Starting phenix.real_space_refine
on Wed Sep 17 06:11:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b4n_44186/09_2025/9b4n_44186.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b4n_44186/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b4n_44186/09_2025/9b4n_44186.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b4n_44186/09_2025/9b4n_44186.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b4n_44186/09_2025/9b4n_44186.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b4n_44186/09_2025/9b4n_44186.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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:
    B, C, D, E, F, G, H, I, J
  Time building chain proxies: 0.77, per 1000 atoms: 0.13
  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: 0.50
  Conformation dependent library (CDL) restraints added in 221.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.26
  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: 0.97

  Time building geometry restraints manager: 0.66 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             6.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.910
  Find NCS groups from input model:        0.050
  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:1.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.540
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.001   0.000   ARG I 349 
 TYR   0.008   0.002   TYR H 310 
 PHE   0.014   0.002   PHE J 346 
 HIS   0.002   0.001   HIS C 374 

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

*********************** 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  : 0.237 
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: 0.0997
  time to fit residues: 35.9343
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  : 0.237 
-------------------------------------------------------------------------------
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 49 optimal weight:   10.0000
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.1980
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    2.0388

-------------------------------------------------------------------------------
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
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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.161305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.136797 restraints weight = 7294.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.140665 restraints weight = 2683.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.143041 restraints weight = 1429.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.144530 restraints weight = 945.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.145400 restraints weight = 724.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.4196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.1667

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= 0.184
  Angle     :  0.616   7.199   7970  Z= 0.315
  Chirality :  0.048   0.131    890
  Planarity :  0.004   0.034   1020
  Dihedral  :  7.840  49.824    819
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.40 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 14.03 %
    Favored  : 79.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.68 (0.26), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.04 (0.20), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG J 349 
 TYR   0.005   0.001   TYR F 310 
 PHE   0.015   0.002   PHE D 346 
 HIS   0.004   0.001   HIS J 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 5960)
  covalent geometry    : angle       0.61597 ( 7970)
  hydrogen bonds       : bond        0.03197 (  128)
  hydrogen bonds       : angle       5.35008 (  384)

*********************** 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
  309 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 268
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A  368 ASN cc_start: 0.8346 (m-40) cc_final: 0.7842 (m-40)
REVERT: B  342 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7411 (mp0)
REVERT: B  353 LYS cc_start: 0.8947 (tttp) cc_final: 0.8672 (tttm)
REVERT: D  340 LYS cc_start: 0.8454 (mtpp) cc_final: 0.7810 (mttt)
REVERT: D  342 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7680 (mp0)
REVERT: E  342 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7484 (mp0)
REVERT: F  340 LYS cc_start: 0.8321 (mtpp) cc_final: 0.7799 (mttt)
REVERT: F  342 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7204 (mp0)
REVERT: G  342 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7267 (mp0)
REVERT: H  342 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7507 (mp0)
REVERT: I  327 ASN cc_start: 0.8254 (t0) cc_final: 0.7633 (t0)
REVERT: I  340 LYS cc_start: 0.8253 (mtpp) cc_final: 0.7565 (mmmt)
REVERT: I  345 ASP cc_start: 0.8313 (m-30) cc_final: 0.8025 (m-30)
  outliers start: 41
  outliers final: 25
  residues processed: 277
  average time/residue: 0.0952
  time to fit residues: 32.7955
Evaluate side-chains
  288 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 257
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
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  306 VAL
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 23 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 40 optimal weight:    4.9990
   chunk 12 optimal weight:    6.9990
   chunk 21 optimal weight:   10.0000
   chunk 45 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 59 optimal weight:    7.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    2.4986

-------------------------------------------------------------------------------
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**
** 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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.160120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.135314 restraints weight = 7266.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.139210 restraints weight = 2740.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.141641 restraints weight = 1462.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.143102 restraints weight = 965.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.144004 restraints weight = 744.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.4208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.1997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   5960  Z= 0.211
  Angle     :  0.614   5.038   7970  Z= 0.321
  Chirality :  0.048   0.133    890
  Planarity :  0.005   0.041   1020
  Dihedral  :  7.586  59.626    817
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.53 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  6.27 %
    Allowed  : 15.07 %
    Favored  : 78.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.001   0.000   ARG G 349 
 TYR   0.007   0.002   TYR I 310 
 PHE   0.017   0.003   PHE D 346 
 HIS   0.004   0.001   HIS J 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 ( 5960)
  covalent geometry    : angle       0.61375 ( 7970)
  hydrogen bonds       : bond        0.03291 (  128)
  hydrogen bonds       : angle       5.22521 (  384)

