Starting phenix.real_space_refine
on Wed Sep 17 06:11:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b4m_44185/09_2025/9b4m_44185.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b4m_44185/09_2025/9b4m_44185.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b4m_44185/09_2025/9b4m_44185.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b4m_44185/09_2025/9b4m_44185.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b4m_44185/09_2025/9b4m_44185.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b4m_44185/09_2025/9b4m_44185.cif"
  }
  resolution = 3.1
  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
  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: 0.85, per 1000 atoms: 0.14
  Number of scatterers: 5870
  At special positions: 0
  Unit cell: (147.58, 81.78, 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: 0.48
  Conformation dependent library (CDL) restraints added in 233.6 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  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, 41.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310
      removed outlier: 6.268A  pdb=" N   VAL A 306 " --> pdb=" O   GLN D 307 " (cutoff:3.500A)
      removed outlier: 7.896A  pdb=" N   VAL D 309 " --> pdb=" O   VAL A 306 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ILE A 308 " --> pdb=" O   VAL D 309 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   VAL D 306 " --> pdb=" O   GLN F 307 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   VAL F 309 " --> pdb=" O   VAL D 306 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ILE D 308 " --> pdb=" O   VAL F 309 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   VAL F 306 " --> pdb=" O   GLN H 307 " (cutoff:3.500A)
      removed outlier: 7.896A  pdb=" N   VAL H 309 " --> pdb=" O   VAL F 306 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ILE F 308 " --> pdb=" O   VAL H 309 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   VAL H 306 " --> pdb=" O   GLN J 307 " (cutoff:3.500A)
      removed outlier: 7.896A  pdb=" N   VAL J 309 " --> pdb=" O   VAL H 306 " (cutoff:3.500A)
      removed outlier: 6.488A  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 325 through 330
      removed outlier: 5.908A  pdb=" N   GLY A 326 " --> pdb=" O   ASN D 327 " (cutoff:3.500A)
      removed outlier: 8.405A  pdb=" N   HIS D 329 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   ILE A 328 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
      removed outlier: 5.907A  pdb=" N   GLY D 326 " --> pdb=" O   ASN F 327 " (cutoff:3.500A)
      removed outlier: 8.405A  pdb=" N   HIS F 329 " --> pdb=" O   GLY D 326 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   ILE D 328 " --> pdb=" O   HIS F 329 " (cutoff:3.500A)
      removed outlier: 5.907A  pdb=" N   GLY F 326 " --> pdb=" O   ASN H 327 " (cutoff:3.500A)
      removed outlier: 8.405A  pdb=" N   HIS H 329 " --> pdb=" O   GLY F 326 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   ILE F 328 " --> pdb=" O   HIS H 329 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   GLY H 326 " --> pdb=" O   ASN J 327 " (cutoff:3.500A)
      removed outlier: 8.405A  pdb=" N   HIS J 329 " --> pdb=" O   GLY H 326 " (cutoff:3.500A)
      removed outlier: 6.259A  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 337 through 338
      removed outlier: 6.550A  pdb=" N   VAL A 337 " --> pdb=" O   GLU D 338 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   VAL D 337 " --> pdb=" O   GLU F 338 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   VAL F 337 " --> pdb=" O   GLU H 338 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   VAL H 337 " --> pdb=" O   GLU J 338 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 346
      removed outlier: 6.458A  pdb=" N   LEU A 344 " --> pdb=" O   ASP D 345 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   LEU D 344 " --> pdb=" O   ASP F 345 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   LEU F 344 " --> pdb=" O   ASP H 345 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   LEU H 344 " --> pdb=" O   ASP J 345 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 362
      removed outlier: 6.915A  pdb=" N   GLY A 355 " --> pdb=" O   SER D 356 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   ASP D 358 " --> pdb=" O   GLY A 355 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   LEU A 357 " --> pdb=" O   ASP D 358 " (cutoff:3.500A)
      removed outlier: 8.350A  pdb=" N   ILE D 360 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   ASN A 359 " --> pdb=" O   ILE D 360 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   HIS D 362 " --> pdb=" O   ASN A 359 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   THR A 361 " --> pdb=" O   HIS D 362 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   GLY D 355 " --> pdb=" O   SER F 356 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   ASP F 358 " --> pdb=" O   GLY D 355 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   LEU D 357 " --> pdb=" O   ASP F 358 " (cutoff:3.500A)
      removed outlier: 8.351A  pdb=" N   ILE F 360 " --> pdb=" O   LEU D 357 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   ASN D 359 " --> pdb=" O   ILE F 360 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   HIS F 362 " --> pdb=" O   ASN D 359 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   THR D 361 " --> pdb=" O   HIS F 362 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   GLY F 355 " --> pdb=" O   SER H 356 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   ASP H 358 " --> pdb=" O   GLY F 355 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   LEU F 357 " --> pdb=" O   ASP H 358 " (cutoff:3.500A)
      removed outlier: 8.351A  pdb=" N   ILE H 360 " --> pdb=" O   LEU F 357 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   ASN F 359 " --> pdb=" O   ILE H 360 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   HIS H 362 " --> pdb=" O   ASN F 359 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   THR F 361 " --> pdb=" O   HIS H 362 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   GLY H 355 " --> pdb=" O   SER J 356 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   ASP J 358 " --> pdb=" O   GLY H 355 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   LEU H 357 " --> pdb=" O   ASP J 358 " (cutoff:3.500A)
      removed outlier: 8.350A  pdb=" N   ILE J 360 " --> pdb=" O   LEU H 357 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   ASN H 359 " --> pdb=" O   ILE J 360 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   HIS J 362 " --> pdb=" O   ASN H 359 " (cutoff:3.500A)
      removed outlier: 6.288A  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: 6.267A  pdb=" N   VAL B 306 " --> pdb=" O   GLN E 307 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   VAL E 309 " --> pdb=" O   VAL B 306 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ILE B 308 " --> pdb=" O   VAL E 309 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   VAL E 306 " --> pdb=" O   GLN G 307 " (cutoff:3.500A)
      removed outlier: 7.896A  pdb=" N   VAL G 309 " --> pdb=" O   VAL E 306 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ILE E 308 " --> pdb=" O   VAL G 309 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   VAL G 306 " --> pdb=" O   GLN I 307 " (cutoff:3.500A)
      removed outlier: 7.896A  pdb=" N   VAL I 309 " --> pdb=" O   VAL G 306 " (cutoff:3.500A)
      removed outlier: 6.488A  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: 6.762A  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: 6.756A  pdb=" N   LYS B 317 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 325 through 330
      removed outlier: 6.848A  pdb=" N   GLY C 326 " --> pdb=" O   LEU B 325 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   ASN B 327 " --> pdb=" O   GLY C 326 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   GLY B 326 " --> pdb=" O   ASN E 327 " (cutoff:3.500A)
      removed outlier: 8.405A  pdb=" N   HIS E 329 " --> pdb=" O   GLY B 326 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   ILE B 328 " --> pdb=" O   HIS E 329 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   GLY E 326 " --> pdb=" O   ASN G 327 " (cutoff:3.500A)
      removed outlier: 8.405A  pdb=" N   HIS G 329 " --> pdb=" O   GLY E 326 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   ILE E 328 " --> pdb=" O   HIS G 329 " (cutoff:3.500A)
      removed outlier: 5.907A  pdb=" N   GLY G 326 " --> pdb=" O   ASN I 327 " (cutoff:3.500A)
      removed outlier: 8.406A  pdb=" N   HIS I 329 " --> pdb=" O   GLY G 326 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   ILE G 328 " --> pdb=" O   HIS I 329 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 337 through 338
      removed outlier: 6.550A  pdb=" N   VAL B 337 " --> pdb=" O   GLU E 338 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   VAL E 337 " --> pdb=" O   GLU G 338 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   VAL G 337 " --> pdb=" O   GLU I 338 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 343 through 346
      removed outlier: 6.458A  pdb=" N   LEU B 344 " --> pdb=" O   ASP E 345 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   LEU E 344 " --> pdb=" O   ASP G 345 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   LEU G 344 " --> pdb=" O   ASP I 345 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 354 through 362
      removed outlier: 6.968A  pdb=" N   GLY C 355 " --> pdb=" O   ILE B 354 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   GLY B 355 " --> pdb=" O   SER E 356 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   ASP E 358 " --> pdb=" O   GLY B 355 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   LEU B 357 " --> pdb=" O   ASP E 358 " (cutoff:3.500A)
      removed outlier: 8.351A  pdb=" N   ILE E 360 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   ASN B 359 " --> pdb=" O   ILE E 360 " (cutoff:3.500A)
      removed outlier: 7.836A  pdb=" N   HIS E 362 " --> pdb=" O   ASN B 359 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   THR B 361 " --> pdb=" O   HIS E 362 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   GLY E 355 " --> pdb=" O   SER G 356 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   ASP G 358 " --> pdb=" O   GLY E 355 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   LEU E 357 " --> pdb=" O   ASP G 358 " (cutoff:3.500A)
      removed outlier: 8.350A  pdb=" N   ILE G 360 " --> pdb=" O   LEU E 357 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   ASN E 359 " --> pdb=" O   ILE G 360 " (cutoff:3.500A)
      removed outlier: 7.836A  pdb=" N   HIS G 362 " --> pdb=" O   ASN E 359 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   THR E 361 " --> pdb=" O   HIS G 362 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   GLY G 355 " --> pdb=" O   SER I 356 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   ASP I 358 " --> pdb=" O   GLY G 355 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   LEU G 357 " --> pdb=" O   ASP I 358 " (cutoff:3.500A)
      removed outlier: 8.351A  pdb=" N   ILE I 360 " --> pdb=" O   LEU G 357 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   ASN G 359 " --> pdb=" O   ILE I 360 " (cutoff:3.500A)
      removed outlier: 7.836A  pdb=" N   HIS I 362 " --> pdb=" O   ASN G 359 " (cutoff:3.500A)
      removed outlier: 6.287A  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: 6.577A  pdb=" N   LYS B 369 " --> pdb=" O   LYS C 370 " (cutoff:3.500A)
      removed outlier: 8.211A  pdb=" N   GLU C 372 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   ILE B 371 " --> pdb=" O   GLU C 372 " (cutoff:3.500A)
      removed outlier: 7.991A  pdb=" N   HIS C 374 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   THR B 373 " --> pdb=" O   HIS C 374 " (cutoff:3.500A)
      removed outlier: 8.125A  pdb=" N   LEU C 376 " --> pdb=" O   THR B 373 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   LYS B 375 " --> pdb=" O   LEU C 376 " (cutoff:3.500A)
      removed outlier: 7.923A  pdb=" N   PHE C 378 " --> pdb=" O   LYS B 375 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   THR B 377 " --> pdb=" O   PHE C 378 " (cutoff:3.500A)

    95 hydrogen bonds defined for protein.
    285 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: 0.89

