0.4037 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3957 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.3957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.5662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5025  Z= 0.131
  Angle     :  0.512   4.887   6723  Z= 0.260
  Chirality :  0.051   0.155    756
  Planarity :  0.003   0.035    855
  Dihedral  :  5.235  29.792    665
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 15.87 %
    Favored  : 80.25 %
  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: -1.44 (0.28), residues: 636
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.09 (0.21), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 374 
 PHE   0.004   0.001   PHE A 346 
 TYR   0.010   0.002   TYR C 310 
 ARG   0.003   0.001   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02127 (   98)
  hydrogen bonds       : angle       4.28655 (  294)
  covalent geometry    : bond        0.00299 ( 5025)
  covalent geometry    : angle       0.51225 ( 6723)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 88
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  314 ASP cc_start: 0.4611 (t0) cc_final: 0.4101 (t70)
REVERT: B  353 LYS cc_start: 0.6016 (tttt) cc_final: 0.5794 (tttm)
REVERT: D  314 ASP cc_start: 0.4366 (t70) cc_final: 0.4069 (t70)
REVERT: D  321 LYS cc_start: 0.2810 (OUTLIER) cc_final: 0.2571 (pmtt)
REVERT: D  331 LYS cc_start: 0.6161 (mttt) cc_final: 0.5253 (pptt)
REVERT: D  368 ASN cc_start: 0.5329 (m-40) cc_final: 0.5080 (m110)
REVERT: D  372 GLU cc_start: 0.4942 (mm-30) cc_final: 0.4179 (mm-30)
REVERT: F  321 LYS cc_start: 0.6318 (OUTLIER) cc_final: 0.5771 (mtpp)
REVERT: F  325 LEU cc_start: 0.3687 (mt) cc_final: 0.2971 (mt)
REVERT: F  327 ASN cc_start: 0.3934 (m-40) cc_final: 0.3465 (m110)
REVERT: F  348 ASP cc_start: 0.4214 (t0) cc_final: 0.3876 (t0)
REVERT: C  311 LYS cc_start: 0.8098 (mtmt) cc_final: 0.7802 (mttt)
REVERT: C  338 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8250 (tt0)
REVERT: C  347 LYS cc_start: 0.8331 (mttt) cc_final: 0.8098 (pmtt)
REVERT: C  375 LYS cc_start: 0.5503 (tmtt) cc_final: 0.4953 (tptp)
REVERT: A  360 ILE cc_start: 0.9033 (mt) cc_final: 0.8714 (mm)
REVERT: E  311 LYS cc_start: 0.7890 (mtmt) cc_final: 0.7125 (mmtm)
REVERT: E  347 LYS cc_start: 0.8363 (mttt) cc_final: 0.8062 (tttt)
REVERT: E  369 LYS cc_start: 0.8329 (ttmt) cc_final: 0.8047 (tttm)
REVERT: H  369 LYS cc_start: 0.8398 (ttmt) cc_final: 0.7867 (ttmt)
REVERT: I  311 LYS cc_start: 0.8045 (mttt) cc_final: 0.7551 (mmtm)
REVERT: I  375 LYS cc_start: 0.8143 (tttt) cc_final: 0.7786 (ttmm)
  outliers start: 22
  outliers final: 13
  residues processed: 105
  average time/residue: 2.3802
  time to fit residues: 260.9225
Evaluate side-chains
  101 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain D residue  321 LYS
Chi-restraints excluded: chain D residue  328 ILE
Chi-restraints excluded: chain D residue  336 GLN
Chi-restraints excluded: chain D residue  339 VAL
Chi-restraints excluded: chain D residue  353 LYS
Chi-restraints excluded: chain F residue  321 LYS
Chi-restraints excluded: chain F residue  328 ILE
Chi-restraints excluded: chain F residue  339 VAL
Chi-restraints excluded: chain C residue  340 LYS
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain G residue  320 SER
Chi-restraints excluded: chain I residue  315 LEU
Chi-restraints excluded: chain I residue  320 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 32 optimal weight:   10.0000
   chunk 11 optimal weight:    6.9990
   chunk 49 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 3 optimal weight:    9.9990
   chunk 16 optimal weight:    4.9990
   chunk 29 optimal weight:    6.9990
   chunk 13 optimal weight:    9.9990
   chunk 54 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 336 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4677 r_free = 0.4677 target = 0.202614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.150592 restraints weight = 17358.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.4147 rms_B_bonded: 2.32