*********************** 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  : 0.229 
Fit side-chains
REVERT: A  368 ASN cc_start: 0.8394 (m-40) cc_final: 0.7904 (m-40)
REVERT: A  369 LYS cc_start: 0.8416 (ttmm) cc_final: 0.8172 (ttmm)
REVERT: B  353 LYS cc_start: 0.8997 (tttp) cc_final: 0.8653 (tttm)
REVERT: D  340 LYS cc_start: 0.8416 (mtpp) cc_final: 0.7772 (mttt)
REVERT: F  340 LYS cc_start: 0.8410 (mtpp) cc_final: 0.7912 (mttt)
REVERT: F  342 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7292 (mp0)
REVERT: G  342 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7356 (mp0)
REVERT: H  340 LYS cc_start: 0.8270 (mtpp) cc_final: 0.7808 (mttt)
REVERT: I  327 ASN cc_start: 0.8332 (t0) cc_final: 0.7742 (t0)
REVERT: I  345 ASP cc_start: 0.8270 (m-30) cc_final: 0.8054 (m-30)
REVERT: I  375 LYS cc_start: 0.8387 (ttmm) cc_final: 0.8173 (ttmm)
  outliers start: 42
  outliers final: 28
  residues processed: 278
  average time/residue: 0.0927
  time to fit residues: 32.1482
Evaluate side-chains
  285 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 255
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
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  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  306 VAL
Chi-restraints excluded: chain J residue  319 THR
Chi-restraints excluded: chain J residue  320 SER
Chi-restraints excluded: chain J residue  337 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 49 optimal weight:   10.0000
   chunk 38 optimal weight:    6.9990
   chunk 7 optimal weight:   10.0000
   chunk 34 optimal weight:    1.9990
   chunk 29 optimal weight:   10.0000
   chunk 18 optimal weight:    6.9990
   chunk 48 optimal weight:    0.0980
   chunk 22 optimal weight:   10.0000
   chunk 41 optimal weight:    4.9990
   chunk 28 optimal weight:    0.5980
   overall best weight:    2.7386

-------------------------------------------------------------------------------
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
B 336 GLN
** 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

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.160132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.135250 restraints weight = 7282.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.139198 restraints weight = 2762.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.141633 restraints weight = 1477.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.143074 restraints weight = 973.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.144057 restraints weight = 751.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.4215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.2282

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= 0.228
  Angle     :  0.656   7.529   7970  Z= 0.340
  Chirality :  0.049   0.127    890
  Planarity :  0.004   0.034   1020
  Dihedral  :  6.276  45.994    805
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 16.57 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.001   0.000   ARG G 349 
 TYR   0.008   0.002   TYR G 310 
 PHE   0.019   0.003   PHE I 346 
 HIS   0.004   0.001   HIS I 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00540 ( 5960)
  covalent geometry    : angle       0.65598 ( 7970)
  hydrogen bonds       : bond        0.03181 (  128)
  hydrogen bonds       : angle       5.14269 (  384)