  Time building geometry restraints manager: 0.65 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 -     1.46: 822
        1.46 -     1.57: 3178
        1.57 -     1.69: 0
        1.69 -     1.80: 10
  Bond restraints: 5960
  Sorted by residual:
  bond pdb=" CA  ASN H 327 "
       pdb=" C   ASN H 327 "
    ideal  model  delta    sigma   weight residual
    1.530  1.519  0.011 1.17e-02 7.31e+03 8.79e-01
  bond pdb=" CA  ASN C 327 "
       pdb=" C   ASN C 327 "
    ideal  model  delta    sigma   weight residual
    1.530  1.519  0.011 1.17e-02 7.31e+03 8.48e-01
  bond pdb=" CA  ASN J 327 "
       pdb=" C   ASN J 327 "
    ideal  model  delta    sigma   weight residual
    1.530  1.519  0.011 1.17e-02 7.31e+03 8.42e-01
  bond pdb=" CA  ASN G 327 "
       pdb=" C   ASN G 327 "
    ideal  model  delta    sigma   weight residual
    1.530  1.520  0.011 1.17e-02 7.31e+03 8.23e-01
  bond pdb=" CA  ASN E 327 "
       pdb=" C   ASN E 327 "
    ideal  model  delta    sigma   weight residual
    1.530  1.520  0.011 1.17e-02 7.31e+03 8.21e-01
  ... (remaining 5955 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.83: 6988
        0.83 -     1.65: 810
        1.65 -     2.48: 92
        2.48 -     3.31: 50
        3.31 -     4.14: 30
  Bond angle restraints: 7970
  Sorted by residual:
  angle pdb=" C   PHE E 346 "
        pdb=" N   LYS E 347 "
        pdb=" CA  LYS E 347 "
      ideal   model   delta    sigma   weight residual
     123.24  119.61    3.63 1.54e+00 4.22e-01 5.56e+00
  angle pdb=" C   PHE F 346 "
        pdb=" N   LYS F 347 "
        pdb=" CA  LYS F 347 "
      ideal   model   delta    sigma   weight residual
     123.24  119.61    3.63 1.54e+00 4.22e-01 5.56e+00
  angle pdb=" C   PHE I 346 "
        pdb=" N   LYS I 347 "
        pdb=" CA  LYS I 347 "
      ideal   model   delta    sigma   weight residual
     123.24  119.61    3.63 1.54e+00 4.22e-01 5.56e+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  119.61    3.63 1.54e+00 4.22e-01 5.55e+00
  angle pdb=" C   PHE H 346 "
        pdb=" N   LYS H 347 "
        pdb=" CA  LYS H 347 "
      ideal   model   delta    sigma   weight residual
     123.24  119.61    3.63 1.54e+00 4.22e-01 5.55e+00
  ... (remaining 7965 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.73: 3090
       11.73 -    23.47: 420
       23.47 -    35.20: 70
       35.20 -    46.93: 30
       46.93 -    58.66: 20
  Dihedral angle restraints: 3630
    sinusoidal: 1520
      harmonic: 2110
  Sorted by residual:
  dihedral pdb=" CA  LYS B 347 "
           pdb=" C   LYS B 347 "
           pdb=" N   ASP B 348 "
           pdb=" CA  ASP B 348 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.18   16.82     0      5.00e+00 4.00e-02 1.13e+01
  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  163.20   16.80     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CA  LYS C 347 "
           pdb=" C   LYS C 347 "
           pdb=" N   ASP C 348 "
           pdb=" CA  ASP C 348 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.20   16.80     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 3627 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.023: 477
       0.023 -    0.047: 222
       0.047 -    0.070: 61
       0.070 -    0.094: 20
       0.094 -    0.117: 110
  Chirality restraints: 890
  Sorted by residual:
  chirality pdb=" CA  VAL E 350 "
            pdb=" N   VAL E 350 "
            pdb=" C   VAL E 350 "
            pdb=" CB  VAL E 350 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.43e-01
  chirality pdb=" CA  VAL A 350 "
            pdb=" N   VAL A 350 "
            pdb=" C   VAL A 350 "
            pdb=" CB  VAL A 350 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.41e-01
  chirality pdb=" CA  VAL J 350 "
            pdb=" N   VAL J 350 "
            pdb=" C   VAL J 350 "
            pdb=" CB  VAL J 350 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.41e-01
  ... (remaining 887 not shown)

  Planarity restraints: 1020
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 331 "    0.022 5.00e-02 4.00e+02   3.32e-02 1.76e+00
        pdb=" N   PRO C 332 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO C 332 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C 332 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS G 331 "    0.022 5.00e-02 4.00e+02   3.32e-02 1.76e+00
        pdb=" N   PRO G 332 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO G 332 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO G 332 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS I 331 "    0.022 5.00e-02 4.00e+02   3.31e-02 1.76e+00
        pdb=" N   PRO I 332 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO I 332 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO I 332 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1017 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 1703
        2.83 -     3.35: 4768
        3.35 -     3.86: 9765
        3.86 -     4.38: 10129
        4.38 -     4.90: 21280
  Nonbonded interactions: 47645
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS I 370 "
            pdb=" OE1 GLU I 372 "
     model   vdw
     2.311 3.120
  nonbonded pdb=" NZ  LYS E 370 "
            pdb=" OE1 GLU E 372 "
     model   vdw
     2.311 3.120
  nonbonded pdb=" NZ  LYS C 370 "
            pdb=" OE1 GLU C 372 "
     model   vdw
     2.311 3.120
  nonbonded pdb=" NZ  LYS H 370 "
            pdb=" OE1 GLU H 372 "
     model   vdw
     2.311 3.120
  nonbonded pdb=" NZ  LYS J 370 "
            pdb=" OE1 GLU J 372 "
     model   vdw
     2.311 3.120
  ... (remaining 47640 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.490
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
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   0.025   5960  Z= 0.274
  Angle     :  0.603   4.136   7970  Z= 0.342
  Chirality :  0.046   0.117    890
  Planarity :  0.004   0.033   1020
  Dihedral  : 11.897  58.665   2290
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.33 %
    Favored  : 90.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.45 %
    Favored  : 89.55 %
  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: -3.19 (0.24), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.42 (0.18), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG J 349 
 TYR   0.011   0.003   TYR C 310 
 PHE   0.007   0.002   PHE F 346 
 HIS   0.002   0.001   HIS J 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00584 ( 5960)
  covalent geometry    : angle       0.60307 ( 7970)
  hydrogen bonds       : bond        0.15568 (   95)
  hydrogen bonds       : angle       7.07756 (  285)

*********************** 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
  410 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 410
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A  317 LYS cc_start: 0.8944 (ptpt) cc_final: 0.8581 (ptpp)
REVERT: A  331 LYS cc_start: 0.9215 (mtmt) cc_final: 0.8983 (mttp)
REVERT: B  317 LYS cc_start: 0.8504 (ptpt) cc_final: 0.8026 (ptpp)
REVERT: B  321 LYS cc_start: 0.9174 (mtmm) cc_final: 0.8844 (mttm)
REVERT: B  331 LYS cc_start: 0.9319 (mtmt) cc_final: 0.9055 (mttt)
REVERT: B  340 LYS cc_start: 0.8827 (ttmm) cc_final: 0.8213 (mttp)
REVERT: B  342 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8413 (mp0)
REVERT: B  356 SER cc_start: 0.9570 (p) cc_final: 0.9154 (p)
REVERT: B  375 LYS cc_start: 0.8827 (ttmm) cc_final: 0.8605 (tttt)
REVERT: C  317 LYS cc_start: 0.9021 (ptpt) cc_final: 0.8559 (ptpp)
REVERT: C  340 LYS cc_start: 0.8938 (ttmm) cc_final: 0.8470 (mttp)
REVERT: C  356 SER cc_start: 0.9224 (p) cc_final: 0.8952 (p)
REVERT: D  317 LYS cc_start: 0.8477 (ptpt) cc_final: 0.8109 (ptpp)
REVERT: D  331 LYS cc_start: 0.9282 (mtmt) cc_final: 0.8899 (mttt)
REVERT: D  340 LYS cc_start: 0.8817 (ttmm) cc_final: 0.8362 (mttp)
REVERT: D  342 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8369 (mm-30)
REVERT: D  356 SER cc_start: 0.9553 (p) cc_final: 0.9230 (p)
REVERT: D  357 LEU cc_start: 0.9152 (tt) cc_final: 0.8945 (tt)
REVERT: E  317 LYS cc_start: 0.8449 (ptpt) cc_final: 0.7999 (ptpp)
REVERT: E  327 ASN cc_start: 0.9120 (t0) cc_final: 0.8740 (t0)
REVERT: E  331 LYS cc_start: 0.9274 (mtmt) cc_final: 0.8915 (mttp)
REVERT: E  338 GLU cc_start: 0.8657 (tt0) cc_final: 0.8385 (tt0)
REVERT: E  340 LYS cc_start: 0.8919 (ttmm) cc_final: 0.8326 (mttm)
REVERT: E  342 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8231 (mp0)
REVERT: E  343 LYS cc_start: 0.8751 (mppt) cc_final: 0.8455 (ttmt)
REVERT: E  356 SER cc_start: 0.9564 (p) cc_final: 0.9227 (p)
REVERT: E  370 LYS cc_start: 0.9091 (tttm) cc_final: 0.8782 (tttm)
REVERT: F  317 LYS cc_start: 0.8423 (ptpt) cc_final: 0.8059 (ptpp)
REVERT: F  340 LYS cc_start: 0.8838 (ttmm) cc_final: 0.8358 (mttp)
REVERT: F  342 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8139 (mm-30)
REVERT: F  343 LYS cc_start: 0.8685 (mppt) cc_final: 0.8439 (mtpp)
REVERT: F  356 SER cc_start: 0.9546 (p) cc_final: 0.9172 (p)
REVERT: G  317 LYS cc_start: 0.8382 (ptpt) cc_final: 0.7983 (ptpp)
REVERT: G  331 LYS cc_start: 0.9327 (mtmt) cc_final: 0.9012 (mttt)
REVERT: G  340 LYS cc_start: 0.8784 (ttmm) cc_final: 0.8245 (mttm)
REVERT: G  342 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8260 (mp0)
REVERT: G  343 LYS cc_start: 0.8721 (mppt) cc_final: 0.8211 (mtpp)
REVERT: G  356 SER cc_start: 0.9537 (p) cc_final: 0.9160 (p)
REVERT: G  370 LYS cc_start: 0.9077 (tttm) cc_final: 0.8867 (tttm)
REVERT: H  317 LYS cc_start: 0.8444 (ptpt) cc_final: 0.8234 (ptmt)
REVERT: H  331 LYS cc_start: 0.9280 (mtmt) cc_final: 0.9000 (mttt)
REVERT: H  340 LYS cc_start: 0.8794 (ttmm) cc_final: 0.8179 (mttp)
REVERT: H  342 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8406 (mp0)
REVERT: H  344 LEU cc_start: 0.9471 (mp) cc_final: 0.9174 (mp)
REVERT: H  356 SER cc_start: 0.9548 (p) cc_final: 0.9204 (p)
REVERT: I  317 LYS cc_start: 0.8558 (ptpt) cc_final: 0.8080 (ptpp)
REVERT: I  325 LEU cc_start: 0.8930 (tp) cc_final: 0.8717 (tp)
REVERT: I  331 LYS cc_start: 0.9339 (mtmt) cc_final: 0.8949 (mttp)
REVERT: I  336 GLN cc_start: 0.9201 (tp40) cc_final: 0.8497 (tp40)
REVERT: I  356 SER cc_start: 0.9364 (p) cc_final: 0.8991 (p)
REVERT: J  317 LYS cc_start: 0.8617 (ptpt) cc_final: 0.8137 (ptpp)
REVERT: J  321 LYS cc_start: 0.9176 (mtmm) cc_final: 0.8891 (mttm)
REVERT: J  331 LYS cc_start: 0.9294 (mtmt) cc_final: 0.7438 (tmtt)
REVERT: J  340 LYS cc_start: 0.8829 (ttmm) cc_final: 0.8138 (mttm)
REVERT: J  343 LYS cc_start: 0.8767 (mppt) cc_final: 0.8390 (ttmt)
REVERT: J  356 SER cc_start: 0.9442 (p) cc_final: 0.9106 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 410
  average time/residue: 0.1105
  time to fit residues: 55.1398
Evaluate side-chains
  371 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 371
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.2980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    0.0770
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.8744

