Starting phenix.real_space_refine
on Sun Apr 27 14:07:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b4n_44186/04_2025/9b4n_44186.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b4n_44186/04_2025/9b4n_44186.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b4n_44186/04_2025/9b4n_44186.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b4n_44186/04_2025/9b4n_44186.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b4n_44186/04_2025/9b4n_44186.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b4n_44186/04_2025/9b4n_44186.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      10      5.16       5
     C    3670      2.51       5
     N    1080      2.21       5
     O    1110      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 5870
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 587
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, J
  Time building chain proxies: 3.81, per 1000 atoms: 0.65
  Number of scatterers: 5870
  At special positions: 0
  Unit cell: (78.96, 147.58, 45.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      10     16.00
     O    1110      8.00
     N    1080      7.00
     C    3670      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.29
  Conformation dependent library (CDL) restraints added in 645.4 milliseconds
  

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1340

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 16 sheets defined
      0.0% alpha, 48.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310
      removed outlier: 6.320A  pdb=" N   VAL A 306 " --> pdb=" O   GLN D 307 " (cutoff:3.500A)
      removed outlier: 7.871A  pdb=" N   VAL D 309 " --> pdb=" O   VAL A 306 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   ILE A 308 " --> pdb=" O   VAL D 309 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   VAL D 306 " --> pdb=" O   GLN F 307 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   VAL F 309 " --> pdb=" O   VAL D 306 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   ILE D 308 " --> pdb=" O   VAL F 309 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   VAL F 306 " --> pdb=" O   GLN H 307 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   VAL H 309 " --> pdb=" O   VAL F 306 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   ILE F 308 " --> pdb=" O   VAL H 309 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   VAL H 306 " --> pdb=" O   GLN J 307 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   VAL J 309 " --> pdb=" O   VAL H 306 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   ILE H 308 " --> pdb=" O   VAL J 309 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314
    Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 318
    Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 330
      removed outlier: 9.069A  pdb=" N   CYS A 322 " --> pdb=" O   GLY D 323 " (cutoff:3.500A)
      removed outlier: 7.258A  pdb=" N   LEU D 325 " --> pdb=" O   CYS A 322 " (cutoff:3.500A)
      removed outlier: 9.439A  pdb=" N   SER A 324 " --> pdb=" O   LEU D 325 " (cutoff:3.500A)
      removed outlier: 10.400A  pdb=" N   ASN D 327 " --> pdb=" O   SER A 324 " (cutoff:3.500A)
      removed outlier: 5.874A  pdb=" N   GLY A 326 " --> pdb=" O   ASN D 327 " (cutoff:3.500A)
      removed outlier: 8.212A  pdb=" N   HIS D 329 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   ILE A 328 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
      removed outlier: 9.070A  pdb=" N   CYS D 322 " --> pdb=" O   GLY F 323 " (cutoff:3.500A)
      removed outlier: 7.258A  pdb=" N   LEU F 325 " --> pdb=" O   CYS D 322 " (cutoff:3.500A)
      removed outlier: 9.438A  pdb=" N   SER D 324 " --> pdb=" O   LEU F 325 " (cutoff:3.500A)
      removed outlier: 10.401A  pdb=" N   ASN F 327 " --> pdb=" O   SER D 324 " (cutoff:3.500A)
      removed outlier: 5.873A  pdb=" N   GLY D 326 " --> pdb=" O   ASN F 327 " (cutoff:3.500A)
      removed outlier: 8.212A  pdb=" N   HIS F 329 " --> pdb=" O   GLY D 326 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   ILE D 328 " --> pdb=" O   HIS F 329 " (cutoff:3.500A)
      removed outlier: 9.070A  pdb=" N   CYS F 322 " --> pdb=" O   GLY H 323 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   LEU H 325 " --> pdb=" O   CYS F 322 " (cutoff:3.500A)
      removed outlier: 9.439A  pdb=" N   SER F 324 " --> pdb=" O   LEU H 325 " (cutoff:3.500A)
      removed outlier: 10.401A  pdb=" N   ASN H 327 " --> pdb=" O   SER F 324 " (cutoff:3.500A)
      removed outlier: 5.874A  pdb=" N   GLY F 326 " --> pdb=" O   ASN H 327 " (cutoff:3.500A)
      removed outlier: 8.211A  pdb=" N   HIS H 329 " --> pdb=" O   GLY F 326 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   ILE F 328 " --> pdb=" O   HIS H 329 " (cutoff:3.500A)
      removed outlier: 9.070A  pdb=" N   CYS H 322 " --> pdb=" O   GLY J 323 " (cutoff:3.500A)
      removed outlier: 7.258A  pdb=" N   LEU J 325 " --> pdb=" O   CYS H 322 " (cutoff:3.500A)
      removed outlier: 9.439A  pdb=" N   SER H 324 " --> pdb=" O   LEU J 325 " (cutoff:3.500A)
      removed outlier: 10.401A  pdb=" N   ASN J 327 " --> pdb=" O   SER H 324 " (cutoff:3.500A)
      removed outlier: 5.874A  pdb=" N   GLY H 326 " --> pdb=" O   ASN J 327 " (cutoff:3.500A)
      removed outlier: 8.212A  pdb=" N   HIS J 329 " --> pdb=" O   GLY H 326 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   ILE H 328 " --> pdb=" O   HIS J 329 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340
    Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 346
    Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 362
      removed outlier: 6.939A  pdb=" N   GLY A 355 " --> pdb=" O   SER D 356 " (cutoff:3.500A)
      removed outlier: 8.179A  pdb=" N   ASP D 358 " --> pdb=" O   GLY A 355 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   LEU A 357 " --> pdb=" O   ASP D 358 " (cutoff:3.500A)
      removed outlier: 8.214A  pdb=" N   ILE D 360 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   ASN A 359 " --> pdb=" O   ILE D 360 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   HIS D 362 " --> pdb=" O   ASN A 359 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   THR A 361 " --> pdb=" O   HIS D 362 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   GLY D 355 " --> pdb=" O   SER F 356 " (cutoff:3.500A)
      removed outlier: 8.179A  pdb=" N   ASP F 358 " --> pdb=" O   GLY D 355 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   LEU D 357 " --> pdb=" O   ASP F 358 " (cutoff:3.500A)
      removed outlier: 8.214A  pdb=" N   ILE F 360 " --> pdb=" O   LEU D 357 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ASN D 359 " --> pdb=" O   ILE F 360 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   HIS F 362 " --> pdb=" O   ASN D 359 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   THR D 361 " --> pdb=" O   HIS F 362 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   GLY F 355 " --> pdb=" O   SER H 356 " (cutoff:3.500A)
      removed outlier: 8.180A  pdb=" N   ASP H 358 " --> pdb=" O   GLY F 355 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   LEU F 357 " --> pdb=" O   ASP H 358 " (cutoff:3.500A)
      removed outlier: 8.215A  pdb=" N   ILE H 360 " --> pdb=" O   LEU F 357 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   ASN F 359 " --> pdb=" O   ILE H 360 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   HIS H 362 " --> pdb=" O   ASN F 359 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   THR F 361 " --> pdb=" O   HIS H 362 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   GLY H 355 " --> pdb=" O   SER J 356 " (cutoff:3.500A)