*********************** 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
  303 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 262
  time to evaluate  : 0.227 
Fit side-chains
REVERT: A  342 GLU cc_start: 0.4356 (pm20) cc_final: 0.3719 (pm20)
REVERT: A  368 ASN cc_start: 0.8328 (m110) cc_final: 0.7914 (m110)
REVERT: B  353 LYS cc_start: 0.9023 (tttp) cc_final: 0.8639 (tttm)
REVERT: D  340 LYS cc_start: 0.8481 (mtpp) cc_final: 0.7813 (mttt)
REVERT: E  310 TYR cc_start: 0.9213 (t80) cc_final: 0.8819 (t80)
REVERT: E  353 LYS cc_start: 0.8865 (tttm) cc_final: 0.8507 (tttp)
REVERT: F  340 LYS cc_start: 0.8363 (mtpp) cc_final: 0.7867 (mttt)
REVERT: G  342 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7099 (mp0)
REVERT: H  340 LYS cc_start: 0.8357 (mtpp) cc_final: 0.7920 (mttt)
REVERT: I  327 ASN cc_start: 0.8290 (t0) cc_final: 0.7716 (t0)
REVERT: I  345 ASP cc_start: 0.8258 (m-30) cc_final: 0.8055 (m-30)
REVERT: I  362 HIS cc_start: 0.7335 (OUTLIER) cc_final: 0.7081 (t70)
REVERT: I  375 LYS cc_start: 0.8378 (ttmm) cc_final: 0.8171 (ttmm)
  outliers start: 41
  outliers final: 35
  residues processed: 269
  average time/residue: 0.0941
  time to fit residues: 31.5443
Evaluate side-chains
  286 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 249
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
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 D residue  306 VAL
Chi-restraints excluded: chain D residue  315 LEU
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  373 THR
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 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  306 VAL
Chi-restraints excluded: chain I residue  319 THR
Chi-restraints excluded: chain I residue  337 VAL
Chi-restraints excluded: chain I residue  362 HIS
Chi-restraints excluded: chain J residue  306 VAL
Chi-restraints excluded: chain J residue  319 THR
Chi-restraints excluded: chain J residue  320 SER
Chi-restraints excluded: chain J residue  337 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 61 optimal weight:    0.4980
   chunk 6 optimal weight:    0.4980
   chunk 42 optimal weight:    2.9990
   chunk 9 optimal weight:    6.9990
   chunk 62 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   overall best weight:    1.9986

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.161369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.136398 restraints weight = 7380.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.140402 restraints weight = 2792.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.142878 restraints weight = 1502.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.144386 restraints weight = 992.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.145363 restraints weight = 762.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.4258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.2445

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= 0.178
  Angle     :  0.629   8.855   7970  Z= 0.324
  Chirality :  0.049   0.125    890
  Planarity :  0.004   0.037   1020
  Dihedral  :  5.842  48.391    802
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 18.51 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.63 (0.26), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.99 (0.20), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 349 
 TYR   0.006   0.001   TYR G 310 
 PHE   0.020   0.003   PHE E 346 
 HIS   0.003   0.001   HIS I 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 5960)
  covalent geometry    : angle       0.62874 ( 7970)
  hydrogen bonds       : bond        0.02862 (  128)
  hydrogen bonds       : angle       4.94111 (  384)

*********************** 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
  306 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 268
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A  310 TYR cc_start: 0.9079 (t80) cc_final: 0.8619 (t80)
REVERT: A  368 ASN cc_start: 0.8369 (m110) cc_final: 0.7963 (m110)
REVERT: A  378 PHE cc_start: 0.8914 (t80) cc_final: 0.8633 (t80)
REVERT: B  353 LYS cc_start: 0.9012 (tttp) cc_final: 0.8650 (tttm)
REVERT: C  342 GLU cc_start: 0.4463 (pm20) cc_final: 0.4103 (pm20)
REVERT: D  310 TYR cc_start: 0.9216 (t80) cc_final: 0.8817 (t80)
REVERT: D  340 LYS cc_start: 0.8411 (mtpp) cc_final: 0.7797 (mttt)
REVERT: E  310 TYR cc_start: 0.9234 (t80) cc_final: 0.8941 (t80)
REVERT: F  310 TYR cc_start: 0.9243 (t80) cc_final: 0.9038 (t80)
REVERT: F  340 LYS cc_start: 0.8391 (mtpp) cc_final: 0.7889 (mttt)
REVERT: G  342 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7053 (mp0)
REVERT: H  316 SER cc_start: 0.9142 (p) cc_final: 0.8875 (p)
REVERT: H  340 LYS cc_start: 0.8414 (mtpp) cc_final: 0.7907 (mttt)
REVERT: H  376 LEU cc_start: 0.8481 (tp) cc_final: 0.8238 (tp)
REVERT: I  327 ASN cc_start: 0.8381 (t0) cc_final: 0.7859 (t0)
REVERT: I  375 LYS cc_start: 0.8429 (ttmm) cc_final: 0.8216 (ttmm)
  outliers start: 38
  outliers final: 34
  residues processed: 276
  average time/residue: 0.0873
  time to fit residues: 30.1998
Evaluate side-chains
  290 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 255
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
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 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 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  306 VAL
Chi-restraints excluded: chain I residue  319 THR
Chi-restraints excluded: chain I residue  337 VAL
Chi-restraints excluded: chain J residue  306 VAL
Chi-restraints excluded: chain J residue  319 THR
Chi-restraints excluded: chain J residue  325 LEU
Chi-restraints excluded: chain J residue  337 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 50 optimal weight:    9.9990
   chunk 66 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 29 optimal weight:    9.9990
   chunk 58 optimal weight:    0.8980
   chunk 48 optimal weight:    8.9990
   chunk 36 optimal weight:    8.9990
   chunk 47 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 6 optimal weight:    0.3980
   overall best weight:    1.6586