r_work: 0.4029 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3950 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.5807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   5025  Z= 0.145
  Angle     :  0.515   5.099   6723  Z= 0.261
  Chirality :  0.050   0.158    756
  Planarity :  0.003   0.037    855
  Dihedral  :  5.218  29.836    665
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 16.23 %
    Favored  : 80.25 %
  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: -1.47 (0.28), residues: 636
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.11 (0.21), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F 329 
 PHE   0.005   0.001   PHE A 346 
 TYR   0.009   0.002   TYR C 310 
 ARG   0.004   0.001   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02211 (   98)
  hydrogen bonds       : angle       4.17174 (  294)
  covalent geometry    : bond        0.00333 ( 5025)
  covalent geometry    : angle       0.51451 ( 6723)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 85
  time to evaluate  : 1.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  314 ASP cc_start: 0.4603 (t0) cc_final: 0.4068 (t70)
REVERT: B  353 LYS cc_start: 0.6101 (tttt) cc_final: 0.5844 (tttm)
REVERT: D  321 LYS cc_start: 0.2873 (OUTLIER) cc_final: 0.2559 (pmtt)
REVERT: D  331 LYS cc_start: 0.6182 (mttt) cc_final: 0.5271 (pptt)
REVERT: D  368 ASN cc_start: 0.5313 (m-40) cc_final: 0.5068 (m110)
REVERT: D  372 GLU cc_start: 0.4879 (mm-30) cc_final: 0.4193 (mm-30)
REVERT: F  321 LYS cc_start: 0.6262 (OUTLIER) cc_final: 0.5681 (mtpp)
REVERT: F  325 LEU cc_start: 0.3663 (mt) cc_final: 0.2962 (mt)
REVERT: F  327 ASN cc_start: 0.3845 (m-40) cc_final: 0.3462 (m110)
REVERT: F  368 ASN cc_start: 0.5091 (OUTLIER) cc_final: 0.4843 (m110)
REVERT: C  311 LYS cc_start: 0.8105 (mtmt) cc_final: 0.7802 (mttt)
REVERT: C  338 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8282 (tt0)
REVERT: C  342 GLU cc_start: 0.8002 (tt0) cc_final: 0.7702 (tp30)
REVERT: C  347 LYS cc_start: 0.8363 (mttt) cc_final: 0.8104 (pmtt)
REVERT: C  375 LYS cc_start: 0.5445 (tmtt) cc_final: 0.4948 (tptp)
REVERT: A  360 ILE cc_start: 0.9044 (mt) cc_final: 0.8717 (mm)
REVERT: E  311 LYS cc_start: 0.7880 (mtmt) cc_final: 0.7145 (mmtm)
REVERT: E  347 LYS cc_start: 0.8373 (mttt) cc_final: 0.8058 (tttt)
REVERT: E  369 LYS cc_start: 0.8334 (ttmt) cc_final: 0.8041 (tttm)
REVERT: H  369 LYS cc_start: 0.8388 (ttmt) cc_final: 0.7945 (ttmt)
REVERT: I  311 LYS cc_start: 0.8106 (mttt) cc_final: 0.7597 (mmtm)
REVERT: I  375 LYS cc_start: 0.8146 (tttt) cc_final: 0.7777 (ttmm)
  outliers start: 20
  outliers final: 14
  residues processed: 102
  average time/residue: 2.6163
  time to fit residues: 279.8441
Evaluate side-chains
  98 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  368 ASN
Chi-restraints excluded: chain D residue  321 LYS
Chi-restraints excluded: chain D residue  328 ILE
Chi-restraints excluded: chain D residue  339 VAL
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain D residue  353 LYS
Chi-restraints excluded: chain F residue  321 LYS
Chi-restraints excluded: chain F residue  328 ILE
Chi-restraints excluded: chain F residue  339 VAL
Chi-restraints excluded: chain F residue  368 ASN
Chi-restraints excluded: chain C residue  340 LYS
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain G residue  320 SER
Chi-restraints excluded: chain I residue  320 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 5 optimal weight:   30.0000
   chunk 16 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   chunk 49 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 18 optimal weight:   20.0000
   chunk 26 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 54 optimal weight:    8.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B 336 GLN ** 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 = 0.4636 r_free = 0.4636 target = 0.198706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.148182 restraints weight = 17363.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.4106 rms_B_bonded: 2.00
