Starting phenix.real_space_refine
on Fri Aug 22 18:32:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q8e_18252/08_2025/8q8e_18252.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q8e_18252/08_2025/8q8e_18252.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q8e_18252/08_2025/8q8e_18252.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q8e_18252/08_2025/8q8e_18252.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q8e_18252/08_2025/8q8e_18252.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q8e_18252/08_2025/8q8e_18252.map"
  }
  resolution = 3.81
  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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      12      5.16       5
     C    4278      2.51       5
     N    1248      2.21       5
     O    1272      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6810
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 578
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "C"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 578
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "E"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 578
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "B"
      Number of atoms: 557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 557
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "D"
      Number of atoms: 557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 557
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "F"
      Number of atoms: 557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 557
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "G"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 578
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "H"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 578
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "I"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 578
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "J"
      Number of atoms: 557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 557
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "K"
      Number of atoms: 557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 557
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "L"
      Number of atoms: 557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 557
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
  Time building chain proxies: 1.43, per 1000 atoms: 0.21
  Number of scatterers: 6810
  At special positions: 0
  Unit cell: (166.448, 164.8, 50.264, 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      12     16.00
     O    1272      8.00
     N    1248      7.00
     C    4278      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: 0.35
  Conformation dependent library (CDL) restraints added in 305.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1560

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 34 sheets defined
      0.0% alpha, 38.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310
      removed outlier: 6.422A  pdb=" N   GLN A 307 " --> pdb=" O   ILE C 308 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   TYR C 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   VAL A 309 " --> pdb=" O   TYR C 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 320
    Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 330
      removed outlier: 6.578A  pdb=" N   HIS A 329 " --> pdb=" O   HIS C 330 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 336 through 340
      removed outlier: 6.429A  pdb=" N   GLN A 336 " --> pdb=" O   VAL C 337 " (cutoff:3.500A)
      removed outlier: 8.244A  pdb=" N   VAL C 339 " --> pdb=" O   GLN A 336 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   GLU A 338 " --> pdb=" O   VAL C 339 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 343 through 346
      removed outlier: 6.587A  pdb=" N   LEU A 344 " --> pdb=" O   ASP E 345 " (cutoff:3.500A)
      removed outlier: 7.970A  pdb=" N   LYS E 347 " --> pdb=" O   LEU A 344 " (cutoff:3.500A)
      removed outlier: 7.372A  pdb=" N   PHE A 346 " --> pdb=" O   LYS E 347 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 351 through 352
      removed outlier: 6.226A  pdb=" N   GLN A 351 " --> pdb=" O   SER C 352 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 357 through 362
      removed outlier: 6.153A  pdb=" N   ASP A 358 " --> pdb=" O   ASN C 359 " (cutoff:3.500A)
      removed outlier: 7.678A  pdb=" N   THR C 361 " --> pdb=" O   ASP A 358 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   ILE A 360 " --> pdb=" O   THR C 361 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 370 through 373
    Processing sheet with id=AA9, first strand: chain 'D' and resid 307 through 310
      removed outlier: 6.959A  pdb=" N   ILE B 308 " --> pdb=" O   VAL D 309 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 313 through 314
      removed outlier: 6.753A  pdb=" N   VAL B 313 " --> pdb=" O   ASP F 314 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 317 through 325
    Processing sheet with id=AB3, first strand: chain 'D' and resid 337 through 340
      removed outlier: 6.689A  pdb=" N   VAL B 337 " --> pdb=" O   GLU D 338 " (cutoff:3.500A)
      removed outlier: 8.353A  pdb=" N   LYS D 340 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   VAL B 339 " --> pdb=" O   LYS D 340 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 343 through 346