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

Flipped N/Q/H residues before XYZ refinement:
B 368 ASN
C 362 HIS
F 368 ASN
H 368 ASN
J 368 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.130923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.112235 restraints weight = 9196.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3861 rms_B_bonded: 3.29
r_work: 0.3738 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   5960  Z= 0.105
  Angle     :  0.636   8.905   7970  Z= 0.298
  Chirality :  0.050   0.139    890
  Planarity :  0.004   0.025   1020
  Dihedral  :  4.358  14.927    790
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 20.15 %
    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: -3.03 (0.24), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.30 (0.18), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG I 349 
 TYR   0.005   0.001   TYR G 310 
 PHE   0.009   0.002   PHE G 378 
 HIS   0.002   0.000   HIS H 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 5960)
  covalent geometry    : angle       0.63585 ( 7970)
  hydrogen bonds       : bond        0.02435 (   95)
  hydrogen bonds       : angle       4.67870 (  285)

*********************** 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
  422 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 414
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 LYS cc_start: 0.8859 (ptpt) cc_final: 0.8455 (ptpp)
REVERT: A  331 LYS cc_start: 0.9221 (mtmt) cc_final: 0.8964 (mttp)
REVERT: A  343 LYS cc_start: 0.8794 (mttp) cc_final: 0.8438 (mtpp)
REVERT: B  317 LYS cc_start: 0.8298 (ptpt) cc_final: 0.7850 (ptpp)
REVERT: B  321 LYS cc_start: 0.9203 (mtmm) cc_final: 0.8860 (mttm)
REVERT: B  331 LYS cc_start: 0.9165 (mtmt) cc_final: 0.8950 (mttt)
REVERT: B  340 LYS cc_start: 0.8810 (ttmm) cc_final: 0.7931 (mttm)
REVERT: B  342 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8379 (mm-30)
REVERT: B  356 SER cc_start: 0.9510 (p) cc_final: 0.9216 (p)
REVERT: B  370 LYS cc_start: 0.8913 (tttm) cc_final: 0.8686 (tttp)
REVERT: B  375 LYS cc_start: 0.8893 (ttmm) cc_final: 0.8572 (tttt)
REVERT: C  317 LYS cc_start: 0.8848 (ptpt) cc_final: 0.8457 (ptpp)
REVERT: C  340 LYS cc_start: 0.8866 (ttmm) cc_final: 0.8565 (mttm)
REVERT: C  341 SER cc_start: 0.9079 (m) cc_final: 0.8788 (p)
REVERT: C  342 GLU cc_start: 0.5320 (pm20) cc_final: 0.5085 (pm20)
REVERT: C  343 LYS cc_start: 0.8796 (ttmt) cc_final: 0.8331 (mtpp)
REVERT: C  356 SER cc_start: 0.9067 (p) cc_final: 0.8749 (p)
REVERT: D  317 LYS cc_start: 0.8098 (ptpt) cc_final: 0.7702 (ptpp)
REVERT: D  331 LYS cc_start: 0.9191 (mtmt) cc_final: 0.8818 (mttp)
REVERT: D  342 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8555 (mp0)
REVERT: D  343 LYS cc_start: 0.9087 (mttt) cc_final: 0.8503 (mtpp)
REVERT: E  310 TYR cc_start: 0.9173 (t80) cc_final: 0.8652 (t80)
REVERT: E  317 LYS cc_start: 0.8024 (ptpt) cc_final: 0.7736 (ptmt)
REVERT: E  327 ASN cc_start: 0.9114 (t0) cc_final: 0.8774 (t0)
REVERT: E  331 LYS cc_start: 0.9184 (mtmt) cc_final: 0.8873 (mttp)
REVERT: E  340 LYS cc_start: 0.8806 (ttmm) cc_final: 0.8260 (mttm)
REVERT: E  342 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8284 (mp0)
REVERT: E  343 LYS cc_start: 0.8674 (mppt) cc_final: 0.8384 (ttmt)
REVERT: E  356 SER cc_start: 0.9575 (p) cc_final: 0.9271 (p)
REVERT: F  317 LYS cc_start: 0.7937 (ptpt) cc_final: 0.7544 (ptpp)
REVERT: F  331 LYS cc_start: 0.9175 (mtmt) cc_final: 0.8772 (mttp)
REVERT: F  340 LYS cc_start: 0.8755 (ttmm) cc_final: 0.8221 (mttp)
REVERT: F  342 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8684 (mp0)
REVERT: F  343 LYS cc_start: 0.8705 (mppt) cc_final: 0.8486 (mttp)
REVERT: F  356 SER cc_start: 0.9501 (p) cc_final: 0.9299 (p)
REVERT: G  317 LYS cc_start: 0.7922 (ptpt) cc_final: 0.7528 (ptpp)
REVERT: G  331 LYS cc_start: 0.9121 (mtmt) cc_final: 0.8914 (mttt)
REVERT: G  342 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8507 (mp0)
REVERT: G  356 SER cc_start: 0.9518 (p) cc_final: 0.9283 (p)
REVERT: G  358 ASP cc_start: 0.8708 (m-30) cc_final: 0.8452 (m-30)
REVERT: H  317 LYS cc_start: 0.8053 (ptpt) cc_final: 0.7403 (ptpp)
REVERT: H  331 LYS cc_start: 0.9126 (mtmt) cc_final: 0.8865 (mtmm)
REVERT: H  342 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8581 (mp0)
REVERT: H  356 SER cc_start: 0.9552 (p) cc_final: 0.9343 (p)
REVERT: I  317 LYS cc_start: 0.7909 (ptpt) cc_final: 0.7427 (ptpp)
REVERT: I  331 LYS cc_start: 0.9156 (mtmt) cc_final: 0.8847 (mttp)
REVERT: I  336 GLN cc_start: 0.9072 (tp40) cc_final: 0.8437 (tp40)
REVERT: I  340 LYS cc_start: 0.8810 (ttmm) cc_final: 0.8280 (mttp)
REVERT: I  343 LYS cc_start: 0.8985 (mttp) cc_final: 0.8506 (mtpp)
REVERT: I  356 SER cc_start: 0.9449 (p) cc_final: 0.9066 (p)
REVERT: J  317 LYS cc_start: 0.8199 (ptpt) cc_final: 0.7624 (ptpp)
REVERT: J  321 LYS cc_start: 0.9190 (mtmm) cc_final: 0.8897 (mttm)
REVERT: J  331 LYS cc_start: 0.9122 (mtmt) cc_final: 0.7341 (tmtt)
REVERT: J  340 LYS cc_start: 0.8793 (ttmm) cc_final: 0.8038 (mttm)
REVERT: J  356 SER cc_start: 0.9427 (p) cc_final: 0.9134 (p)
  outliers start: 8
  outliers final: 6
  residues processed: 416
  average time/residue: 0.1055
  time to fit residues: 53.9206
Evaluate side-chains
  398 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 392
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain E residue  373 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 23 optimal weight:    9.9990
   chunk 17 optimal weight:    7.9990
   chunk 64 optimal weight:   10.0000
   chunk 14 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 12 optimal weight:    6.9990
   chunk 21 optimal weight:    8.9990
   chunk 45 optimal weight:    7.9990
   chunk 32 optimal weight:    8.9990
   chunk 59 optimal weight:    4.9990
   chunk 33 optimal weight:    0.6980
   overall best weight:    4.5388

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

Flipped N/Q/H residues before XYZ refinement:
B 368 ASN
D 368 ASN
F 368 ASN
G 368 ASN
H 368 ASN
I 359 ASN
J 359 ASN
J 368 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.128213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.109523 restraints weight = 9185.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3811 rms_B_bonded: 3.20
r_work: 0.3687 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.034   5960  Z= 0.335
  Angle     :  0.736   8.207   7970  Z= 0.361
  Chirality :  0.051   0.141    890
  Planarity :  0.005   0.038   1020
  Dihedral  :  4.910  17.743    790
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 19.85 %
    Favored  : 75.07 %
  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: -3.13 (0.24), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.38 (0.18), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 349 
 TYR   0.023   0.004   TYR A 310 
 PHE   0.012   0.002   PHE G 378 
 HIS   0.005   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00767 ( 5960)
  covalent geometry    : angle       0.73598 ( 7970)
  hydrogen bonds       : bond        0.03938 (   95)
  hydrogen bonds       : angle       5.06633 (  285)