r_work: 0.3964 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3883 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.6134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   5025  Z= 0.220
  Angle     :  0.568   4.341   6723  Z= 0.291
  Chirality :  0.050   0.158    756
  Planarity :  0.004   0.039    855
  Dihedral  :  5.637  30.654    665
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 16.05 %
    Favored  : 80.07 %
  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: -1.59 (0.28), residues: 636
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.20 (0.21), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 374 
 PHE   0.010   0.002   PHE D 346 
 TYR   0.013   0.002   TYR A 310 
 ARG   0.002   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02391 (   98)
  hydrogen bonds       : angle       4.35639 (  294)
  covalent geometry    : bond        0.00495 ( 5025)
  covalent geometry    : angle       0.56831 ( 6723)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 80
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  314 ASP cc_start: 0.4821 (t0) cc_final: 0.4373 (t70)
REVERT: B  353 LYS cc_start: 0.6132 (tttt) cc_final: 0.5858 (mptp)
REVERT: D  321 LYS cc_start: 0.3013 (OUTLIER) cc_final: 0.2683 (pmtt)
REVERT: D  331 LYS cc_start: 0.6247 (mttt) cc_final: 0.5396 (pptt)
REVERT: D  372 GLU cc_start: 0.4901 (mm-30) cc_final: 0.4181 (mm-30)
REVERT: F  321 LYS cc_start: 0.6411 (OUTLIER) cc_final: 0.6133 (mmpt)
REVERT: F  325 LEU cc_start: 0.3914 (mt) cc_final: 0.3301 (mt)
REVERT: F  327 ASN cc_start: 0.4087 (m-40) cc_final: 0.3749 (m110)
REVERT: F  368 ASN cc_start: 0.5061 (OUTLIER) cc_final: 0.4798 (m110)
REVERT: C  342 GLU cc_start: 0.8074 (tt0) cc_final: 0.7826 (tp30)
REVERT: A  349 ARG cc_start: 0.8093 (mtm180) cc_final: 0.7819 (mtp85)
REVERT: E  311 LYS cc_start: 0.7988 (mtmt) cc_final: 0.7143 (mmpt)
REVERT: E  347 LYS cc_start: 0.8371 (mttt) cc_final: 0.8112 (tttt)
REVERT: E  369 LYS cc_start: 0.8403 (ttmt) cc_final: 0.8104 (tttm)
REVERT: E  372 GLU cc_start: 0.8093 (tt0) cc_final: 0.7763 (tt0)
REVERT: H  369 LYS cc_start: 0.8433 (ttmt) cc_final: 0.8026 (ttmt)
REVERT: I  375 LYS cc_start: 0.8164 (tttt) cc_final: 0.7818 (ttmm)
  outliers start: 22
  outliers final: 13
  residues processed: 97
  average time/residue: 2.3973
  time to fit residues: 242.8055
Evaluate side-chains
  87 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  368 ASN
Chi-restraints excluded: chain D residue  321 LYS
Chi-restraints excluded: chain D residue  339 VAL
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain D residue  353 LYS
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain F residue  321 LYS
Chi-restraints excluded: chain F residue  328 ILE
Chi-restraints excluded: chain F residue  356 SER
Chi-restraints excluded: chain F residue  368 ASN
Chi-restraints excluded: chain C residue  340 LYS
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain G residue  320 SER
Chi-restraints excluded: chain I residue  320 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 34 optimal weight:    1.9990
   chunk 13 optimal weight:    9.9990
   chunk 50 optimal weight:    8.9990
   chunk 25 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 10 optimal weight:   10.0000
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
B 336 GLN
B 368 ASN
D 368 ASN
F 368 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4655 r_free = 0.4655 target = 0.200987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.150758 restraints weight = 17470.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.4134 rms_B_bonded: 2.31
r_work: 0.3995 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3907 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.6402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   5025  Z= 0.111
  Angle     :  0.509   4.155   6723  Z= 0.256