-------------------------------------------------------------------------------
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
** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 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 = 0.4456 r_free = 0.4456 target = 0.164444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.139446 restraints weight = 7270.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.143486 restraints weight = 2767.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.145993 restraints weight = 1490.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.147500 restraints weight = 985.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.148443 restraints weight = 757.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.4306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.2642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   5960  Z= 0.162
  Angle     :  0.647   8.888   7970  Z= 0.333
  Chirality :  0.050   0.152    890
  Planarity :  0.004   0.033   1020
  Dihedral  :  5.775  55.234    802
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  5.52 %
    Allowed  : 19.10 %
    Favored  : 75.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.58 (0.26), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.96 (0.20), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG J 349 
 TYR   0.005   0.001   TYR I 310 
 PHE   0.019   0.003   PHE G 346 
 HIS   0.003   0.001   HIS I 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 5960)
  covalent geometry    : angle       0.64653 ( 7970)
  hydrogen bonds       : bond        0.02689 (  128)
  hydrogen bonds       : angle       4.83371 (  384)

*********************** 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
  307 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 270
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A  310 TYR cc_start: 0.9022 (t80) cc_final: 0.8590 (t80)
REVERT: A  368 ASN cc_start: 0.8323 (m110) cc_final: 0.7900 (m110)
REVERT: A  378 PHE cc_start: 0.8842 (t80) cc_final: 0.8618 (t80)
REVERT: B  353 LYS cc_start: 0.8980 (ttpp) cc_final: 0.8623 (tttm)
REVERT: C  342 GLU cc_start: 0.4254 (pm20) cc_final: 0.3971 (pm20)
REVERT: D  310 TYR cc_start: 0.9200 (t80) cc_final: 0.8785 (t80)
REVERT: D  340 LYS cc_start: 0.8425 (mtpp) cc_final: 0.7801 (mttt)
REVERT: E  310 TYR cc_start: 0.9225 (t80) cc_final: 0.8910 (t80)
REVERT: F  310 TYR cc_start: 0.9216 (t80) cc_final: 0.8995 (t80)
REVERT: F  325 LEU cc_start: 0.8871 (tp) cc_final: 0.8610 (pp)
REVERT: F  340 LYS cc_start: 0.8334 (mtpp) cc_final: 0.7823 (mttt)
REVERT: H  316 SER cc_start: 0.9118 (p) cc_final: 0.8844 (p)
REVERT: H  340 LYS cc_start: 0.8379 (mtpp) cc_final: 0.7883 (mttt)
REVERT: I  327 ASN cc_start: 0.8257 (t0) cc_final: 0.7735 (t0)
REVERT: I  375 LYS cc_start: 0.8376 (ttmm) cc_final: 0.8161 (ttmm)
REVERT: J  316 SER cc_start: 0.8796 (p) cc_final: 0.8590 (p)
REVERT: J  327 ASN cc_start: 0.7694 (t0) cc_final: 0.7080 (t0)
REVERT: J  362 HIS cc_start: 0.6802 (OUTLIER) cc_final: 0.6055 (t-90)
  outliers start: 37
  outliers final: 31
  residues processed: 279
  average time/residue: 0.0857
  time to fit residues: 30.2330
Evaluate side-chains
  288 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 256
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
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 D residue  306 VAL
Chi-restraints excluded: chain D residue  315 LEU
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 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  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
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 20 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0870
   chunk 33 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 47 optimal weight:    3.9990
   chunk 68 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0270
   chunk 36 optimal weight:   10.0000
   chunk 58 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.9620