*********************** 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
  431 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 397
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A  317 LYS cc_start: 0.8917 (ptpt) cc_final: 0.8517 (ptpp)
REVERT: A  331 LYS cc_start: 0.9334 (mtmt) cc_final: 0.8952 (mttp)
REVERT: A  340 LYS cc_start: 0.9131 (ttmm) cc_final: 0.8817 (mttp)
REVERT: A  343 LYS cc_start: 0.8776 (mttp) cc_final: 0.8463 (mtpp)
REVERT: B  317 LYS cc_start: 0.8349 (ptpt) cc_final: 0.7932 (ptpp)
REVERT: B  321 LYS cc_start: 0.9143 (mtmm) cc_final: 0.8773 (mttm)
REVERT: B  331 LYS cc_start: 0.9263 (mtmt) cc_final: 0.8896 (mttt)
REVERT: B  340 LYS cc_start: 0.8905 (ttmm) cc_final: 0.8099 (mttm)
REVERT: B  342 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8573 (mp0)
REVERT: B  356 SER cc_start: 0.9577 (p) cc_final: 0.9374 (p)
REVERT: B  370 LYS cc_start: 0.9063 (tttm) cc_final: 0.8666 (tttm)
REVERT: B  375 LYS cc_start: 0.8966 (ttmm) cc_final: 0.8606 (tttt)
REVERT: C  310 TYR cc_start: 0.9077 (t80) cc_final: 0.8684 (t80)
REVERT: C  317 LYS cc_start: 0.8947 (ptpt) cc_final: 0.8550 (ptpp)
REVERT: C  340 LYS cc_start: 0.8997 (ttmm) cc_final: 0.8518 (mttp)
REVERT: C  356 SER cc_start: 0.9097 (p) cc_final: 0.8865 (p)
REVERT: D  317 LYS cc_start: 0.8172 (ptpt) cc_final: 0.7780 (ptpp)
REVERT: D  331 LYS cc_start: 0.9218 (mtmt) cc_final: 0.8755 (mttt)
REVERT: D  340 LYS cc_start: 0.8908 (ttmm) cc_final: 0.8343 (mttp)
REVERT: D  343 LYS cc_start: 0.9150 (mttt) cc_final: 0.8569 (mtpp)
REVERT: E  310 TYR cc_start: 0.9239 (t80) cc_final: 0.8686 (t80)
REVERT: E  317 LYS cc_start: 0.8173 (ptpt) cc_final: 0.7702 (ptpp)
REVERT: E  327 ASN cc_start: 0.9156 (t0) cc_final: 0.8697 (t0)
REVERT: E  331 LYS cc_start: 0.9260 (mtmt) cc_final: 0.8964 (mttt)
REVERT: E  338 GLU cc_start: 0.8890 (tt0) cc_final: 0.8467 (tt0)
REVERT: E  340 LYS cc_start: 0.8988 (ttmm) cc_final: 0.8351 (mttm)
REVERT: E  342 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8379 (mp0)
REVERT: E  343 LYS cc_start: 0.8803 (mppt) cc_final: 0.8516 (ttmt)
REVERT: E  372 GLU cc_start: 0.8924 (tt0) cc_final: 0.8555 (tt0)
REVERT: F  317 LYS cc_start: 0.8178 (ptpt) cc_final: 0.7819 (ptpp)
REVERT: F  325 LEU cc_start: 0.9400 (tp) cc_final: 0.9072 (tp)
REVERT: F  331 LYS cc_start: 0.9226 (mtmt) cc_final: 0.8734 (mttp)
REVERT: F  340 LYS cc_start: 0.8887 (ttmm) cc_final: 0.8398 (mttp)
REVERT: F  342 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8438 (mm-30)
REVERT: F  343 LYS cc_start: 0.8805 (mppt) cc_final: 0.8581 (mmtp)
REVERT: G  310 TYR cc_start: 0.9308 (t80) cc_final: 0.8845 (t80)
REVERT: G  317 LYS cc_start: 0.8135 (ptpt) cc_final: 0.7685 (ptpp)
REVERT: G  331 LYS cc_start: 0.9220 (mtmt) cc_final: 0.8857 (mttp)
REVERT: G  342 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8328 (mp0)
REVERT: H  317 LYS cc_start: 0.8122 (ptpt) cc_final: 0.7721 (ptpp)
REVERT: H  331 LYS cc_start: 0.9133 (mtmt) cc_final: 0.8778 (mttm)
REVERT: H  340 LYS cc_start: 0.8860 (ttmm) cc_final: 0.8182 (mttm)
REVERT: H  342 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8368 (mp0)
REVERT: H  343 LYS cc_start: 0.9073 (mttt) cc_final: 0.8666 (mtpp)
REVERT: H  356 SER cc_start: 0.9607 (p) cc_final: 0.9352 (p)
REVERT: I  317 LYS cc_start: 0.8170 (ptpt) cc_final: 0.7714 (ptpp)
REVERT: I  331 LYS cc_start: 0.9274 (mtmt) cc_final: 0.8876 (mttp)
REVERT: I  336 GLN cc_start: 0.9153 (tp40) cc_final: 0.8549 (tp40)
REVERT: I  343 LYS cc_start: 0.9064 (mttp) cc_final: 0.8601 (mtpp)
REVERT: I  353 LYS cc_start: 0.9158 (tttp) cc_final: 0.8944 (tttp)
REVERT: J  317 LYS cc_start: 0.8305 (ptpt) cc_final: 0.7874 (ptpp)
REVERT: J  321 LYS cc_start: 0.9224 (mtmm) cc_final: 0.8875 (mttm)
REVERT: J  331 LYS cc_start: 0.9182 (mtmt) cc_final: 0.7375 (tmtt)
REVERT: J  340 LYS cc_start: 0.8885 (ttmm) cc_final: 0.8149 (mttm)
  outliers start: 34
  outliers final: 30
  residues processed: 400
  average time/residue: 0.1076
  time to fit residues: 52.7214
Evaluate side-chains
  411 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 380
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain G residue  319 THR
Chi-restraints excluded: chain G residue  320 SER
Chi-restraints excluded: chain G residue  342 GLU
Chi-restraints excluded: chain H residue  319 THR
Chi-restraints excluded: chain H residue  320 SER
Chi-restraints excluded: chain H residue  328 ILE
Chi-restraints excluded: chain I residue  319 THR
Chi-restraints excluded: chain I residue  320 SER
Chi-restraints excluded: chain I residue  324 SER
Chi-restraints excluded: chain I residue  358 ASP
Chi-restraints excluded: chain J residue  319 THR
Chi-restraints excluded: chain J residue  320 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 7 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 22 optimal weight:    8.9990
   chunk 41 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
B 368 ASN
G 368 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.131208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.112342 restraints weight = 9209.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.3864 rms_B_bonded: 3.29
r_work: 0.3738 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.2478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   5960  Z= 0.230
  Angle     :  0.680   8.968   7970  Z= 0.328
  Chirality :  0.050   0.180    890
  Planarity :  0.005   0.040   1020
  Dihedral  :  4.743  14.870    790
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.47 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 22.99 %
    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: -3.10 (0.24), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.35 (0.18), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 349 
 TYR   0.018   0.003   TYR A 310 
 PHE   0.010   0.002   PHE G 378 
 HIS   0.003   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00528 ( 5960)
  covalent geometry    : angle       0.68025 ( 7970)
  hydrogen bonds       : bond        0.03309 (   95)
  hydrogen bonds       : angle       4.86259 (  285)

*********************** 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
  429 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 395
  time to evaluate  : 0.271 
Fit side-chains
REVERT: A  317 LYS cc_start: 0.8925 (ptpt) cc_final: 0.8507 (ptpp)
REVERT: A  331 LYS cc_start: 0.9329 (mtmt) cc_final: 0.8964 (mttp)
REVERT: A  340 LYS cc_start: 0.9063 (ttmm) cc_final: 0.8789 (mttp)
REVERT: A  343 LYS cc_start: 0.8632 (mttp) cc_final: 0.8394 (mtpp)
REVERT: B  317 LYS cc_start: 0.8346 (ptpt) cc_final: 0.7936 (ptpp)
REVERT: B  321 LYS cc_start: 0.9146 (mtmm) cc_final: 0.8763 (mttp)
REVERT: B  331 LYS cc_start: 0.9246 (mtmt) cc_final: 0.8917 (mttt)
REVERT: B  340 LYS cc_start: 0.8899 (ttmm) cc_final: 0.8129 (mttm)
REVERT: B  342 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8490 (mp0)
REVERT: B  370 LYS cc_start: 0.9039 (tttm) cc_final: 0.8664 (tttm)
REVERT: B  375 LYS cc_start: 0.8962 (ttmm) cc_final: 0.8609 (tttt)
REVERT: C  310 TYR cc_start: 0.9025 (t80) cc_final: 0.8593 (t80)
REVERT: C  317 LYS cc_start: 0.8921 (ptpt) cc_final: 0.8513 (ptpp)
REVERT: C  340 LYS cc_start: 0.9081 (ttmm) cc_final: 0.8515 (mttp)
REVERT: C  356 SER cc_start: 0.8970 (p) cc_final: 0.8763 (p)
REVERT: D  317 LYS cc_start: 0.8135 (ptpt) cc_final: 0.7753 (ptpp)
REVERT: D  331 LYS cc_start: 0.9178 (mtmt) cc_final: 0.8759 (mttt)
REVERT: D  340 LYS cc_start: 0.8897 (ttmm) cc_final: 0.8298 (mttp)
REVERT: D  343 LYS cc_start: 0.9129 (mttt) cc_final: 0.8554 (mtpp)
REVERT: E  310 TYR cc_start: 0.9203 (t80) cc_final: 0.8699 (t80)
REVERT: E  327 ASN cc_start: 0.9157 (t0) cc_final: 0.8669 (t0)
REVERT: E  331 LYS cc_start: 0.9246 (mtmt) cc_final: 0.8991 (mttt)
REVERT: E  338 GLU cc_start: 0.8891 (tt0) cc_final: 0.8384 (tt0)
REVERT: E  340 LYS cc_start: 0.8944 (ttmm) cc_final: 0.8207 (mttm)
REVERT: E  342 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8442 (mp0)
REVERT: E  343 LYS cc_start: 0.8743 (mppt) cc_final: 0.8474 (ttmt)
REVERT: E  372 GLU cc_start: 0.8884 (tt0) cc_final: 0.8530 (tt0)
REVERT: F  317 LYS cc_start: 0.8130 (ptpt) cc_final: 0.7753 (ptpp)
REVERT: F  331 LYS cc_start: 0.9186 (mtmt) cc_final: 0.8764 (mttp)
REVERT: F  340 LYS cc_start: 0.8829 (ttmm) cc_final: 0.8236 (mttp)
REVERT: F  342 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8590 (mp0)
REVERT: G  310 TYR cc_start: 0.9252 (t80) cc_final: 0.8932 (t80)
REVERT: G  317 LYS cc_start: 0.8084 (ptpt) cc_final: 0.7609 (ptpp)
REVERT: G  331 LYS cc_start: 0.9181 (mtmt) cc_final: 0.8833 (mttp)
REVERT: G  372 GLU cc_start: 0.8712 (tt0) cc_final: 0.8495 (tt0)
REVERT: H  317 LYS cc_start: 0.8105 (ptpt) cc_final: 0.7699 (ptpp)
REVERT: H  331 LYS cc_start: 0.9119 (mtmt) cc_final: 0.8875 (mtmm)
REVERT: H  340 LYS cc_start: 0.8820 (ttmm) cc_final: 0.8172 (mttp)
REVERT: H  342 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8444 (mp0)
REVERT: H  343 LYS cc_start: 0.9080 (mttt) cc_final: 0.8699 (mtpp)
REVERT: H  356 SER cc_start: 0.9631 (p) cc_final: 0.9272 (p)
REVERT: H  358 ASP cc_start: 0.8672 (m-30) cc_final: 0.8407 (m-30)
REVERT: I  317 LYS cc_start: 0.8150 (ptpt) cc_final: 0.7657 (ptpp)
REVERT: I  331 LYS cc_start: 0.9248 (mtmt) cc_final: 0.8820 (mttp)
REVERT: I  336 GLN cc_start: 0.9138 (tp40) cc_final: 0.8564 (tp40)
REVERT: I  340 LYS cc_start: 0.8914 (ttmm) cc_final: 0.8321 (mmtp)
REVERT: J  317 LYS cc_start: 0.8270 (ptpt) cc_final: 0.7844 (ptpp)
REVERT: J  321 LYS cc_start: 0.9234 (mtmm) cc_final: 0.8896 (mttm)
REVERT: J  331 LYS cc_start: 0.9163 (mtmt) cc_final: 0.7385 (tmtt)
REVERT: J  340 LYS cc_start: 0.8865 (ttmm) cc_final: 0.8216 (mttm)
REVERT: J  345 ASP cc_start: 0.8624 (t0) cc_final: 0.8331 (t0)
  outliers start: 34
  outliers final: 30
  residues processed: 397
  average time/residue: 0.1035
  time to fit residues: 50.4744
Evaluate side-chains
  415 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 385
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain F residue  356 SER
Chi-restraints excluded: chain G residue  319 THR
Chi-restraints excluded: chain G residue  320 SER
Chi-restraints excluded: chain H residue  319 THR
Chi-restraints excluded: chain H residue  320 SER
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain I residue  319 THR
Chi-restraints excluded: chain I residue  320 SER
Chi-restraints excluded: chain I residue  358 ASP
Chi-restraints excluded: chain J residue  319 THR
Chi-restraints excluded: chain J residue  320 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   chunk 6 optimal weight:    5.9990
   chunk 42 optimal weight:    8.9990
   chunk 9 optimal weight:    7.9990
   chunk 62 optimal weight:    7.9990
   chunk 11 optimal weight:    7.9990
   chunk 51 optimal weight:    6.9990
   chunk 13 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
B 368 ASN
G 368 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.130122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.111372 restraints weight = 9349.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3851 rms_B_bonded: 3.28
r_work: 0.3722 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.2591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.031   5960  Z= 0.272
  Angle     :  0.709   8.414   7970  Z= 0.345
  Chirality :  0.051   0.209    890
  Planarity :  0.005   0.046   1020
  Dihedral  :  4.840  15.643    790
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.07 %
    Favored  : 90.93 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 23.73 %
    Favored  : 70.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.09 (0.24), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.35 (0.18), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 349 
 TYR   0.020   0.004   TYR A 310 
 PHE   0.011   0.002   PHE C 346 
 HIS   0.003   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00625 ( 5960)
  covalent geometry    : angle       0.70936 ( 7970)
  hydrogen bonds       : bond        0.03528 (   95)
  hydrogen bonds       : angle       4.90391 (  285)