  Chirality :  0.051   0.158    756
  Planarity :  0.004   0.043    855
  Dihedral  :  5.215  29.846    665
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 18.52 %
    Favored  : 79.01 %
  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: -1.62 (0.27), residues: 636
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.22 (0.21), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 374 
 PHE   0.004   0.001   PHE D 346 
 TYR   0.009   0.001   TYR C 310 
 ARG   0.001   0.000   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02177 (   98)
  hydrogen bonds       : angle       4.18817 (  294)
  covalent geometry    : bond        0.00258 ( 5025)
  covalent geometry    : angle       0.50852 ( 6723)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.940 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  314 ASP cc_start: 0.4813 (t0) cc_final: 0.4131 (t70)
REVERT: B  353 LYS cc_start: 0.6076 (tttt) cc_final: 0.5854 (mptp)
REVERT: D  321 LYS cc_start: 0.3067 (OUTLIER) cc_final: 0.2727 (pmtt)
REVERT: D  331 LYS cc_start: 0.6218 (mttt) cc_final: 0.5365 (pptt)
REVERT: D  372 GLU cc_start: 0.4880 (mm-30) cc_final: 0.4237 (mm-30)
REVERT: F  321 LYS cc_start: 0.6401 (OUTLIER) cc_final: 0.6119 (mmpt)
REVERT: F  325 LEU cc_start: 0.3947 (mt) cc_final: 0.3342 (mt)
REVERT: F  327 ASN cc_start: 0.4186 (m-40) cc_final: 0.3859 (m110)
REVERT: F  368 ASN cc_start: 0.5051 (OUTLIER) cc_final: 0.4812 (m-40)
REVERT: C  342 GLU cc_start: 0.8094 (tt0) cc_final: 0.7857 (tp30)
REVERT: A  349 ARG cc_start: 0.8063 (mtm180) cc_final: 0.7825 (mtp85)
REVERT: E  311 LYS cc_start: 0.7931 (mtmt) cc_final: 0.7231 (mmtm)
REVERT: E  347 LYS cc_start: 0.8367 (mttt) cc_final: 0.8094 (tttt)
REVERT: E  369 LYS cc_start: 0.8419 (ttmt) cc_final: 0.8138 (tttm)
REVERT: H  369 LYS cc_start: 0.8422 (ttmt) cc_final: 0.8029 (ttmt)
REVERT: I  375 LYS cc_start: 0.8190 (tttt) cc_final: 0.7849 (ttmm)
  outliers start: 14
  outliers final: 10
  residues processed: 84
  average time/residue: 2.3497
  time to fit residues: 206.9873
Evaluate side-chains
  83 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  368 ASN
Chi-restraints excluded: chain D residue  321 LYS
Chi-restraints excluded: chain D residue  339 VAL
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain D residue  353 LYS
Chi-restraints excluded: chain D residue  368 ASN
Chi-restraints excluded: chain F residue  321 LYS
Chi-restraints excluded: chain F residue  328 ILE
Chi-restraints excluded: chain F residue  368 ASN
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain G residue  320 SER
Chi-restraints excluded: chain I residue  320 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 5 optimal weight:    7.9990
   chunk 6 optimal weight:   10.0000
   chunk 52 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 50 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 27 optimal weight:   10.0000
   chunk 55 optimal weight:    0.9990
   overall best weight:    1.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4658 r_free = 0.4658 target = 0.201166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.150005 restraints weight = 17502.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.4128 rms_B_bonded: 2.08
r_work: 0.4011 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3929 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.3929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.6437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5025  Z= 0.119
  Angle     :  0.515   4.141   6723  Z= 0.265
  Chirality :  0.051   0.198    756
  Planarity :  0.003   0.043    855
  Dihedral  :  5.204  29.507    665
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 18.87 %
    Favored  : 78.84 %
  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: -1.60 (0.28), residues: 636
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.21 (0.21), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 374 
 PHE   0.005   0.001   PHE D 346 
 TYR   0.009   0.001   TYR C 310 