      removed outlier: 8.180A  pdb=" N   ASP J 358 " --> pdb=" O   GLY H 355 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   LEU H 357 " --> pdb=" O   ASP J 358 " (cutoff:3.500A)
      removed outlier: 8.214A  pdb=" N   ILE J 360 " --> pdb=" O   LEU H 357 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   ASN H 359 " --> pdb=" O   ILE J 360 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   HIS J 362 " --> pdb=" O   ASN H 359 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   THR H 361 " --> pdb=" O   HIS J 362 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 378
    Processing sheet with id=AA9, first strand: chain 'C' and resid 306 through 310
      removed outlier: 6.320A  pdb=" N   VAL B 306 " --> pdb=" O   GLN E 307 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   VAL E 309 " --> pdb=" O   VAL B 306 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   ILE B 308 " --> pdb=" O   VAL E 309 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   VAL E 306 " --> pdb=" O   GLN G 307 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   VAL G 309 " --> pdb=" O   VAL E 306 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   ILE E 308 " --> pdb=" O   VAL G 309 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   VAL G 306 " --> pdb=" O   GLN I 307 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   VAL I 309 " --> pdb=" O   VAL G 306 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   ILE G 308 " --> pdb=" O   VAL I 309 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 313 through 314
      removed outlier: 6.655A  pdb=" N   VAL B 313 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 317 through 318
      removed outlier: 6.701A  pdb=" N   LYS B 317 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 321 through 330
      removed outlier: 6.819A  pdb=" N   SER C 324 " --> pdb=" O   GLY B 323 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   LEU B 325 " --> pdb=" O   SER C 324 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   GLY C 326 " --> pdb=" O   LEU B 325 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   ASN B 327 " --> pdb=" O   GLY C 326 " (cutoff:3.500A)
      removed outlier: 9.069A  pdb=" N   CYS B 322 " --> pdb=" O   GLY E 323 " (cutoff:3.500A)
      removed outlier: 7.258A  pdb=" N   LEU E 325 " --> pdb=" O   CYS B 322 " (cutoff:3.500A)
      removed outlier: 9.439A  pdb=" N   SER B 324 " --> pdb=" O   LEU E 325 " (cutoff:3.500A)
      removed outlier: 10.400A  pdb=" N   ASN E 327 " --> pdb=" O   SER B 324 " (cutoff:3.500A)
      removed outlier: 5.874A  pdb=" N   GLY B 326 " --> pdb=" O   ASN E 327 " (cutoff:3.500A)
      removed outlier: 8.212A  pdb=" N   HIS E 329 " --> pdb=" O   GLY B 326 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   ILE B 328 " --> pdb=" O   HIS E 329 " (cutoff:3.500A)
      removed outlier: 9.070A  pdb=" N   CYS E 322 " --> pdb=" O   GLY G 323 " (cutoff:3.500A)
      removed outlier: 7.258A  pdb=" N   LEU G 325 " --> pdb=" O   CYS E 322 " (cutoff:3.500A)
      removed outlier: 9.439A  pdb=" N   SER E 324 " --> pdb=" O   LEU G 325 " (cutoff:3.500A)
      removed outlier: 10.401A  pdb=" N   ASN G 327 " --> pdb=" O   SER E 324 " (cutoff:3.500A)
      removed outlier: 5.874A  pdb=" N   GLY E 326 " --> pdb=" O   ASN G 327 " (cutoff:3.500A)
      removed outlier: 8.212A  pdb=" N   HIS G 329 " --> pdb=" O   GLY E 326 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   ILE E 328 " --> pdb=" O   HIS G 329 " (cutoff:3.500A)
      removed outlier: 9.070A  pdb=" N   CYS G 322 " --> pdb=" O   GLY I 323 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   LEU I 325 " --> pdb=" O   CYS G 322 " (cutoff:3.500A)
      removed outlier: 9.439A  pdb=" N   SER G 324 " --> pdb=" O   LEU I 325 " (cutoff:3.500A)
      removed outlier: 10.400A  pdb=" N   ASN I 327 " --> pdb=" O   SER G 324 " (cutoff:3.500A)
      removed outlier: 5.873A  pdb=" N   GLY G 326 " --> pdb=" O   ASN I 327 " (cutoff:3.500A)
      removed outlier: 8.212A  pdb=" N   HIS I 329 " --> pdb=" O   GLY G 326 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   ILE G 328 " --> pdb=" O   HIS I 329 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 336 through 340
      removed outlier: 6.627A  pdb=" N   GLN B 336 " --> pdb=" O   VAL C 337 " (cutoff:3.500A)
      removed outlier: 8.423A  pdb=" N   VAL C 339 " --> pdb=" O   GLN B 336 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   GLU B 338 " --> pdb=" O   VAL C 339 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 345 through 346
      removed outlier: 6.394A  pdb=" N   ASP B 345 " --> pdb=" O   PHE C 346 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 354 through 362
      removed outlier: 6.964A  pdb=" N   GLY C 355 " --> pdb=" O   ILE B 354 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   GLY B 355 " --> pdb=" O   SER E 356 " (cutoff:3.500A)
      removed outlier: 8.180A  pdb=" N   ASP E 358 " --> pdb=" O   GLY B 355 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   LEU B 357 " --> pdb=" O   ASP E 358 " (cutoff:3.500A)
      removed outlier: 8.214A  pdb=" N   ILE E 360 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ASN B 359 " --> pdb=" O   ILE E 360 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   HIS E 362 " --> pdb=" O   ASN B 359 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   THR B 361 " --> pdb=" O   HIS E 362 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   GLY E 355 " --> pdb=" O   SER G 356 " (cutoff:3.500A)
      removed outlier: 8.180A  pdb=" N   ASP G 358 " --> pdb=" O   GLY E 355 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   LEU E 357 " --> pdb=" O   ASP G 358 " (cutoff:3.500A)
      removed outlier: 8.214A  pdb=" N   ILE G 360 " --> pdb=" O   LEU E 357 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   ASN E 359 " --> pdb=" O   ILE G 360 " (cutoff:3.500A)
      removed outlier: 7.773A  pdb=" N   HIS G 362 " --> pdb=" O   ASN E 359 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   THR E 361 " --> pdb=" O   HIS G 362 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   GLY G 355 " --> pdb=" O   SER I 356 " (cutoff:3.500A)
      removed outlier: 8.180A  pdb=" N   ASP I 358 " --> pdb=" O   GLY G 355 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   LEU G 357 " --> pdb=" O   ASP I 358 " (cutoff:3.500A)
      removed outlier: 8.214A  pdb=" N   ILE I 360 " --> pdb=" O   LEU G 357 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   ASN G 359 " --> pdb=" O   ILE I 360 " (cutoff:3.500A)
      removed outlier: 7.775A  pdb=" N   HIS I 362 " --> pdb=" O   ASN G 359 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   THR G 361 " --> pdb=" O   HIS I 362 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 369 through 378
      removed outlier: 6.570A  pdb=" N   LYS B 369 " --> pdb=" O   LYS C 370 " (cutoff:3.500A)
      removed outlier: 8.191A  pdb=" N   GLU C 372 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   ILE B 371 " --> pdb=" O   GLU C 372 " (cutoff:3.500A)
      removed outlier: 7.937A  pdb=" N   HIS C 374 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   THR B 373 " --> pdb=" O   HIS C 374 " (cutoff:3.500A)
      removed outlier: 8.101A  pdb=" N   LEU C 376 " --> pdb=" O   THR B 373 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   LYS B 375 " --> pdb=" O   LEU C 376 " (cutoff:3.500A)
      removed outlier: 8.044A  pdb=" N   PHE C 378 " --> pdb=" O   LYS B 375 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   THR B 377 " --> pdb=" O   PHE C 378 " (cutoff:3.500A)

    128 hydrogen bonds defined for protein.