-------------------------------------------------------------------------------
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
G 336 GLN
H 336 GLN
** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.168001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.142481 restraints weight = 7311.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.146697 restraints weight = 2790.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.149270 restraints weight = 1498.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.150930 restraints weight = 990.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.151831 restraints weight = 755.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.4356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.2857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5960  Z= 0.125
  Angle     :  0.627   9.018   7970  Z= 0.322
  Chirality :  0.049   0.149    890
  Planarity :  0.004   0.037   1020
  Dihedral  :  5.051  24.528    798
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 20.00 %
    Favored  : 75.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.53 (0.26), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.92 (0.20), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG I 349 
 TYR   0.004   0.001   TYR B 310 
 PHE   0.016   0.002   PHE G 346 
 HIS   0.002   0.001   HIS D 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 5960)
  covalent geometry    : angle       0.62714 ( 7970)
  hydrogen bonds       : bond        0.02425 (  128)
  hydrogen bonds       : angle       4.62719 (  384)

*********************** 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
  295 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 266
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A  310 TYR cc_start: 0.9048 (t80) cc_final: 0.8709 (t80)
REVERT: A  368 ASN cc_start: 0.8327 (m110) cc_final: 0.7994 (m110)
REVERT: B  353 LYS cc_start: 0.9061 (ttpp) cc_final: 0.8727 (tttm)
REVERT: D  310 TYR cc_start: 0.9164 (t80) cc_final: 0.8792 (t80)
REVERT: D  340 LYS cc_start: 0.8565 (mtpp) cc_final: 0.7958 (mttt)
REVERT: E  327 ASN cc_start: 0.8579 (t0) cc_final: 0.7871 (t0)
REVERT: F  310 TYR cc_start: 0.9170 (t80) cc_final: 0.8941 (t80)
REVERT: F  340 LYS cc_start: 0.8379 (mtpp) cc_final: 0.7954 (mttt)
REVERT: H  316 SER cc_start: 0.9128 (p) cc_final: 0.8866 (p)
REVERT: H  327 ASN cc_start: 0.8597 (t0) cc_final: 0.8083 (t0)
REVERT: H  340 LYS cc_start: 0.8479 (mtpp) cc_final: 0.8013 (mttt)
REVERT: I  327 ASN cc_start: 0.8377 (t0) cc_final: 0.8014 (t0)
REVERT: I  375 LYS cc_start: 0.8415 (ttmm) cc_final: 0.8169 (ttmm)
REVERT: J  311 LYS cc_start: 0.5480 (tptt) cc_final: 0.3806 (pttp)
REVERT: J  316 SER cc_start: 0.8877 (p) cc_final: 0.8664 (p)
REVERT: J  327 ASN cc_start: 0.7862 (t0) cc_final: 0.7405 (t0)
REVERT: J  362 HIS cc_start: 0.6995 (OUTLIER) cc_final: 0.6366 (t-90)
  outliers start: 29
  outliers final: 25
  residues processed: 270
  average time/residue: 0.0878
  time to fit residues: 29.5912
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  : 0.161 
-------------------------------------------------------------------------------
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  315 LEU
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  320 SER
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 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 H residue  322 CYS
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 13 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 34 optimal weight:    0.8980
   chunk 26 optimal weight:    6.9990
   chunk 25 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9980
   chunk 7 optimal weight:   10.0000
   chunk 18 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 14 optimal weight:    6.9990
   overall best weight:    3.7786

-------------------------------------------------------------------------------
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
** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 368 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.158295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.133230 restraints weight = 7371.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.137138 restraints weight = 2878.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.139580 restraints weight = 1572.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.141072 restraints weight = 1046.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.142025 restraints weight = 806.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.4219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.2719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.061   5960  Z= 0.304
  Angle     :  0.756   8.640   7970  Z= 0.391
  Chirality :  0.052   0.199    890
  Planarity :  0.004   0.039   1020
  Dihedral  :  5.647  29.803    797
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.60 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 20.60 %
    Favored  : 74.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.63 (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
 ARG   0.001   0.000   ARG G 349 
 TYR   0.010   0.002   TYR F 310 
 PHE   0.024   0.004   PHE G 346 
 HIS   0.006   0.002   HIS F 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00726 ( 5960)
  covalent geometry    : angle       0.75636 ( 7970)
  hydrogen bonds       : bond        0.03543 (  128)
  hydrogen bonds       : angle       5.19543 (  384)