 ARG   0.001   0.000   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02182 (   98)
  hydrogen bonds       : angle       4.16136 (  294)
  covalent geometry    : bond        0.00277 ( 5025)
  covalent geometry    : angle       0.51524 ( 6723)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 1.030 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  353 LYS cc_start: 0.6061 (tttt) cc_final: 0.5856 (mptp)
REVERT: B  358 ASP cc_start: 0.7526 (p0) cc_final: 0.7289 (p0)
REVERT: D  321 LYS cc_start: 0.3037 (OUTLIER) cc_final: 0.2692 (pmtt)
REVERT: D  331 LYS cc_start: 0.6263 (mttt) cc_final: 0.5409 (pptt)
REVERT: D  372 GLU cc_start: 0.4863 (mm-30) cc_final: 0.4229 (mm-30)
REVERT: F  321 LYS cc_start: 0.6461 (OUTLIER) cc_final: 0.6180 (mmpt)
REVERT: F  325 LEU cc_start: 0.4037 (mt) cc_final: 0.3443 (mp)
REVERT: F  327 ASN cc_start: 0.4209 (m-40) cc_final: 0.3906 (m110)
REVERT: F  368 ASN cc_start: 0.4956 (OUTLIER) cc_final: 0.4663 (m110)
REVERT: C  342 GLU cc_start: 0.8062 (tt0) cc_final: 0.7835 (tp30)
REVERT: A  349 ARG cc_start: 0.8067 (mtm180) cc_final: 0.7837 (mtp85)
REVERT: E  311 LYS cc_start: 0.7928 (mtmt) cc_final: 0.7245 (mmtm)
REVERT: E  347 LYS cc_start: 0.8371 (mttt) cc_final: 0.8113 (tttt)
REVERT: E  369 LYS cc_start: 0.8403 (ttmt) cc_final: 0.8126 (tttm)
REVERT: E  372 GLU cc_start: 0.8092 (tt0) cc_final: 0.7790 (tt0)
REVERT: H  369 LYS cc_start: 0.8413 (ttmt) cc_final: 0.8017 (ttmt)
REVERT: I  375 LYS cc_start: 0.8167 (tttt) cc_final: 0.7813 (ttmm)
  outliers start: 13
  outliers final: 9
  residues processed: 84
  average time/residue: 2.6310
  time to fit residues: 230.9957
Evaluate side-chains
  82 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain D residue  321 LYS
Chi-restraints excluded: chain D residue  339 VAL
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain D residue  353 LYS
Chi-restraints excluded: chain F residue  321 LYS
Chi-restraints excluded: chain F residue  328 ILE
Chi-restraints excluded: chain F residue  368 ASN
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain G residue  320 SER
Chi-restraints excluded: chain I residue  320 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 56 optimal weight:    5.9990
   chunk 4 optimal weight:   10.0000
   chunk 22 optimal weight:    7.9990
   chunk 28 optimal weight:   10.0000
   chunk 26 optimal weight:    0.3980
   chunk 45 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 3 optimal weight:    5.9990
   chunk 6 optimal weight:   20.0000
   chunk 29 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   overall best weight:    2.4786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4661 r_free = 0.4661 target = 0.201099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.145545 restraints weight = 17322.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.4106 rms_B_bonded: 1.81
r_work: 0.4027 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.3953 rms_B_bonded: 2.96 restraints_weight: 0.2500
r_work (final): 0.3953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.6562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5025  Z= 0.131
  Angle     :  0.504   4.149   6723  Z= 0.254
  Chirality :  0.050   0.154    756
  Planarity :  0.003   0.043    855
  Dihedral  :  5.087  29.015    665
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 19.22 %
    Favored  : 78.66 %
  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: -1.61 (0.27), residues: 636
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.22 (0.21), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C 374 
 PHE   0.006   0.001   PHE D 346 
 TYR   0.010   0.001   TYR C 310 
 ARG   0.001   0.000   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02151 (   98)
  hydrogen bonds       : angle       4.12193 (  294)
  covalent geometry    : bond        0.00301 ( 5025)
  covalent geometry    : angle       0.50401 ( 6723)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9119.42 seconds
wall clock time: 158 minutes 34.27 seconds (9514.27 seconds total)