    384 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.49

  Time building geometry restraints manager: 1.56 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1950
        1.34 -     1.45: 781
        1.45 -     1.57: 3219
        1.57 -     1.68: 0
        1.68 -     1.80: 10
  Bond restraints: 5960
  Sorted by residual:
  bond pdb=" CA  ASP A 348 "
       pdb=" CB  ASP A 348 "
    ideal  model  delta    sigma   weight residual
    1.530  1.516  0.014 1.36e-02 5.41e+03 9.87e-01
  bond pdb=" CA  ASP J 348 "
       pdb=" CB  ASP J 348 "
    ideal  model  delta    sigma   weight residual
    1.530  1.517  0.013 1.36e-02 5.41e+03 9.75e-01
  bond pdb=" CA  ASP H 348 "
       pdb=" CB  ASP H 348 "
    ideal  model  delta    sigma   weight residual
    1.530  1.517  0.013 1.36e-02 5.41e+03 9.74e-01
  bond pdb=" CA  ASP D 348 "
       pdb=" CB  ASP D 348 "
    ideal  model  delta    sigma   weight residual
    1.530  1.517  0.013 1.36e-02 5.41e+03 9.73e-01
  bond pdb=" CA  ASP E 348 "
       pdb=" CB  ASP E 348 "
    ideal  model  delta    sigma   weight residual
    1.530  1.517  0.013 1.36e-02 5.41e+03 9.72e-01
  ... (remaining 5955 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.75: 6719
        0.75 -     1.51: 1023
        1.51 -     2.26: 158
        2.26 -     3.02: 38
        3.02 -     3.77: 32
  Bond angle restraints: 7970
  Sorted by residual:
  angle pdb=" C   PHE J 346 "
        pdb=" N   LYS J 347 "
        pdb=" CA  LYS J 347 "
      ideal   model   delta    sigma   weight residual
     123.24  119.47    3.77 1.54e+00 4.22e-01 6.01e+00
  angle pdb=" C   PHE D 346 "
        pdb=" N   LYS D 347 "
        pdb=" CA  LYS D 347 "
      ideal   model   delta    sigma   weight residual
     123.24  119.47    3.77 1.54e+00 4.22e-01 5.99e+00
  angle pdb=" C   PHE C 346 "
        pdb=" N   LYS C 347 "
        pdb=" CA  LYS C 347 "
      ideal   model   delta    sigma   weight residual
     123.24  119.47    3.77 1.54e+00 4.22e-01 5.99e+00
  angle pdb=" C   PHE A 346 "
        pdb=" N   LYS A 347 "
        pdb=" CA  LYS A 347 "
      ideal   model   delta    sigma   weight residual
     123.24  119.48    3.76 1.54e+00 4.22e-01 5.97e+00
  angle pdb=" C   PHE B 346 "
        pdb=" N   LYS B 347 "
        pdb=" CA  LYS B 347 "
      ideal   model   delta    sigma   weight residual
     123.24  119.48    3.76 1.54e+00 4.22e-01 5.96e+00
  ... (remaining 7965 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.79: 3046
       10.79 -    21.58: 404
       21.58 -    32.37: 110
       32.37 -    43.17: 50
       43.17 -    53.96: 20
  Dihedral angle restraints: 3630
    sinusoidal: 1520
      harmonic: 2110
  Sorted by residual:
  dihedral pdb=" CA  LYS E 347 "
           pdb=" C   LYS E 347 "
           pdb=" N   ASP E 348 "
           pdb=" CA  ASP E 348 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.42   15.58     0      5.00e+00 4.00e-02 9.72e+00
  dihedral pdb=" CA  LYS D 347 "
           pdb=" C   LYS D 347 "
           pdb=" N   ASP D 348 "
           pdb=" CA  ASP D 348 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.43   15.57     0      5.00e+00 4.00e-02 9.70e+00
  dihedral pdb=" CA  LYS G 347 "
           pdb=" C   LYS G 347 "
           pdb=" N   ASP G 348 "
           pdb=" CA  ASP G 348 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.43   15.57     0      5.00e+00 4.00e-02 9.70e+00
  ... (remaining 3627 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.023: 445
       0.023 -    0.046: 245
       0.046 -    0.068: 57
       0.068 -    0.091: 33
       0.091 -    0.114: 110
  Chirality restraints: 890
  Sorted by residual:
  chirality pdb=" CA  ILE F 371 "
            pdb=" N   ILE F 371 "
            pdb=" C   ILE F 371 "
            pdb=" CB  ILE F 371 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.24e-01
  chirality pdb=" CA  ILE I 371 "
            pdb=" N   ILE I 371 "
            pdb=" C   ILE I 371 "
            pdb=" CB  ILE I 371 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.23e-01
  chirality pdb=" CA  ILE H 371 "
            pdb=" N   ILE H 371 "
            pdb=" C   ILE H 371 "
            pdb=" CB  ILE H 371 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.22e-01
  ... (remaining 887 not shown)

  Planarity restraints: 1020
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 363 "   -0.024 5.00e-02 4.00e+02   3.65e-02 2.13e+00
        pdb=" N   PRO A 364 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 364 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 364 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL J 363 "   -0.024 5.00e-02 4.00e+02   3.64e-02 2.12e+00
        pdb=" N   PRO J 364 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO J 364 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO J 364 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 363 "    0.024 5.00e-02 4.00e+02   3.64e-02 2.12e+00
        pdb=" N   PRO B 364 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO B 364 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 364 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1017 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1611
        2.82 -     3.34: 4802
        3.34 -     3.86: 9769
        3.86 -     4.38: 9797
        4.38 -     4.90: 21368
  Nonbonded interactions: 47347
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS I 370 "
            pdb=" OE1 GLU I 372 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" NZ  LYS A 370 "
            pdb=" OE1 GLU A 372 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" NZ  LYS D 370 "
            pdb=" OE1 GLU D 372 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" NZ  LYS F 370 "
            pdb=" OE1 GLU F 372 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" NZ  LYS B 370 "
            pdb=" OE1 GLU B 372 "
     model   vdw
     2.305 3.120
  ... (remaining 47342 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             5.860
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.090
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.010
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
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      :  0.006   0.028   5960  Z= 0.280
  Angle     :  0.594   3.775   7970  Z= 0.338
  Chirality :  0.046   0.114    890
  Planarity :  0.005   0.036   1020
  Dihedral  : 11.995  53.957   2290
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.67 %
    Favored  : 89.33 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 10.45 %
    Favored  : 85.07 %
  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: -2.81 (0.25), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.13 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C 374 
 PHE   0.014   0.002   PHE J 346 
 TYR   0.008   0.002   TYR H 310 
 ARG   0.001   0.000   ARG I 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15650 (  128)
  hydrogen bonds       : angle       7.79137 (  384)
  covalent geometry    : bond        0.00600 ( 5960)
  covalent geometry    : angle       0.59419 ( 7970)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 282
  time to evaluate  : 0.743 
Fit side-chains
REVERT: A  363 VAL cc_start: 0.9351 (t) cc_final: 0.9122 (p)