*********************** 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
  425 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 389
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A  317 LYS cc_start: 0.8942 (ptpt) cc_final: 0.8479 (ptpp)
REVERT: A  331 LYS cc_start: 0.9346 (mtmt) cc_final: 0.8980 (mttp)
REVERT: A  343 LYS cc_start: 0.8608 (mttp) cc_final: 0.8388 (mtpp)
REVERT: B  317 LYS cc_start: 0.8348 (ptpt) cc_final: 0.7943 (ptpp)
REVERT: B  321 LYS cc_start: 0.9149 (mtmm) cc_final: 0.8777 (mttm)
REVERT: B  331 LYS cc_start: 0.9271 (mtmt) cc_final: 0.8931 (mttt)
REVERT: B  340 LYS cc_start: 0.8952 (ttmm) cc_final: 0.8167 (mttm)
REVERT: B  342 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8466 (mp0)
REVERT: B  370 LYS cc_start: 0.9055 (tttm) cc_final: 0.8672 (tttm)
REVERT: B  375 LYS cc_start: 0.8949 (ttmm) cc_final: 0.8581 (tttt)
REVERT: C  310 TYR cc_start: 0.9020 (t80) cc_final: 0.8708 (t80)
REVERT: C  317 LYS cc_start: 0.8938 (ptpt) cc_final: 0.8532 (ptpp)
REVERT: C  340 LYS cc_start: 0.9107 (ttmm) cc_final: 0.8528 (mttp)
REVERT: C  343 LYS cc_start: 0.8690 (ttmt) cc_final: 0.8356 (mtpp)
REVERT: C  356 SER cc_start: 0.9051 (p) cc_final: 0.8837 (p)
REVERT: D  317 LYS cc_start: 0.8096 (ptpt) cc_final: 0.7726 (ptpp)
REVERT: D  331 LYS cc_start: 0.9201 (mtmt) cc_final: 0.8756 (mttt)
REVERT: D  340 LYS cc_start: 0.8934 (ttmm) cc_final: 0.8361 (mttp)
REVERT: D  343 LYS cc_start: 0.9136 (mttt) cc_final: 0.8559 (mtpp)
REVERT: E  310 TYR cc_start: 0.9207 (t80) cc_final: 0.8693 (t80)
REVERT: E  327 ASN cc_start: 0.9151 (t0) cc_final: 0.8654 (t0)
REVERT: E  331 LYS cc_start: 0.9264 (mtmt) cc_final: 0.8991 (mttt)
REVERT: E  338 GLU cc_start: 0.8908 (tt0) cc_final: 0.8521 (tt0)
REVERT: E  340 LYS cc_start: 0.8944 (ttmm) cc_final: 0.8346 (mttm)
REVERT: E  342 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8402 (mp0)
REVERT: E  343 LYS cc_start: 0.8773 (mppt) cc_final: 0.8530 (ttmt)
REVERT: E  372 GLU cc_start: 0.8914 (tt0) cc_final: 0.8559 (tt0)
REVERT: F  317 LYS cc_start: 0.8179 (ptpt) cc_final: 0.7808 (ptpp)
REVERT: F  331 LYS cc_start: 0.9188 (mtmt) cc_final: 0.8767 (mttp)
REVERT: F  340 LYS cc_start: 0.8846 (ttmm) cc_final: 0.8387 (mttp)
REVERT: F  342 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8430 (mm-30)
REVERT: F  343 LYS cc_start: 0.8942 (mttp) cc_final: 0.8433 (mtpp)
REVERT: G  310 TYR cc_start: 0.9252 (t80) cc_final: 0.8974 (t80)
REVERT: G  317 LYS cc_start: 0.8082 (ptpt) cc_final: 0.7603 (ptpp)
REVERT: G  331 LYS cc_start: 0.9211 (mtmt) cc_final: 0.8856 (mttp)
REVERT: G  342 GLU cc_start: 0.7951 (mp0) cc_final: 0.7741 (mp0)
REVERT: G  372 GLU cc_start: 0.8737 (tt0) cc_final: 0.8476 (tt0)
REVERT: H  317 LYS cc_start: 0.8080 (ptpt) cc_final: 0.7673 (ptpp)
REVERT: H  331 LYS cc_start: 0.9126 (mtmt) cc_final: 0.8867 (mtmm)
REVERT: H  340 LYS cc_start: 0.8838 (ttmm) cc_final: 0.8221 (mttp)
REVERT: H  342 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8280 (mp0)
REVERT: H  343 LYS cc_start: 0.9098 (mttt) cc_final: 0.8685 (mtpp)
REVERT: H  356 SER cc_start: 0.9633 (p) cc_final: 0.9284 (p)
REVERT: H  358 ASP cc_start: 0.8667 (m-30) cc_final: 0.8395 (m-30)
REVERT: I  317 LYS cc_start: 0.8200 (ptpt) cc_final: 0.7698 (ptpp)
REVERT: I  331 LYS cc_start: 0.9233 (mtmt) cc_final: 0.8865 (mttp)
REVERT: I  336 GLN cc_start: 0.9146 (tp40) cc_final: 0.8663 (tp40)
REVERT: I  340 LYS cc_start: 0.8932 (ttmm) cc_final: 0.8351 (mmtp)
REVERT: J  321 LYS cc_start: 0.9228 (mtmm) cc_final: 0.8876 (mttp)
REVERT: J  340 LYS cc_start: 0.8889 (ttmm) cc_final: 0.8197 (mttm)
REVERT: J  345 ASP cc_start: 0.8709 (t0) cc_final: 0.8286 (t0)
  outliers start: 36
  outliers final: 32
  residues processed: 392
  average time/residue: 0.1042
  time to fit residues: 50.1096
Evaluate side-chains
  417 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 382
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain E residue  373 THR
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 F residue  352 SER
Chi-restraints excluded: chain F residue  356 SER
Chi-restraints excluded: chain G residue  319 THR
Chi-restraints excluded: chain G residue  320 SER
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  352 SER
Chi-restraints excluded: chain I residue  319 THR
Chi-restraints excluded: chain I residue  320 SER
Chi-restraints excluded: chain I residue  358 ASP
Chi-restraints excluded: chain J residue  319 THR
Chi-restraints excluded: chain J residue  320 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 66 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 29 optimal weight:    5.9990
   chunk 58 optimal weight:    5.9990
   chunk 48 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 368 ASN
G 368 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.134227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.115722 restraints weight = 9181.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.3909 rms_B_bonded: 3.25
r_work: 0.3784 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.2738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5960  Z= 0.174
  Angle     :  0.659   9.374   7970  Z= 0.315
  Chirality :  0.050   0.143    890
  Planarity :  0.005   0.045   1020
  Dihedral  :  4.658  15.073    790
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 25.07 %
    Favored  : 70.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.04 (0.24), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.31 (0.18), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G 349 
 TYR   0.017   0.003   TYR A 310 
 PHE   0.008   0.002   PHE J 378 
 HIS   0.002   0.000   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 5960)
  covalent geometry    : angle       0.65851 ( 7970)
  hydrogen bonds       : bond        0.02890 (   95)
  hydrogen bonds       : angle       4.69311 (  285)