*********************** 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
  295 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 260
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  310 TYR cc_start: 0.9103 (t80) cc_final: 0.8654 (t80)
REVERT: A  368 ASN cc_start: 0.8422 (m110) cc_final: 0.8040 (m110)
REVERT: B  353 LYS cc_start: 0.9069 (ttpp) cc_final: 0.8645 (tttm)
REVERT: C  341 SER cc_start: 0.8596 (m) cc_final: 0.8291 (p)
REVERT: D  340 LYS cc_start: 0.8507 (mtpp) cc_final: 0.7913 (mttt)
REVERT: F  310 TYR cc_start: 0.9267 (t80) cc_final: 0.8869 (t80)
REVERT: F  340 LYS cc_start: 0.8466 (mtpp) cc_final: 0.7986 (mttt)
REVERT: F  342 GLU cc_start: 0.7178 (mp0) cc_final: 0.6825 (mp0)
REVERT: H  316 SER cc_start: 0.9112 (p) cc_final: 0.8866 (p)
REVERT: H  340 LYS cc_start: 0.8348 (mtpp) cc_final: 0.7869 (mttt)
REVERT: I  327 ASN cc_start: 0.8171 (t0) cc_final: 0.7481 (t0)
REVERT: I  375 LYS cc_start: 0.8472 (ttmm) cc_final: 0.8229 (ttmm)
REVERT: J  362 HIS cc_start: 0.7172 (OUTLIER) cc_final: 0.6172 (t-90)
  outliers start: 35
  outliers final: 31
  residues processed: 266
  average time/residue: 0.0877
  time to fit residues: 29.2782
Evaluate side-chains
  287 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 255
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
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  325 LEU
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  325 LEU
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 H residue  350 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 0 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 42 optimal weight:    9.9990
   chunk 59 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
** I 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 = 0.4451 r_free = 0.4451 target = 0.163933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.138570 restraints weight = 7379.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.142717 restraints weight = 2853.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.145209 restraints weight = 1545.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.146836 restraints weight = 1028.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.147731 restraints weight = 784.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.4299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.2892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5960  Z= 0.181
  Angle     :  0.696   9.049   7970  Z= 0.358
  Chirality :  0.051   0.210    890
  Planarity :  0.004   0.037   1020
  Dihedral  :  5.325  24.742    797
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 22.24 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.62 (0.26), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.99 (0.20), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG J 349 
 TYR   0.006   0.001   TYR A 310 
 PHE   0.020   0.003   PHE G 346 
 HIS   0.003   0.001   HIS I 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 5960)
  covalent geometry    : angle       0.69551 ( 7970)
  hydrogen bonds       : bond        0.02912 (  128)
  hydrogen bonds       : angle       4.86990 (  384)

*********************** 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
  297 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 267
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A  310 TYR cc_start: 0.9070 (t80) cc_final: 0.8667 (t80)
REVERT: A  368 ASN cc_start: 0.8393 (m110) cc_final: 0.8028 (m110)
REVERT: B  353 LYS cc_start: 0.9052 (ttpp) cc_final: 0.8661 (tttm)
REVERT: C  341 SER cc_start: 0.8607 (m) cc_final: 0.8287 (p)
REVERT: D  310 TYR cc_start: 0.9205 (t80) cc_final: 0.8825 (t80)
REVERT: D  340 LYS cc_start: 0.8530 (mtpp) cc_final: 0.7919 (mttt)
REVERT: F  310 TYR cc_start: 0.9230 (t80) cc_final: 0.8990 (t80)
REVERT: F  340 LYS cc_start: 0.8408 (mtpp) cc_final: 0.7938 (mttt)
REVERT: H  316 SER cc_start: 0.9113 (p) cc_final: 0.8840 (p)
REVERT: H  340 LYS cc_start: 0.8381 (mtpp) cc_final: 0.7888 (mttt)
REVERT: I  327 ASN cc_start: 0.8103 (t0) cc_final: 0.7494 (t0)
REVERT: I  375 LYS cc_start: 0.8429 (ttmm) cc_final: 0.8180 (ttmm)
REVERT: J  316 SER cc_start: 0.8846 (p) cc_final: 0.8640 (p)
REVERT: J  362 HIS cc_start: 0.7059 (OUTLIER) cc_final: 0.6300 (t-90)
  outliers start: 30
  outliers final: 29
  residues processed: 272
  average time/residue: 0.0881
  time to fit residues: 30.3548
Evaluate side-chains
  288 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 258
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
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  325 LEU
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 F residue  325 LEU
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 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  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 45 optimal weight:    0.7980
   chunk 12 optimal weight:    5.9990
   chunk 40 optimal weight:    6.9990
   chunk 49 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 7 optimal weight:   10.0000
   chunk 44 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 68 optimal weight:    0.6980
   chunk 59 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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
F 336 GLN
** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.170991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.145095 restraints weight = 7266.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.149466 restraints weight = 2814.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.152133 restraints weight = 1523.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.153846 restraints weight = 1007.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.154875 restraints weight = 766.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.4404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.3229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5960  Z= 0.122
  Angle     :  0.658   9.104   7970  Z= 0.337
  Chirality :  0.050   0.153    890
  Planarity :  0.004   0.040   1020
  Dihedral  :  5.035  21.556    797
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 24.78 %
    Favored  : 71.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.54 (0.26), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.93 (0.20), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG I 349 
 TYR   0.022   0.001   TYR J 310 
 PHE   0.017   0.002   PHE G 346 
 HIS   0.002   0.000   HIS C 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 5960)
  covalent geometry    : angle       0.65763 ( 7970)
  hydrogen bonds       : bond        0.02307 (  128)
  hydrogen bonds       : angle       4.49002 (  384)