REVERT: A  368 ASN cc_start: 0.8278 (m-40) cc_final: 0.7886 (m-40)
REVERT: B  342 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7453 (mp0)
REVERT: D  340 LYS cc_start: 0.8450 (mtpp) cc_final: 0.8037 (mttt)
REVERT: D  342 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7498 (mp0)
REVERT: D  368 ASN cc_start: 0.8562 (m-40) cc_final: 0.8184 (m-40)
REVERT: E  342 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7418 (mp0)
REVERT: F  340 LYS cc_start: 0.8399 (mtpp) cc_final: 0.7970 (mttt)
REVERT: F  342 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7270 (mp0)
REVERT: G  342 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7361 (mp0)
REVERT: H  322 CYS cc_start: 0.8408 (t) cc_final: 0.8146 (t)
REVERT: H  342 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7303 (mp0)
REVERT: I  345 ASP cc_start: 0.8436 (m-30) cc_final: 0.8203 (m-30)
REVERT: I  375 LYS cc_start: 0.8755 (ttmm) cc_final: 0.8531 (ttmm)
  outliers start: 30
  outliers final: 11
  residues processed: 292
  average time/residue: 0.2336
  time to fit residues: 84.2130
Evaluate side-chains
  287 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 270
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain E residue  306 VAL
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  342 GLU
Chi-restraints excluded: chain G residue  306 VAL
Chi-restraints excluded: chain G residue  342 GLU
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  342 GLU
Chi-restraints excluded: chain I residue  306 VAL
Chi-restraints excluded: chain I residue  337 VAL
Chi-restraints excluded: chain J residue  306 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 29 optimal weight:    9.9990
   chunk 18 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 54 optimal weight:    7.9990
   chunk 21 optimal weight:    0.3980
   chunk 33 optimal weight:    6.9990
   chunk 40 optimal weight:    1.9990
   chunk 63 optimal weight:    6.9990
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 374 HIS
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 336 GLN
G 336 GLN
G 374 HIS
** J 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.162599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.137967 restraints weight = 7205.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.141903 restraints weight = 2681.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.144346 restraints weight = 1429.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.4190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.1701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5960  Z= 0.159
  Angle     :  0.602   6.983   7970  Z= 0.309
  Chirality :  0.048   0.134    890
  Planarity :  0.004   0.033   1020
  Dihedral  :  7.699  48.677    819
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  5.97 %
    Allowed  : 13.88 %
    Favored  : 80.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.67 (0.26), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.03 (0.20), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS J 374 
 PHE   0.014   0.002   PHE D 346 
 TYR   0.004   0.001   TYR B 310 
 ARG   0.001   0.000   ARG J 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03041 (  128)
  hydrogen bonds       : angle       5.29711 (  384)
  covalent geometry    : bond        0.00370 ( 5960)
  covalent geometry    : angle       0.60242 ( 7970)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 275
  time to evaluate  : 0.739 
Fit side-chains
REVERT: A  368 ASN cc_start: 0.8305 (m-40) cc_final: 0.7798 (m-40)
REVERT: B  342 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7428 (mp0)
REVERT: B  353 LYS cc_start: 0.8913 (tttp) cc_final: 0.8615 (tttp)
REVERT: D  340 LYS cc_start: 0.8413 (mtpp) cc_final: 0.7756 (mttt)
REVERT: D  342 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7678 (mp0)
REVERT: E  342 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7445 (mp0)
REVERT: F  340 LYS cc_start: 0.8231 (mtpp) cc_final: 0.7686 (mttt)
REVERT: F  342 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7360 (mp0)
REVERT: G  342 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7246 (mp0)
REVERT: H  342 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7595 (mp0)
REVERT: I  327 ASN cc_start: 0.8275 (t0) cc_final: 0.7654 (t0)
REVERT: I  340 LYS cc_start: 0.8151 (mtpp) cc_final: 0.7529 (mmmt)
REVERT: I  345 ASP cc_start: 0.8308 (m-30) cc_final: 0.8009 (m-30)
REVERT: J  327 ASN cc_start: 0.7853 (t0) cc_final: 0.7259 (t0)
  outliers start: 40
  outliers final: 24
  residues processed: 283
  average time/residue: 0.2067
  time to fit residues: 72.4617
Evaluate side-chains
  292 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 262
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain E residue  306 VAL
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain F residue  342 GLU
Chi-restraints excluded: chain G residue  306 VAL
Chi-restraints excluded: chain G residue  319 THR
Chi-restraints excluded: chain G residue  337 VAL
Chi-restraints excluded: chain G residue  342 GLU
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  319 THR
Chi-restraints excluded: chain H residue  320 SER
Chi-restraints excluded: chain H residue  342 GLU
Chi-restraints excluded: chain H residue  350 VAL
Chi-restraints excluded: chain I residue  319 THR
Chi-restraints excluded: chain J residue  319 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 30 optimal weight:    8.9990
   chunk 56 optimal weight:   10.0000
   chunk 28 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 47 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 46 optimal weight:    6.9990
   chunk 32 optimal weight:    0.7980
   chunk 39 optimal weight:   10.0000
   chunk 17 optimal weight:    7.9990
   chunk 66 optimal weight:    2.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 336 GLN
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.159290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.134460 restraints weight = 7287.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.138343 restraints weight = 2751.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.140725 restraints weight = 1472.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.4160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   5960  Z= 0.231
  Angle     :  0.620   5.037   7970  Z= 0.324
  Chirality :  0.048   0.132    890
  Planarity :  0.005   0.041   1020
  Dihedral  :  7.567  57.347    816
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.93 %
    Favored  : 91.07 %
  Rotamer:
    Outliers :  6.27 %
    Allowed  : 15.82 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.67 (0.26), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.02 (0.20), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS I 374 
 PHE   0.019   0.003   PHE H 346 
 TYR   0.008   0.002   TYR G 310 
 ARG   0.001   0.000   ARG E 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03359 (  128)
  hydrogen bonds       : angle       5.26082 (  384)
  covalent geometry    : bond        0.00546 ( 5960)
  covalent geometry    : angle       0.61963 ( 7970)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 268
  time to evaluate  : 0.705 
Fit side-chains
REVERT: A  368 ASN cc_start: 0.8391 (m-40) cc_final: 0.7882 (m-40)
REVERT: A  369 LYS cc_start: 0.8423 (ttmm) cc_final: 0.8179 (ttmm)