*********************** 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
  424 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 395
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A  317 LYS cc_start: 0.8944 (ptpt) cc_final: 0.8465 (ptpp)
REVERT: A  331 LYS cc_start: 0.9327 (mtmt) cc_final: 0.8956 (mttp)
REVERT: B  317 LYS cc_start: 0.8343 (ptpt) cc_final: 0.7881 (ptpp)
REVERT: B  331 LYS cc_start: 0.9262 (mtmt) cc_final: 0.8934 (mttt)
REVERT: B  340 LYS cc_start: 0.8912 (ttmm) cc_final: 0.8162 (mttm)
REVERT: B  342 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8422 (mp0)
REVERT: B  370 LYS cc_start: 0.9024 (tttm) cc_final: 0.8678 (tttm)
REVERT: B  375 LYS cc_start: 0.8942 (ttmm) cc_final: 0.8585 (tttt)
REVERT: C  310 TYR cc_start: 0.9004 (t80) cc_final: 0.8581 (t80)
REVERT: C  317 LYS cc_start: 0.8910 (ptpt) cc_final: 0.8500 (ptpp)
REVERT: C  340 LYS cc_start: 0.9085 (ttmm) cc_final: 0.8521 (mttp)
REVERT: C  356 SER cc_start: 0.8989 (p) cc_final: 0.8763 (p)
REVERT: D  317 LYS cc_start: 0.8094 (ptpt) cc_final: 0.7711 (ptpp)
REVERT: D  331 LYS cc_start: 0.9191 (mtmt) cc_final: 0.8754 (mttt)
REVERT: D  340 LYS cc_start: 0.8906 (ttmm) cc_final: 0.8310 (mttp)
REVERT: D  343 LYS cc_start: 0.9124 (mttt) cc_final: 0.8558 (mtpp)
REVERT: E  310 TYR cc_start: 0.9223 (t80) cc_final: 0.8716 (t80)
REVERT: E  327 ASN cc_start: 0.9134 (t0) cc_final: 0.8709 (t0)
REVERT: E  331 LYS cc_start: 0.9228 (mtmt) cc_final: 0.8990 (mttt)
REVERT: E  338 GLU cc_start: 0.8849 (tt0) cc_final: 0.8364 (tt0)
REVERT: E  340 LYS cc_start: 0.8945 (ttmm) cc_final: 0.8227 (mttm)
REVERT: E  342 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8378 (mp0)
REVERT: E  343 LYS cc_start: 0.8739 (mppt) cc_final: 0.8508 (ttmt)
REVERT: E  372 GLU cc_start: 0.8861 (tt0) cc_final: 0.8548 (tt0)
REVERT: F  317 LYS cc_start: 0.8174 (ptpt) cc_final: 0.7796 (ptpp)
REVERT: F  331 LYS cc_start: 0.9168 (mtmt) cc_final: 0.8756 (mttp)
REVERT: F  340 LYS cc_start: 0.8827 (ttmm) cc_final: 0.8263 (mttp)
REVERT: F  342 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8451 (mp0)
REVERT: F  343 LYS cc_start: 0.8853 (mttp) cc_final: 0.8424 (mtpt)
REVERT: G  317 LYS cc_start: 0.8049 (ptpt) cc_final: 0.7561 (ptpp)
REVERT: G  331 LYS cc_start: 0.9171 (mtmt) cc_final: 0.8899 (mttt)
REVERT: H  317 LYS cc_start: 0.8126 (ptpt) cc_final: 0.7684 (ptpp)
REVERT: H  331 LYS cc_start: 0.9131 (mtmt) cc_final: 0.8852 (mttm)
REVERT: H  340 LYS cc_start: 0.8815 (ttmm) cc_final: 0.8199 (mttm)
REVERT: H  342 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8579 (mp0)
REVERT: H  343 LYS cc_start: 0.9085 (mttt) cc_final: 0.8712 (mtpp)
REVERT: H  345 ASP cc_start: 0.8526 (t0) cc_final: 0.8306 (t0)
REVERT: H  356 SER cc_start: 0.9626 (p) cc_final: 0.9304 (p)
REVERT: H  358 ASP cc_start: 0.8705 (m-30) cc_final: 0.8446 (m-30)
REVERT: I  317 LYS cc_start: 0.8124 (ptpt) cc_final: 0.7606 (ptpp)
REVERT: I  331 LYS cc_start: 0.9213 (mtmt) cc_final: 0.8822 (mttp)
REVERT: I  336 GLN cc_start: 0.9111 (tp40) cc_final: 0.8519 (tp40)
REVERT: I  340 LYS cc_start: 0.8894 (ttmm) cc_final: 0.8342 (mmtp)
REVERT: I  343 LYS cc_start: 0.9137 (mttp) cc_final: 0.8712 (mmmt)
REVERT: J  317 LYS cc_start: 0.8228 (ptpt) cc_final: 0.7797 (ptpp)
REVERT: J  321 LYS cc_start: 0.9245 (mtmm) cc_final: 0.8892 (mttm)
REVERT: J  331 LYS cc_start: 0.9142 (mtmt) cc_final: 0.7362 (tmtt)
REVERT: J  340 LYS cc_start: 0.8860 (ttmm) cc_final: 0.8196 (mttm)
REVERT: J  345 ASP cc_start: 0.8712 (t0) cc_final: 0.8408 (t0)
  outliers start: 29
  outliers final: 29
  residues processed: 398
  average time/residue: 0.1069
  time to fit residues: 52.2922
Evaluate side-chains
  417 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 388
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain G residue  319 THR
Chi-restraints excluded: chain G residue  320 SER
Chi-restraints excluded: chain H residue  319 THR
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain I residue  319 THR
Chi-restraints excluded: chain I residue  320 SER
Chi-restraints excluded: chain I residue  358 ASP
Chi-restraints excluded: chain J residue  319 THR
Chi-restraints excluded: chain J residue  320 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 20 optimal weight:    0.0970
   chunk 17 optimal weight:    3.9990
   chunk 33 optimal weight:    7.9990
   chunk 23 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9990
   chunk 68 optimal weight:    0.0170
   chunk 24 optimal weight:    2.9990
   chunk 36 optimal weight:   10.0000
   chunk 58 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   overall best weight:    1.0222

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

Flipped N/Q/H residues before XYZ refinement:
B 368 ASN
G 368 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.132442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.113266 restraints weight = 9216.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.3922 rms_B_bonded: 3.46
r_work: 0.3808 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.2980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5960  Z= 0.108
  Angle     :  0.651   9.423   7970  Z= 0.303
  Chirality :  0.050   0.125    890
  Planarity :  0.005   0.045   1020
  Dihedral  :  4.483  15.281    790
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 25.82 %
    Favored  : 69.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.97 (0.24), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.25 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG I 349 
 TYR   0.015   0.003   TYR A 310 
 PHE   0.008   0.002   PHE I 378 
 HIS   0.001   0.000   HIS G 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 5960)
  covalent geometry    : angle       0.65059 ( 7970)
  hydrogen bonds       : bond        0.02230 (   95)
  hydrogen bonds       : angle       4.47270 (  285)

*********************** 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
  428 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 395
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 LYS cc_start: 0.8704 (ptpt) cc_final: 0.8284 (ptpp)
REVERT: A  331 LYS cc_start: 0.9164 (mtmt) cc_final: 0.8755 (mttp)
REVERT: B  317 LYS cc_start: 0.7790 (ptpt) cc_final: 0.7345 (ptpp)
REVERT: B  331 LYS cc_start: 0.8958 (mtmt) cc_final: 0.8637 (mttt)
REVERT: B  340 LYS cc_start: 0.8734 (ttmm) cc_final: 0.7916 (mttm)
REVERT: B  370 LYS cc_start: 0.8729 (tttm) cc_final: 0.8389 (tttm)
REVERT: B  375 LYS cc_start: 0.8831 (ttmm) cc_final: 0.8369 (tttt)
REVERT: C  310 TYR cc_start: 0.8936 (t80) cc_final: 0.8394 (t80)
REVERT: C  317 LYS cc_start: 0.8655 (ptpt) cc_final: 0.8217 (ptpp)
REVERT: C  325 LEU cc_start: 0.8583 (tp) cc_final: 0.8376 (tp)
REVERT: C  340 LYS cc_start: 0.9084 (ttmm) cc_final: 0.8502 (mttp)
REVERT: C  356 SER cc_start: 0.8554 (p) cc_final: 0.8330 (p)
REVERT: D  317 LYS cc_start: 0.7585 (ptpt) cc_final: 0.7222 (ptpp)
REVERT: D  331 LYS cc_start: 0.8886 (mtmt) cc_final: 0.8338 (mttp)
REVERT: D  340 LYS cc_start: 0.8767 (ttmm) cc_final: 0.8131 (mttp)
REVERT: D  343 LYS cc_start: 0.9013 (mttt) cc_final: 0.8333 (mtpp)
REVERT: E  310 TYR cc_start: 0.9226 (t80) cc_final: 0.8595 (t80)
REVERT: E  325 LEU cc_start: 0.9193 (tt) cc_final: 0.8876 (tp)
REVERT: E  327 ASN cc_start: 0.8823 (t0) cc_final: 0.8441 (t0)
REVERT: E  331 LYS cc_start: 0.8933 (mtmt) cc_final: 0.8689 (mttt)
REVERT: E  338 GLU cc_start: 0.8852 (tt0) cc_final: 0.8423 (tt0)
REVERT: E  340 LYS cc_start: 0.8605 (ttmm) cc_final: 0.8042 (mttm)
REVERT: E  342 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8230 (mp0)
REVERT: E  343 LYS cc_start: 0.8392 (mppt) cc_final: 0.8168 (ttmt)
REVERT: F  317 LYS cc_start: 0.7580 (ptpt) cc_final: 0.7205 (ptpp)
REVERT: F  331 LYS cc_start: 0.8828 (mtmt) cc_final: 0.8426 (mttp)
REVERT: F  340 LYS cc_start: 0.8643 (ttmm) cc_final: 0.8089 (mttp)
REVERT: F  342 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8363 (mp0)
REVERT: F  343 LYS cc_start: 0.8646 (mttp) cc_final: 0.8147 (mtpt)
REVERT: G  310 TYR cc_start: 0.9351 (t80) cc_final: 0.8991 (t80)
REVERT: G  331 LYS cc_start: 0.8871 (mtmt) cc_final: 0.8595 (mttt)
REVERT: G  342 GLU cc_start: 0.7685 (mp0) cc_final: 0.7481 (mp0)
REVERT: H  317 LYS cc_start: 0.7561 (ptpt) cc_final: 0.7139 (ptpp)
REVERT: H  331 LYS cc_start: 0.8834 (mtmt) cc_final: 0.8537 (mttm)
REVERT: H  340 LYS cc_start: 0.8589 (ttmm) cc_final: 0.7959 (mttm)
REVERT: H  342 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8535 (mp0)
REVERT: H  343 LYS cc_start: 0.8839 (mttt) cc_final: 0.8443 (mtpp)
REVERT: H  345 ASP cc_start: 0.8210 (t0) cc_final: 0.7988 (t0)
REVERT: I  317 LYS cc_start: 0.7577 (ptpt) cc_final: 0.7209 (ptpp)
REVERT: I  331 LYS cc_start: 0.8963 (mtmt) cc_final: 0.8569 (mttp)
REVERT: I  336 GLN cc_start: 0.9101 (tp40) cc_final: 0.8289 (tp40)
REVERT: I  340 LYS cc_start: 0.8772 (ttmm) cc_final: 0.8330 (mttp)
REVERT: I  343 LYS cc_start: 0.8907 (mttp) cc_final: 0.8434 (mmmt)
REVERT: J  317 LYS cc_start: 0.7733 (ptpt) cc_final: 0.7296 (ptpp)
REVERT: J  321 LYS cc_start: 0.9029 (mtmm) cc_final: 0.8670 (mttm)
REVERT: J  331 LYS cc_start: 0.8835 (mtmt) cc_final: 0.6936 (tmtt)
REVERT: J  340 LYS cc_start: 0.8707 (ttmm) cc_final: 0.8065 (mttm)
REVERT: J  345 ASP cc_start: 0.8494 (t0) cc_final: 0.8220 (t0)
  outliers start: 33
  outliers final: 30
  residues processed: 399
  average time/residue: 0.1066
  time to fit residues: 52.3233
Evaluate side-chains
  420 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 390
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  344 LEU
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain F residue  356 SER
Chi-restraints excluded: chain G residue  319 THR
Chi-restraints excluded: chain G residue  320 SER
Chi-restraints excluded: chain H residue  319 THR
Chi-restraints excluded: chain H residue  320 SER
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain I residue  319 THR
Chi-restraints excluded: chain I residue  320 SER
Chi-restraints excluded: chain I residue  358 ASP
Chi-restraints excluded: chain J residue  319 THR
Chi-restraints excluded: chain J residue  320 SER
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:    8.9990
   chunk 38 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 18 optimal weight:    8.9990
   chunk 53 optimal weight:    7.9990
   chunk 14 optimal weight:    6.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 368 ASN
G 368 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.121898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.103689 restraints weight = 9522.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3768 rms_B_bonded: 3.27
r_work: 0.3648 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.2787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.043   5960  Z= 0.414
  Angle     :  0.799   9.198   7970  Z= 0.395
  Chirality :  0.053   0.225    890
  Planarity :  0.006   0.055   1020
  Dihedral  :  5.040  15.681    790
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.40 %
    Favored  : 89.60 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 26.42 %
    Favored  : 68.51 %
  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: -3.05 (0.24), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.31 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG D 349 
 TYR   0.021   0.004   TYR A 310 
 PHE   0.013   0.003   PHE I 346 
 HIS   0.004   0.001   HIS A 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00949 ( 5960)
  covalent geometry    : angle       0.79870 ( 7970)
  hydrogen bonds       : bond        0.04031 (   95)
  hydrogen bonds       : angle       5.00026 (  285)