********************** 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
  292 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 270
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A  310 TYR cc_start: 0.9082 (t80) cc_final: 0.8733 (t80)
REVERT: A  368 ASN cc_start: 0.8339 (m110) cc_final: 0.7989 (m110)
REVERT: B  353 LYS cc_start: 0.9061 (ttpp) cc_final: 0.8691 (tttm)
REVERT: C  341 SER cc_start: 0.8621 (m) cc_final: 0.8341 (p)
REVERT: D  310 TYR cc_start: 0.9167 (t80) cc_final: 0.8859 (t80)
REVERT: E  327 ASN cc_start: 0.8525 (t0) cc_final: 0.7816 (t0)
REVERT: F  340 LYS cc_start: 0.8384 (mtpp) cc_final: 0.7938 (mttt)
REVERT: H  316 SER cc_start: 0.9143 (p) cc_final: 0.8876 (p)
REVERT: H  327 ASN cc_start: 0.8638 (t0) cc_final: 0.8412 (t0)
REVERT: H  340 LYS cc_start: 0.8362 (mtpp) cc_final: 0.7999 (mttt)
REVERT: I  327 ASN cc_start: 0.8350 (t0) cc_final: 0.7840 (t0)
REVERT: J  311 LYS cc_start: 0.5630 (tptt) cc_final: 0.3683 (pttm)
REVERT: J  316 SER cc_start: 0.8850 (p) cc_final: 0.8632 (p)
REVERT: J  327 ASN cc_start: 0.7789 (t0) cc_final: 0.7319 (t0)
REVERT: J  362 HIS cc_start: 0.6964 (OUTLIER) cc_final: 0.6339 (t-90)
  outliers start: 22
  outliers final: 19
  residues processed: 275
  average time/residue: 0.0851
  time to fit residues: 29.6446
Evaluate side-chains
  284 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 264
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
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  325 LEU
Chi-restraints excluded: chain C residue  306 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  376 LEU
Chi-restraints excluded: chain E residue  306 VAL
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 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  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 8 optimal weight:    2.9990
   chunk 63 optimal weight:    8.9990
   chunk 33 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 18 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 21 optimal weight:   10.0000
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
B 336 GLN
** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 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 = 0.4454 r_free = 0.4454 target = 0.163491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.138269 restraints weight = 7321.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.142327 restraints weight = 2881.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.144921 restraints weight = 1578.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.146472 restraints weight = 1047.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.147421 restraints weight = 801.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.4298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.3048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   5960  Z= 0.224
  Angle     :  0.718   8.713   7970  Z= 0.372
  Chirality :  0.051   0.188    890
  Planarity :  0.004   0.043   1020
  Dihedral  :  5.372  26.204    796
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 24.33 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.57 (0.26), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.95 (0.20), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 349 
 TYR   0.009   0.002   TYR D 310 
 PHE   0.023   0.003   PHE G 346 
 HIS   0.005   0.001   HIS J 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 ( 5960)
  covalent geometry    : angle       0.71816 ( 7970)
  hydrogen bonds       : bond        0.03227 (  128)
  hydrogen bonds       : angle       4.93745 (  384)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1307.75 seconds
wall clock time: 23 minutes 46.18 seconds (1426.18 seconds total)