REVERT: B  353 LYS cc_start: 0.9026 (tttp) cc_final: 0.8684 (tttm)
REVERT: D  340 LYS cc_start: 0.8413 (mtpp) cc_final: 0.7788 (mttt)
REVERT: F  340 LYS cc_start: 0.8397 (mtpp) cc_final: 0.7902 (mttt)
REVERT: F  342 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7284 (mp0)
REVERT: G  342 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7373 (mp0)
REVERT: H  340 LYS cc_start: 0.8270 (mtpp) cc_final: 0.7782 (mttt)
REVERT: I  327 ASN cc_start: 0.8161 (t0) cc_final: 0.7527 (t0)
REVERT: I  345 ASP cc_start: 0.8274 (m-30) cc_final: 0.8023 (m-30)
REVERT: I  375 LYS cc_start: 0.8393 (ttmm) cc_final: 0.8180 (ttmm)
  outliers start: 42
  outliers final: 27
  residues processed: 279
  average time/residue: 0.2015
  time to fit residues: 69.9001
Evaluate side-chains
  286 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 257
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  350 VAL
Chi-restraints excluded: chain D residue  376 LEU
Chi-restraints excluded: chain E residue  306 VAL
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain F residue  342 GLU
Chi-restraints excluded: chain G residue  306 VAL
Chi-restraints excluded: chain G residue  319 THR
Chi-restraints excluded: chain G residue  337 VAL
Chi-restraints excluded: chain G residue  342 GLU
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  319 THR
Chi-restraints excluded: chain H residue  320 SER
Chi-restraints excluded: chain H residue  350 VAL
Chi-restraints excluded: chain I residue  319 THR
Chi-restraints excluded: chain J residue  319 THR
Chi-restraints excluded: chain J residue  320 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 56 optimal weight:    7.9990
   chunk 2 optimal weight:    1.9990
   chunk 22 optimal weight:    9.9990
   chunk 23 optimal weight:    2.9990
   chunk 28 optimal weight:   10.0000
   chunk 5 optimal weight:    0.7980
   chunk 12 optimal weight:    4.9990
   chunk 11 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9990
   chunk 47 optimal weight:    3.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
A 368 ASN
** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 368 ASN
** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 368 ASN
G 336 GLN
** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 368 ASN
H 374 HIS
J 336 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.162483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.137354 restraints weight = 7393.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.141355 restraints weight = 2787.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.143834 restraints weight = 1492.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.4223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.2324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   5960  Z= 0.191
  Angle     :  0.633   7.757   7970  Z= 0.329
  Chirality :  0.049   0.131    890
  Planarity :  0.004   0.034   1020
  Dihedral  :  6.092  45.304    804
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 17.01 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.64 (0.26), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.00 (0.20), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS I 374 
 PHE   0.019   0.003   PHE G 346 
 TYR   0.007   0.002   TYR G 310 
 ARG   0.001   0.000   ARG J 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02983 (  128)
  hydrogen bonds       : angle       5.03439 (  384)
  covalent geometry    : bond        0.00455 ( 5960)
  covalent geometry    : angle       0.63321 ( 7970)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 267
  time to evaluate  : 0.656 
Fit side-chains
REVERT: A  368 ASN cc_start: 0.8324 (m110) cc_final: 0.7902 (m110)
REVERT: B  353 LYS cc_start: 0.8964 (tttp) cc_final: 0.8613 (tttm)
REVERT: C  336 GLN cc_start: 0.8113 (tt0) cc_final: 0.7908 (tt0)
REVERT: D  340 LYS cc_start: 0.8416 (mtpp) cc_final: 0.7686 (mttt)
REVERT: E  310 TYR cc_start: 0.9212 (t80) cc_final: 0.8789 (t80)
REVERT: E  342 GLU cc_start: 0.7839 (mp0) cc_final: 0.7334 (mp0)
REVERT: F  340 LYS cc_start: 0.8286 (mtpp) cc_final: 0.7793 (mttt)
REVERT: F  342 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7668 (mp0)
REVERT: H  340 LYS cc_start: 0.8288 (mtpp) cc_final: 0.7798 (mttt)
REVERT: H  376 LEU cc_start: 0.8406 (tp) cc_final: 0.8170 (tp)
REVERT: I  327 ASN cc_start: 0.8231 (t0) cc_final: 0.7611 (t0)
REVERT: I  345 ASP cc_start: 0.8189 (m-30) cc_final: 0.7945 (m-30)
REVERT: I  375 LYS cc_start: 0.8335 (ttmm) cc_final: 0.8129 (ttmm)
REVERT: J  327 ASN cc_start: 0.7707 (t0) cc_final: 0.7138 (t0)
  outliers start: 38
  outliers final: 30
  residues processed: 274
  average time/residue: 0.2069
  time to fit residues: 69.9970
Evaluate side-chains
  285 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 254
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  350 VAL
Chi-restraints excluded: chain D residue  376 LEU
Chi-restraints excluded: chain E residue  306 VAL
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain F residue  342 GLU
Chi-restraints excluded: chain G residue  306 VAL
Chi-restraints excluded: chain G residue  319 THR
Chi-restraints excluded: chain G residue  337 VAL
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  319 THR
Chi-restraints excluded: chain H residue  320 SER
Chi-restraints excluded: chain H residue  350 VAL
Chi-restraints excluded: chain I residue  319 THR
Chi-restraints excluded: chain J residue  315 LEU
Chi-restraints excluded: chain J residue  319 THR
Chi-restraints excluded: chain J residue  320 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   chunk 59 optimal weight:    3.9990
   chunk 7 optimal weight:   10.0000
   chunk 40 optimal weight:    7.9990
   chunk 12 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 37 optimal weight:    6.9990
   chunk 4 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 368 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.160998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.136201 restraints weight = 7231.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.140177 restraints weight = 2790.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.142637 restraints weight = 1509.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.4217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.2441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   5960  Z= 0.230
  Angle     :  0.662   8.596   7970  Z= 0.342
  Chirality :  0.049   0.135    890
  Planarity :  0.004   0.039   1020
  Dihedral  :  5.489  26.990    801
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.93 %
    Favored  : 91.07 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 19.70 %
    Favored  : 75.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.66 (0.26), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.02 (0.20), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F 374 
 PHE   0.022   0.003   PHE G 346 
 TYR   0.008   0.002   TYR G 310 
 ARG   0.001   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03228 (  128)
  hydrogen bonds       : angle       5.09220 (  384)
  covalent geometry    : bond        0.00546 ( 5960)
  covalent geometry    : angle       0.66236 ( 7970)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 267