*********************** 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
  408 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 374
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 LYS cc_start: 0.8751 (ptpt) cc_final: 0.8281 (ptpp)
REVERT: A  331 LYS cc_start: 0.9221 (mtmt) cc_final: 0.8798 (mttp)
REVERT: B  317 LYS cc_start: 0.7860 (ptpt) cc_final: 0.7487 (ptpp)
REVERT: B  331 LYS cc_start: 0.9011 (mtmt) cc_final: 0.8627 (mttt)
REVERT: B  340 LYS cc_start: 0.8805 (ttmm) cc_final: 0.7937 (mttm)
REVERT: B  370 LYS cc_start: 0.8867 (tttm) cc_final: 0.8489 (tttm)
REVERT: B  375 LYS cc_start: 0.8801 (ttmm) cc_final: 0.8324 (tttt)
REVERT: C  310 TYR cc_start: 0.8944 (t80) cc_final: 0.8684 (t80)
REVERT: C  317 LYS cc_start: 0.8777 (ptpt) cc_final: 0.8367 (ptpp)
REVERT: C  340 LYS cc_start: 0.9199 (ttmm) cc_final: 0.8614 (mttp)
REVERT: C  356 SER cc_start: 0.8788 (p) cc_final: 0.8567 (p)
REVERT: D  317 LYS cc_start: 0.7595 (ptpt) cc_final: 0.7263 (ptpp)
REVERT: D  331 LYS cc_start: 0.8938 (mtmt) cc_final: 0.8411 (mttt)
REVERT: D  340 LYS cc_start: 0.8815 (ttmm) cc_final: 0.8223 (mttp)
REVERT: D  342 GLU cc_start: 0.8420 (mp0) cc_final: 0.8159 (mp0)
REVERT: D  343 LYS cc_start: 0.9021 (mttt) cc_final: 0.8411 (mtpp)
REVERT: E  327 ASN cc_start: 0.8900 (t0) cc_final: 0.8340 (t0)
REVERT: E  331 LYS cc_start: 0.9007 (mtmt) cc_final: 0.8688 (mttt)
REVERT: E  338 GLU cc_start: 0.8897 (tt0) cc_final: 0.8510 (tt0)
REVERT: E  340 LYS cc_start: 0.8813 (ttmm) cc_final: 0.8253 (mttm)
REVERT: E  342 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8280 (mp0)
REVERT: E  343 LYS cc_start: 0.8540 (mppt) cc_final: 0.8311 (ttmt)
REVERT: E  370 LYS cc_start: 0.8899 (tttm) cc_final: 0.8409 (tttm)
REVERT: E  372 GLU cc_start: 0.9001 (tt0) cc_final: 0.8560 (tt0)
REVERT: F  317 LYS cc_start: 0.7715 (ptpt) cc_final: 0.7357 (ptpp)
REVERT: F  331 LYS cc_start: 0.8926 (mtmt) cc_final: 0.8437 (mttp)
REVERT: F  340 LYS cc_start: 0.8696 (ttmm) cc_final: 0.8211 (mttp)
REVERT: F  342 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8386 (mm-30)
REVERT: F  343 LYS cc_start: 0.8670 (mttp) cc_final: 0.8183 (mtpt)
REVERT: G  310 TYR cc_start: 0.9343 (t80) cc_final: 0.8818 (t80)
REVERT: G  331 LYS cc_start: 0.8951 (mtmt) cc_final: 0.8545 (mttp)
REVERT: H  317 LYS cc_start: 0.7707 (ptpt) cc_final: 0.7304 (ptpp)
REVERT: H  331 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8558 (mtmm)
REVERT: H  340 LYS cc_start: 0.8652 (ttmm) cc_final: 0.8061 (mttp)
REVERT: H  342 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8139 (mm-30)
REVERT: H  343 LYS cc_start: 0.8904 (mttt) cc_final: 0.8491 (mtpp)
REVERT: I  317 LYS cc_start: 0.7752 (ptpt) cc_final: 0.7264 (ptpp)
REVERT: I  331 LYS cc_start: 0.9009 (mtmt) cc_final: 0.8486 (mttp)
REVERT: I  336 GLN cc_start: 0.9129 (tp40) cc_final: 0.8411 (tp40)
REVERT: I  340 LYS cc_start: 0.8774 (ttmm) cc_final: 0.8278 (mttp)
REVERT: I  343 LYS cc_start: 0.8829 (mttp) cc_final: 0.8358 (mmmt)
REVERT: J  317 LYS cc_start: 0.7829 (ptpt) cc_final: 0.7409 (ptpp)
REVERT: J  321 LYS cc_start: 0.9078 (mtmm) cc_final: 0.8709 (mttm)
REVERT: J  331 LYS cc_start: 0.8913 (mtmt) cc_final: 0.7039 (tmtt)
REVERT: J  345 ASP cc_start: 0.8441 (t0) cc_final: 0.8205 (t0)
  outliers start: 34
  outliers final: 30
  residues processed: 382
  average time/residue: 0.1079
  time to fit residues: 50.5052
Evaluate side-chains
  397 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 365
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain E residue  373 THR
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 F residue  352 SER
Chi-restraints excluded: chain F residue  356 SER
Chi-restraints excluded: chain G residue  319 THR
Chi-restraints excluded: chain G residue  320 SER
Chi-restraints excluded: chain H residue  319 THR
Chi-restraints excluded: chain H residue  320 SER
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain I residue  319 THR
Chi-restraints excluded: chain I residue  320 SER
Chi-restraints excluded: chain I residue  358 ASP
Chi-restraints excluded: chain J residue  319 THR
Chi-restraints excluded: chain J residue  320 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 35 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 42 optimal weight:   10.0000
   chunk 59 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   chunk 53 optimal weight:    0.5980
   chunk 63 optimal weight:    4.9990
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 368 ASN
G 368 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.128313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.109034 restraints weight = 9462.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3837 rms_B_bonded: 3.45
r_work: 0.3719 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5960  Z= 0.189
  Angle     :  0.718   9.889   7970  Z= 0.340
  Chirality :  0.050   0.167    890
  Planarity :  0.005   0.048   1020
  Dihedral  :  4.765  14.582    790
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 27.91 %
    Favored  : 67.76 %
  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: -2.99 (0.24), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.27 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 349 
 TYR   0.019   0.003   TYR A 310 
 PHE   0.009   0.002   PHE J 378 
 HIS   0.002   0.001   HIS A 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 5960)
  covalent geometry    : angle       0.71794 ( 7970)
  hydrogen bonds       : bond        0.02966 (   95)
  hydrogen bonds       : angle       4.69943 (  285)