  time to evaluate  : 0.641 
Fit side-chains
REVERT: A  310 TYR cc_start: 0.9122 (t80) cc_final: 0.8769 (t80)
REVERT: A  368 ASN cc_start: 0.8393 (m110) cc_final: 0.7941 (m110)
REVERT: A  369 LYS cc_start: 0.8415 (ttmm) cc_final: 0.8195 (ttmm)
REVERT: A  378 PHE cc_start: 0.8883 (t80) cc_final: 0.8607 (t80)
REVERT: B  353 LYS cc_start: 0.9019 (tttp) cc_final: 0.8679 (tttm)
REVERT: C  336 GLN cc_start: 0.8131 (tt0) cc_final: 0.7915 (tt0)
REVERT: D  340 LYS cc_start: 0.8467 (mtpp) cc_final: 0.7892 (mttt)
REVERT: E  310 TYR cc_start: 0.9252 (t80) cc_final: 0.8933 (t80)
REVERT: F  310 TYR cc_start: 0.9282 (t80) cc_final: 0.8924 (t80)
REVERT: F  340 LYS cc_start: 0.8396 (mtpp) cc_final: 0.7904 (mttt)
REVERT: H  316 SER cc_start: 0.9123 (p) cc_final: 0.8863 (p)
REVERT: H  340 LYS cc_start: 0.8382 (mtpp) cc_final: 0.7904 (mttt)
REVERT: I  327 ASN cc_start: 0.8230 (t0) cc_final: 0.7651 (t0)
REVERT: I  345 ASP cc_start: 0.8216 (m-30) cc_final: 0.7952 (m-30)
REVERT: I  375 LYS cc_start: 0.8432 (ttmm) cc_final: 0.8197 (ttmm)
  outliers start: 32
  outliers final: 31
  residues processed: 273
  average time/residue: 0.1966
  time to fit residues: 66.9112
Evaluate side-chains
  286 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 255
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  350 VAL
Chi-restraints excluded: chain D residue  376 LEU
Chi-restraints excluded: chain E residue  306 VAL
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain G residue  306 VAL
Chi-restraints excluded: chain G residue  319 THR
Chi-restraints excluded: chain G residue  337 VAL
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  319 THR
Chi-restraints excluded: chain H residue  320 SER
Chi-restraints excluded: chain H residue  350 VAL
Chi-restraints excluded: chain I residue  306 VAL
Chi-restraints excluded: chain I residue  319 THR
Chi-restraints excluded: chain I residue  337 VAL
Chi-restraints excluded: chain J residue  319 THR
Chi-restraints excluded: chain J residue  325 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 2 optimal weight:    3.9990
   chunk 46 optimal weight:    6.9990
   chunk 60 optimal weight:    0.6980
   chunk 51 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 362 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.159962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.134950 restraints weight = 7269.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.138916 restraints weight = 2826.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.141339 restraints weight = 1532.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.4223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.2590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   5960  Z= 0.242
  Angle     :  0.697   8.903   7970  Z= 0.360
  Chirality :  0.050   0.164    890
  Planarity :  0.004   0.035   1020
  Dihedral  :  5.457  25.757    798
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.40 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  5.52 %
    Allowed  : 19.25 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.66 (0.26), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.02 (0.20), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS J 374 
 PHE   0.023   0.003   PHE G 346 
 TYR   0.008   0.002   TYR F 310 
 ARG   0.001   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03241 (  128)
  hydrogen bonds       : angle       5.11671 (  384)
  covalent geometry    : bond        0.00574 ( 5960)
  covalent geometry    : angle       0.69710 ( 7970)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 260
  time to evaluate  : 0.721 
Fit side-chains
REVERT: A  310 TYR cc_start: 0.9066 (t80) cc_final: 0.8628 (t80)
REVERT: A  368 ASN cc_start: 0.8395 (m110) cc_final: 0.7955 (m110)
REVERT: A  369 LYS cc_start: 0.8391 (ttmm) cc_final: 0.8147 (ttmm)
REVERT: A  378 PHE cc_start: 0.8899 (t80) cc_final: 0.8577 (t80)
REVERT: B  353 LYS cc_start: 0.9023 (ttpp) cc_final: 0.8663 (tttm)
REVERT: D  310 TYR cc_start: 0.9252 (t80) cc_final: 0.8865 (t80)
REVERT: D  340 LYS cc_start: 0.8458 (mtpp) cc_final: 0.7853 (mttt)
REVERT: F  310 TYR cc_start: 0.9262 (t80) cc_final: 0.9053 (t80)
REVERT: F  340 LYS cc_start: 0.8420 (mtpp) cc_final: 0.7897 (mttt)
REVERT: H  316 SER cc_start: 0.9109 (p) cc_final: 0.8841 (p)
REVERT: H  340 LYS cc_start: 0.8367 (mtpp) cc_final: 0.7838 (mttt)
REVERT: H  376 LEU cc_start: 0.8430 (tp) cc_final: 0.8192 (tp)
REVERT: I  327 ASN cc_start: 0.8230 (t0) cc_final: 0.7651 (t0)
REVERT: I  375 LYS cc_start: 0.8417 (ttmm) cc_final: 0.8183 (ttmm)
REVERT: J  316 SER cc_start: 0.8850 (p) cc_final: 0.8638 (p)
REVERT: J  362 HIS cc_start: 0.7065 (OUTLIER) cc_final: 0.6219 (t-90)
  outliers start: 37
  outliers final: 34
  residues processed: 266
  average time/residue: 0.2056
  time to fit residues: 67.9890
Evaluate side-chains
  287 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 252
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  337 VAL
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  350 VAL
Chi-restraints excluded: chain D residue  376 LEU
Chi-restraints excluded: chain E residue  306 VAL
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain G residue  306 VAL
Chi-restraints excluded: chain G residue  319 THR
Chi-restraints excluded: chain G residue  337 VAL
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  319 THR
Chi-restraints excluded: chain H residue  320 SER
Chi-restraints excluded: chain H residue  350 VAL
Chi-restraints excluded: chain I residue  306 VAL
Chi-restraints excluded: chain I residue  319 THR
Chi-restraints excluded: chain I residue  337 VAL
Chi-restraints excluded: chain J residue  310 TYR
Chi-restraints excluded: chain J residue  319 THR
Chi-restraints excluded: chain J residue  325 LEU
Chi-restraints excluded: chain J residue  362 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 46 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 58 optimal weight:    6.9990
   chunk 53 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 60 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   overall best weight:    2.9788

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.159807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.134719 restraints weight = 7339.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.138849 restraints weight = 2869.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.141383 restraints weight = 1549.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.4217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.2656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   5960  Z= 0.243
  Angle     :  0.706   9.214   7970  Z= 0.363
  Chirality :  0.050   0.174    890
  Planarity :  0.004   0.039   1020
  Dihedral  :  5.491  25.832    798
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  5.52 %
    Allowed  : 19.55 %
    Favored  : 74.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.67 (0.26), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.02 (0.20), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS I 374 
 PHE   0.024   0.003   PHE G 346 
 TYR   0.009   0.002   TYR F 310 
 ARG   0.001   0.000   ARG G 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03238 (  128)
  hydrogen bonds       : angle       5.14967 (  384)
  covalent geometry    : bond        0.00575 ( 5960)
  covalent geometry    : angle       0.70580 ( 7970)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 263
  time to evaluate  : 0.684 
Fit side-chains
REVERT: A  310 TYR cc_start: 0.9060 (t80) cc_final: 0.8671 (t80)
REVERT: A  368 ASN cc_start: 0.8390 (m110) cc_final: 0.7982 (m110)
REVERT: A  378 PHE cc_start: 0.8899 (t80) cc_final: 0.8640 (t80)
REVERT: B  353 LYS cc_start: 0.9071 (ttpp) cc_final: 0.8698 (tttm)
REVERT: C  336 GLN cc_start: 0.8147 (tt0) cc_final: 0.7930 (tt0)
REVERT: C  341 SER cc_start: 0.8561 (m) cc_final: 0.8276 (p)
REVERT: D  310 TYR cc_start: 0.9250 (t80) cc_final: 0.8900 (t80)
REVERT: D  340 LYS cc_start: 0.8486 (mtpp) cc_final: 0.7878 (mttt)
REVERT: E  353 LYS cc_start: 0.9037 (tttp) cc_final: 0.8792 (tttp)
REVERT: F  340 LYS cc_start: 0.8484 (mtpp) cc_final: 0.8000 (mttt)
REVERT: H  316 SER cc_start: 0.9124 (p) cc_final: 0.8855 (p)
REVERT: H  340 LYS cc_start: 0.8324 (mtpp) cc_final: 0.7915 (mttt)
REVERT: H  342 GLU cc_start: 0.7400 (pm20) cc_final: 0.7139 (mp0)
REVERT: I  327 ASN cc_start: 0.8219 (t0) cc_final: 0.7641 (t0)
REVERT: I  375 LYS cc_start: 0.8462 (ttmm) cc_final: 0.8218 (ttmm)
REVERT: J  316 SER cc_start: 0.8884 (p) cc_final: 0.8671 (p)
REVERT: J  362 HIS cc_start: 0.7146 (OUTLIER) cc_final: 0.6242 (t-90)
  outliers start: 37
  outliers final: 34
  residues processed: 271
  average time/residue: 0.2027
  time to fit residues: 68.8350
Evaluate side-chains
  295 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 260
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  337 VAL
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  350 VAL
Chi-restraints excluded: chain D residue  376 LEU
Chi-restraints excluded: chain E residue  306 VAL
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain G residue  306 VAL
Chi-restraints excluded: chain G residue  319 THR
Chi-restraints excluded: chain G residue  337 VAL
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  319 THR
Chi-restraints excluded: chain H residue  320 SER
Chi-restraints excluded: chain H residue  350 VAL
Chi-restraints excluded: chain I residue  306 VAL
Chi-restraints excluded: chain I residue  319 THR
Chi-restraints excluded: chain I residue  337 VAL
Chi-restraints excluded: chain J residue  310 TYR
Chi-restraints excluded: chain J residue  319 THR
Chi-restraints excluded: chain J residue  325 LEU
Chi-restraints excluded: chain J residue  362 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 47 optimal weight:    3.9990
   chunk 35 optimal weight:   10.0000
   chunk 33 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 8 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9980
   chunk 57 optimal weight:    8.9990
   chunk 4 optimal weight:    0.0970
   chunk 69 optimal weight:    0.0970
   overall best weight:    0.9978

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.166956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.141710 restraints weight = 7230.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.145881 restraints weight = 2810.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.148465 restraints weight = 1533.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.4328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.2973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5960  Z= 0.124
  Angle     :  0.654   9.857   7970  Z= 0.331
  Chirality :  0.049   0.167    890
  Planarity :  0.004   0.031   1020
  Dihedral  :  5.041  20.756    798
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 21.19 %
    Favored  : 74.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.56 (0.26), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.94 (0.20), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS I 374 
 PHE   0.019   0.002   PHE E 346 
 TYR   0.012   0.001   TYR F 310 
 ARG   0.001   0.000   ARG I 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02360 (  128)
  hydrogen bonds       : angle       4.59215 (  384)
  covalent geometry    : bond        0.00292 ( 5960)
  covalent geometry    : angle       0.65409 ( 7970)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 273
  time to evaluate  : 0.736 
Fit side-chains
REVERT: A  310 TYR cc_start: 0.9037 (t80) cc_final: 0.8690 (t80)
REVERT: A  368 ASN cc_start: 0.8294 (m110) cc_final: 0.7895 (m110)
REVERT: A  378 PHE cc_start: 0.8778 (t80) cc_final: 0.8537 (t80)
REVERT: B  353 LYS cc_start: 0.8987 (ttpp) cc_final: 0.8651 (tttm)
REVERT: C  341 SER cc_start: 0.8634 (m) cc_final: 0.8334 (p)
REVERT: D  340 LYS cc_start: 0.8515 (mtpp) cc_final: 0.7889 (mttt)
REVERT: F  340 LYS cc_start: 0.8378 (mtpp) cc_final: 0.7892 (mttt)
REVERT: H  316 SER cc_start: 0.9111 (p) cc_final: 0.8830 (p)
REVERT: H  327 ASN cc_start: 0.8631 (t0) cc_final: 0.7710 (t0)
REVERT: H  340 LYS cc_start: 0.8345 (mtpp) cc_final: 0.7885 (mttt)
REVERT: I  327 ASN cc_start: 0.8299 (t0) cc_final: 0.7829 (t0)
REVERT: I  375 LYS cc_start: 0.8423 (ttmm) cc_final: 0.8170 (ttmm)
REVERT: J  311 LYS cc_start: 0.5556 (tptt) cc_final: 0.3704 (pttp)
REVERT: J  316 SER cc_start: 0.8794 (p) cc_final: 0.8568 (p)
REVERT: J  362 HIS cc_start: 0.6945 (OUTLIER) cc_final: 0.6323 (t-90)
  outliers start: 28
  outliers final: 22
  residues processed: 278
  average time/residue: 0.2268
  time to fit residues: 78.4696
Evaluate side-chains
  281 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 258
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain C residue  337 VAL
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  376 LEU
Chi-restraints excluded: chain E residue  306 VAL
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain G residue  306 VAL
Chi-restraints excluded: chain G residue  337 VAL
Chi-restraints excluded: chain I residue  306 VAL
Chi-restraints excluded: chain I residue  319 THR
Chi-restraints excluded: chain J residue  319 THR
Chi-restraints excluded: chain J residue  325 LEU
Chi-restraints excluded: chain J residue  362 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 64 optimal weight:    6.9990
   chunk 55 optimal weight:    6.9990
   chunk 7 optimal weight:    9.9990
   chunk 20 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 34 optimal weight:    7.9990
   chunk 9 optimal weight:    5.9990
   chunk 40 optimal weight:    0.8980
   chunk 43 optimal weight:    4.9990
   chunk 60 optimal weight:    4.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
B 336 GLN
** H 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.161701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.136445 restraints weight = 7311.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.140526 restraints weight = 2878.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.143036 restraints weight = 1576.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.4256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.2911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   5960  Z= 0.234
  Angle     :  0.735   9.274   7970  Z= 0.377
  Chirality :  0.050   0.186    890
  Planarity :  0.004   0.040   1020
  Dihedral  :  5.465  27.735    797
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.33 %
    Favored  : 90.67 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 23.28 %