*********************** 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
  421 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 392
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A  317 LYS cc_start: 0.8685 (ptpt) cc_final: 0.8192 (ptpp)
REVERT: A  331 LYS cc_start: 0.9196 (mtmt) cc_final: 0.8777 (mttp)
REVERT: B  317 LYS cc_start: 0.7700 (ptpt) cc_final: 0.7284 (ptpp)
REVERT: B  331 LYS cc_start: 0.8927 (mtmt) cc_final: 0.8571 (mttt)
REVERT: B  340 LYS cc_start: 0.8719 (ttmm) cc_final: 0.7893 (mttm)
REVERT: B  375 LYS cc_start: 0.8766 (ttmm) cc_final: 0.8320 (tttt)
REVERT: C  310 TYR cc_start: 0.8911 (t80) cc_final: 0.8452 (t80)
REVERT: C  317 LYS cc_start: 0.8653 (ptpt) cc_final: 0.8231 (ptpp)
REVERT: C  340 LYS cc_start: 0.9112 (ttmm) cc_final: 0.8525 (mttp)
REVERT: C  356 SER cc_start: 0.8587 (p) cc_final: 0.8372 (p)
REVERT: D  317 LYS cc_start: 0.7464 (ptpt) cc_final: 0.7119 (ptpp)
REVERT: D  331 LYS cc_start: 0.8815 (mtmt) cc_final: 0.8324 (mttt)
REVERT: D  340 LYS cc_start: 0.8737 (ttmm) cc_final: 0.8124 (mttp)
REVERT: D  342 GLU cc_start: 0.8420 (mp0) cc_final: 0.8033 (mp0)
REVERT: D  343 LYS cc_start: 0.8933 (mttt) cc_final: 0.8295 (mtpp)
REVERT: E  310 TYR cc_start: 0.9232 (t80) cc_final: 0.8704 (t80)
REVERT: E  327 ASN cc_start: 0.8788 (t0) cc_final: 0.8318 (t0)
REVERT: E  331 LYS cc_start: 0.8918 (mtmt) cc_final: 0.8655 (mttt)
REVERT: E  338 GLU cc_start: 0.8840 (tt0) cc_final: 0.8418 (tt0)
REVERT: E  340 LYS cc_start: 0.8694 (ttmm) cc_final: 0.8025 (mttm)
REVERT: E  342 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8268 (mp0)
REVERT: E  343 LYS cc_start: 0.8334 (mppt) cc_final: 0.8130 (ttmt)
REVERT: E  370 LYS cc_start: 0.8716 (tttm) cc_final: 0.8252 (tttm)
REVERT: E  372 GLU cc_start: 0.8921 (tt0) cc_final: 0.8536 (tt0)
REVERT: F  317 LYS cc_start: 0.7626 (ptpt) cc_final: 0.7263 (ptpp)
REVERT: F  331 LYS cc_start: 0.8803 (mtmt) cc_final: 0.8361 (mttp)
REVERT: F  340 LYS cc_start: 0.8623 (ttmm) cc_final: 0.8133 (mttp)
REVERT: F  342 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8302 (mp0)
REVERT: F  343 LYS cc_start: 0.8566 (mttp) cc_final: 0.8100 (mtpt)
REVERT: G  310 TYR cc_start: 0.9307 (t80) cc_final: 0.8870 (t80)
REVERT: G  331 LYS cc_start: 0.8852 (mtmt) cc_final: 0.8548 (mttt)
REVERT: H  317 LYS cc_start: 0.7539 (ptpt) cc_final: 0.7135 (ptpp)
REVERT: H  331 LYS cc_start: 0.8830 (mtmt) cc_final: 0.8582 (mtmm)
REVERT: H  340 LYS cc_start: 0.8563 (ttmm) cc_final: 0.7949 (mttm)
REVERT: H  342 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8479 (mp0)
REVERT: H  343 LYS cc_start: 0.8792 (mttt) cc_final: 0.8402 (mtpp)
REVERT: I  317 LYS cc_start: 0.7494 (ptpt) cc_final: 0.7025 (ptpp)
REVERT: I  331 LYS cc_start: 0.8917 (mtmt) cc_final: 0.8475 (mttp)
REVERT: I  336 GLN cc_start: 0.9058 (tp40) cc_final: 0.8279 (tp40)
REVERT: I  340 LYS cc_start: 0.8685 (ttmm) cc_final: 0.8201 (mttm)
REVERT: I  343 LYS cc_start: 0.8882 (mttp) cc_final: 0.8420 (mmmt)
REVERT: I  353 LYS cc_start: 0.8820 (tttp) cc_final: 0.8527 (tttp)
REVERT: J  317 LYS cc_start: 0.7680 (ptpt) cc_final: 0.7281 (ptpp)
REVERT: J  321 LYS cc_start: 0.8970 (mtmm) cc_final: 0.8600 (mttp)
REVERT: J  331 LYS cc_start: 0.8809 (mtmt) cc_final: 0.6925 (tmtt)
REVERT: J  340 LYS cc_start: 0.8703 (ttmm) cc_final: 0.8061 (mttm)
REVERT: J  345 ASP cc_start: 0.8513 (t0) cc_final: 0.8193 (t0)
  outliers start: 29
  outliers final: 28
  residues processed: 393
  average time/residue: 0.1074
  time to fit residues: 51.7183
Evaluate side-chains
  415 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 386
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  320 SER
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain F residue  356 SER
Chi-restraints excluded: chain G residue  319 THR
Chi-restraints excluded: chain G residue  320 SER
Chi-restraints excluded: chain H residue  319 THR
Chi-restraints excluded: chain H residue  320 SER
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain I residue  319 THR
Chi-restraints excluded: chain I residue  320 SER
Chi-restraints excluded: chain J residue  319 THR
Chi-restraints excluded: chain J residue  320 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 45 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   chunk 40 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 7 optimal weight:   10.0000
   chunk 44 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 68 optimal weight:    4.9990
   chunk 59 optimal weight:    0.0020
   chunk 63 optimal weight:    2.9990
   overall best weight:    2.1994

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 368 ASN
G 368 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.128570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.109268 restraints weight = 9418.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3840 rms_B_bonded: 3.45
r_work: 0.3723 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.2954

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= 0.182
  Angle     :  0.714   9.960   7970  Z= 0.337
  Chirality :  0.050   0.167    890
  Planarity :  0.005   0.052   1020
  Dihedral  :  4.698  15.283    790
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.93 %
    Favored  : 91.07 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 28.36 %
    Favored  : 67.31 %
  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: -2.93 (0.25), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.22 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 349 
 TYR   0.019   0.003   TYR A 310 
 PHE   0.008   0.002   PHE J 378 
 HIS   0.002   0.001   HIS A 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 5960)
  covalent geometry    : angle       0.71356 ( 7970)
  hydrogen bonds       : bond        0.02924 (   95)
  hydrogen bonds       : angle       4.68046 (  285)

********************** 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
  424 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 395
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A  317 LYS cc_start: 0.8676 (ptpt) cc_final: 0.8184 (ptpp)
REVERT: A  331 LYS cc_start: 0.9172 (mtmt) cc_final: 0.8740 (mttp)
REVERT: B  317 LYS cc_start: 0.7657 (ptpt) cc_final: 0.7247 (ptpp)
REVERT: B  331 LYS cc_start: 0.8893 (mtmt) cc_final: 0.8545 (mttt)
REVERT: B  340 LYS cc_start: 0.8708 (ttmm) cc_final: 0.7869 (mttm)
REVERT: B  370 LYS cc_start: 0.8682 (tttm) cc_final: 0.8369 (tttm)
REVERT: B  375 LYS cc_start: 0.8741 (ttmm) cc_final: 0.8294 (tttt)
REVERT: C  310 TYR cc_start: 0.8899 (t80) cc_final: 0.8452 (t80)
REVERT: C  317 LYS cc_start: 0.8628 (ptpt) cc_final: 0.8201 (ptpp)
REVERT: C  340 LYS cc_start: 0.9105 (ttmm) cc_final: 0.8513 (mttp)
REVERT: C  356 SER cc_start: 0.8531 (p) cc_final: 0.8324 (p)
REVERT: D  317 LYS cc_start: 0.7422 (ptpt) cc_final: 0.7080 (ptpp)
REVERT: D  331 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8319 (mttt)
REVERT: D  340 LYS cc_start: 0.8735 (ttmm) cc_final: 0.8128 (mttp)
REVERT: D  342 GLU cc_start: 0.8381 (mp0) cc_final: 0.8019 (mp0)
REVERT: D  343 LYS cc_start: 0.8948 (mttt) cc_final: 0.8298 (mtpp)
REVERT: E  327 ASN cc_start: 0.8749 (t0) cc_final: 0.8290 (t0)
REVERT: E  331 LYS cc_start: 0.8883 (mtmt) cc_final: 0.8631 (mttt)
REVERT: E  338 GLU cc_start: 0.8836 (tt0) cc_final: 0.8425 (tt0)
REVERT: E  340 LYS cc_start: 0.8617 (ttmm) cc_final: 0.7959 (mttm)
REVERT: E  342 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8228 (mp0)
REVERT: E  343 LYS cc_start: 0.8328 (mppt) cc_final: 0.8110 (ttmt)
REVERT: E  356 SER cc_start: 0.9019 (p) cc_final: 0.8808 (t)
REVERT: E  370 LYS cc_start: 0.8671 (tttm) cc_final: 0.8218 (tttm)
REVERT: E  372 GLU cc_start: 0.8945 (tt0) cc_final: 0.8555 (tt0)
REVERT: F  317 LYS cc_start: 0.7593 (ptpt) cc_final: 0.7232 (ptpp)
REVERT: F  331 LYS cc_start: 0.8769 (mtmt) cc_final: 0.8323 (mttp)
REVERT: F  340 LYS cc_start: 0.8623 (ttmm) cc_final: 0.8132 (mttp)
REVERT: F  342 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8296 (mp0)
REVERT: F  343 LYS cc_start: 0.8581 (mttp) cc_final: 0.8089 (mtpp)
REVERT: G  310 TYR cc_start: 0.9275 (t80) cc_final: 0.8796 (t80)
REVERT: G  331 LYS cc_start: 0.8824 (mtmt) cc_final: 0.8527 (mttt)
REVERT: H  317 LYS cc_start: 0.7462 (ptpt) cc_final: 0.7057 (ptpp)
REVERT: H  331 LYS cc_start: 0.8787 (mtmt) cc_final: 0.8537 (mtmm)
REVERT: H  340 LYS cc_start: 0.8537 (ttmm) cc_final: 0.7924 (mttm)
REVERT: H  342 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8470 (mp0)
REVERT: H  343 LYS cc_start: 0.8788 (mttt) cc_final: 0.8383 (mtpp)
REVERT: I  317 LYS cc_start: 0.7504 (ptpt) cc_final: 0.7133 (ptpp)
REVERT: I  331 LYS cc_start: 0.8896 (mtmt) cc_final: 0.8458 (mttp)
REVERT: I  336 GLN cc_start: 0.9049 (tp40) cc_final: 0.8249 (tp40)
REVERT: I  340 LYS cc_start: 0.8716 (ttmm) cc_final: 0.8235 (mttp)
REVERT: I  343 LYS cc_start: 0.8862 (mttp) cc_final: 0.8415 (mmmt)
REVERT: I  353 LYS cc_start: 0.8801 (tttp) cc_final: 0.8508 (tttp)
REVERT: J  317 LYS cc_start: 0.7662 (ptpt) cc_final: 0.7244 (ptpp)
REVERT: J  321 LYS cc_start: 0.8974 (mtmm) cc_final: 0.8613 (mttm)
REVERT: J  331 LYS cc_start: 0.8771 (mtmt) cc_final: 0.6891 (tmtt)
REVERT: J  340 LYS cc_start: 0.8693 (ttmm) cc_final: 0.8043 (mttm)
REVERT: J  345 ASP cc_start: 0.8481 (t0) cc_final: 0.8124 (t0)
  outliers start: 29
  outliers final: 28
  residues processed: 396
  average time/residue: 0.1070
  time to fit residues: 52.1036
Evaluate side-chains
  419 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 390
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  320 SER
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  320 SER
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain E residue  373 THR
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  320 SER
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain F residue  356 SER
Chi-restraints excluded: chain G residue  319 THR
Chi-restraints excluded: chain G residue  320 SER
Chi-restraints excluded: chain H residue  319 THR
Chi-restraints excluded: chain H residue  320 SER
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain I residue  319 THR
Chi-restraints excluded: chain I residue  320 SER
Chi-restraints excluded: chain I residue  358 ASP
Chi-restraints excluded: chain J residue  319 THR
Chi-restraints excluded: chain J residue  320 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 63 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 18 optimal weight:    6.9990
   chunk 49 optimal weight:    4.9990
   chunk 31 optimal weight:    6.9990
   chunk 58 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   overall best weight:    3.3188

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

Flipped N/Q/H residues before XYZ refinement:
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 368 ASN
G 368 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.126566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.107458 restraints weight = 9410.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3807 rms_B_bonded: 3.43
r_work: 0.3685 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.2932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.033   5960  Z= 0.257
  Angle     :  0.747   9.542   7970  Z= 0.358
  Chirality :  0.051   0.210    890
  Planarity :  0.005   0.052   1020
  Dihedral  :  4.814  15.320    790
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.20 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 28.66 %
    Favored  : 67.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.98 (0.24), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.26 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 349 
 TYR   0.018   0.004   TYR A 310 
 PHE   0.010   0.002   PHE A 346 
 HIS   0.003   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00593 ( 5960)
  covalent geometry    : angle       0.74651 ( 7970)
  hydrogen bonds       : bond        0.03361 (   95)
  hydrogen bonds       : angle       4.80632 (  285)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1833.00 seconds
wall clock time: 32 minutes 35.32 seconds (1955.32 seconds total)