    Favored  : 72.84 %
  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: -2.60 (0.26), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.97 (0.20), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS I 374 
 PHE   0.022   0.003   PHE E 346 
 TYR   0.018   0.002   TYR E 310 
 ARG   0.001   0.000   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03264 (  128)
  hydrogen bonds       : angle       4.96367 (  384)
  covalent geometry    : bond        0.00563 ( 5960)
  covalent geometry    : angle       0.73475 ( 7970)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 259
  time to evaluate  : 1.064 
Fit side-chains
REVERT: A  368 ASN cc_start: 0.8344 (m110) cc_final: 0.7973 (m110)
REVERT: A  378 PHE cc_start: 0.8863 (t80) cc_final: 0.8629 (t80)
REVERT: B  353 LYS cc_start: 0.9053 (ttpp) cc_final: 0.8659 (tttm)
REVERT: C  341 SER cc_start: 0.8655 (m) cc_final: 0.8357 (p)
REVERT: D  340 LYS cc_start: 0.8543 (mtpp) cc_final: 0.7954 (mttt)
REVERT: F  340 LYS cc_start: 0.8446 (mtpp) cc_final: 0.7954 (mttt)
REVERT: H  316 SER cc_start: 0.9077 (p) cc_final: 0.8809 (p)
REVERT: H  340 LYS cc_start: 0.8358 (mtpp) cc_final: 0.7869 (mttt)
REVERT: H  342 GLU cc_start: 0.7148 (pm20) cc_final: 0.6917 (mm-30)
REVERT: I  327 ASN cc_start: 0.8218 (t0) cc_final: 0.7686 (t0)
REVERT: I  375 LYS cc_start: 0.8463 (ttmm) cc_final: 0.8212 (ttmm)
REVERT: J  316 SER cc_start: 0.8868 (p) cc_final: 0.8655 (p)
REVERT: J  362 HIS cc_start: 0.6964 (OUTLIER) cc_final: 0.6258 (t-90)
  outliers start: 26
  outliers final: 25
  residues processed: 262
  average time/residue: 0.2014
  time to fit residues: 66.6121
Evaluate side-chains
  281 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 255
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  337 VAL
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  306 VAL
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain G residue  306 VAL
Chi-restraints excluded: chain G residue  319 THR
Chi-restraints excluded: chain G residue  337 VAL
Chi-restraints excluded: chain H residue  319 THR
Chi-restraints excluded: chain H residue  320 SER
Chi-restraints excluded: chain I residue  306 VAL
Chi-restraints excluded: chain I residue  319 THR
Chi-restraints excluded: chain J residue  319 THR
Chi-restraints excluded: chain J residue  325 LEU
Chi-restraints excluded: chain J residue  362 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 18 optimal weight:    0.1980
   chunk 44 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 50 optimal weight:   10.0000
   chunk 24 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 58 optimal weight:    0.0980
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
** H 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4574 r_free = 0.4574 target = 0.173434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.147580 restraints weight = 7287.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.151975 restraints weight = 2827.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.154701 restraints weight = 1541.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.4391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.3327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5960  Z= 0.118
  Angle     :  0.683   9.515   7970  Z= 0.348
  Chirality :  0.049   0.157    890
  Planarity :  0.003   0.033   1020
  Dihedral  :  5.040  20.227    797
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 25.97 %
    Favored  : 71.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.56 (0.26), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.94 (0.20), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 362 
 PHE   0.016   0.002   PHE J 346 
 TYR   0.015   0.001   TYR A 310 
 ARG   0.001   0.000   ARG I 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02239 (  128)
  hydrogen bonds       : angle       4.46199 (  384)
  covalent geometry    : bond        0.00279 ( 5960)
  covalent geometry    : angle       0.68307 ( 7970)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 269
  time to evaluate  : 0.739 
Fit side-chains
REVERT: A  368 ASN cc_start: 0.8361 (m110) cc_final: 0.8015 (m110)
REVERT: B  353 LYS cc_start: 0.9037 (ttpp) cc_final: 0.8691 (tttm)
REVERT: C  341 SER cc_start: 0.8714 (m) cc_final: 0.8315 (p)
REVERT: D  340 LYS cc_start: 0.8509 (mtpp) cc_final: 0.7905 (mttt)
REVERT: F  340 LYS cc_start: 0.8403 (mtpp) cc_final: 0.7951 (mttt)
REVERT: H  316 SER cc_start: 0.9124 (p) cc_final: 0.8851 (p)
REVERT: H  327 ASN cc_start: 0.8680 (t0) cc_final: 0.8405 (t0)
REVERT: H  340 LYS cc_start: 0.8413 (mtpp) cc_final: 0.7962 (mttt)
REVERT: I  327 ASN cc_start: 0.8347 (t0) cc_final: 0.7948 (t0)
REVERT: J  316 SER cc_start: 0.8847 (p) cc_final: 0.8629 (p)
REVERT: J  327 ASN cc_start: 0.7834 (t0) cc_final: 0.7367 (t0)
REVERT: J  362 HIS cc_start: 0.6850 (OUTLIER) cc_final: 0.6435 (t-90)
  outliers start: 16
  outliers final: 12
  residues processed: 273
  average time/residue: 0.2169
  time to fit residues: 74.3413
Evaluate side-chains
  276 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 263
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  337 VAL
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain E residue  306 VAL
Chi-restraints excluded: chain G residue  306 VAL
Chi-restraints excluded: chain H residue  319 THR
Chi-restraints excluded: chain I residue  306 VAL
Chi-restraints excluded: chain J residue  325 LEU
Chi-restraints excluded: chain J residue  362 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 30 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 55 optimal weight:    3.9990
   chunk 68 optimal weight:    5.9990
   chunk 34 optimal weight:    0.7980
   chunk 24 optimal weight:    4.9990
   chunk 36 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 336 GLN
D 336 GLN
** H 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.160619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.135527 restraints weight = 7413.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.139546 restraints weight = 2913.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.142061 restraints weight = 1595.516|
|-----------------------------------------------------------------------------|
r_work (final): 0.4256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.3055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058   5960  Z= 0.264
  Angle     :  0.756   9.132   7970  Z= 0.388
  Chirality :  0.050   0.219    890
  Planarity :  0.004   0.049   1020
  Dihedral  :  5.481  27.642    796
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 25.67 %
    Favored  : 71.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.61 (0.26), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.98 (0.20), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS I 374 
 PHE   0.023   0.004   PHE E 346 
 TYR   0.013   0.002   TYR G 310 
 ARG   0.001   0.000   ARG G 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03435 (  128)
  hydrogen bonds       : angle       5.00860 (  384)
  covalent geometry    : bond        0.00633 ( 5960)
  covalent geometry    : angle       0.75552 ( 7970)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2609.40 seconds
wall clock time: 46 minutes 43.18 seconds (2803.18 seconds total)