      removed outlier: 6.400A  pdb=" N   LYS B 343 " --> pdb=" O   LEU F 344 " (cutoff:3.500A)
      removed outlier: 8.344A  pdb=" N   PHE F 346 " --> pdb=" O   LYS B 343 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   ASP B 345 " --> pdb=" O   PHE F 346 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 351 through 354
      removed outlier: 6.213A  pdb=" N   GLN B 351 " --> pdb=" O   SER F 352 " (cutoff:3.500A)
      removed outlier: 7.971A  pdb=" N   ILE F 354 " --> pdb=" O   GLN B 351 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   LYS B 353 " --> pdb=" O   ILE F 354 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 361 through 362
      removed outlier: 6.571A  pdb=" N   THR B 361 " --> pdb=" O   HIS D 362 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 368 through 373
      removed outlier: 6.298A  pdb=" N   ASN B 368 " --> pdb=" O   LYS D 369 " (cutoff:3.500A)
      removed outlier: 8.059A  pdb=" N   ILE D 371 " --> pdb=" O   ASN B 368 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   LYS B 370 " --> pdb=" O   ILE D 371 " (cutoff:3.500A)
      removed outlier: 8.330A  pdb=" N   THR D 373 " --> pdb=" O   LYS B 370 " (cutoff:3.500A)
      removed outlier: 7.471A  pdb=" N   GLU B 372 " --> pdb=" O   THR D 373 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   LYS B 369 " --> pdb=" O   LYS F 370 " (cutoff:3.500A)
      removed outlier: 7.996A  pdb=" N   GLU F 372 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   ILE B 371 " --> pdb=" O   GLU F 372 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'D' and resid 376 through 377
      removed outlier: 6.742A  pdb=" N   LEU B 376 " --> pdb=" O   THR D 377 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'H' and resid 306 through 310
      removed outlier: 6.422A  pdb=" N   GLN G 307 " --> pdb=" O   ILE H 308 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   TYR H 310 " --> pdb=" O   GLN G 307 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   VAL G 309 " --> pdb=" O   TYR H 310 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'H' and resid 313 through 320
    Processing sheet with id=AC2, first strand: chain 'H' and resid 329 through 330
      removed outlier: 6.578A  pdb=" N   HIS G 329 " --> pdb=" O   HIS H 330 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'H' and resid 336 through 340
      removed outlier: 6.429A  pdb=" N   GLN G 336 " --> pdb=" O   VAL H 337 " (cutoff:3.500A)
      removed outlier: 8.244A  pdb=" N   VAL H 339 " --> pdb=" O   GLN G 336 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   GLU G 338 " --> pdb=" O   VAL H 339 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'H' and resid 343 through 346
      removed outlier: 6.588A  pdb=" N   LEU G 344 " --> pdb=" O   ASP I 345 " (cutoff:3.500A)
      removed outlier: 7.970A  pdb=" N   LYS I 347 " --> pdb=" O   LEU G 344 " (cutoff:3.500A)
      removed outlier: 7.372A  pdb=" N   PHE G 346 " --> pdb=" O   LYS I 347 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'H' and resid 351 through 352
      removed outlier: 6.226A  pdb=" N   GLN G 351 " --> pdb=" O   SER H 352 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'H' and resid 357 through 362
      removed outlier: 6.153A  pdb=" N   ASP G 358 " --> pdb=" O   ASN H 359 " (cutoff:3.500A)
      removed outlier: 7.678A  pdb=" N   THR H 361 " --> pdb=" O   ASP G 358 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   ILE G 360 " --> pdb=" O   THR H 361 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'H' and resid 370 through 373
    Processing sheet with id=AC8, first strand: chain 'K' and resid 307 through 310
      removed outlier: 6.959A  pdb=" N   ILE J 308 " --> pdb=" O   VAL K 309 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'K' and resid 313 through 314
      removed outlier: 6.754A  pdb=" N   VAL J 313 " --> pdb=" O   ASP L 314 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'K' and resid 317 through 325
    Processing sheet with id=AD2, first strand: chain 'K' and resid 337 through 340
      removed outlier: 6.689A  pdb=" N   VAL J 337 " --> pdb=" O   GLU K 338 " (cutoff:3.500A)
      removed outlier: 8.353A  pdb=" N   LYS K 340 " --> pdb=" O   VAL J 337 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   VAL J 339 " --> pdb=" O   LYS K 340 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'K' and resid 343 through 346
      removed outlier: 6.400A  pdb=" N   LYS J 343 " --> pdb=" O   LEU L 344 " (cutoff:3.500A)
      removed outlier: 8.344A  pdb=" N   PHE L 346 " --> pdb=" O   LYS J 343 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   ASP J 345 " --> pdb=" O   PHE L 346 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'K' and resid 351 through 354
      removed outlier: 6.213A  pdb=" N   GLN J 351 " --> pdb=" O   SER L 352 " (cutoff:3.500A)
      removed outlier: 7.971A  pdb=" N   ILE L 354 " --> pdb=" O   GLN J 351 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   LYS J 353 " --> pdb=" O   ILE L 354 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'K' and resid 361 through 362
      removed outlier: 6.571A  pdb=" N   THR J 361 " --> pdb=" O   HIS K 362 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'K' and resid 368 through 373
      removed outlier: 6.299A  pdb=" N   ASN J 368 " --> pdb=" O   LYS K 369 " (cutoff:3.500A)
      removed outlier: 8.059A  pdb=" N   ILE K 371 " --> pdb=" O   ASN J 368 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   LYS J 370 " --> pdb=" O   ILE K 371 " (cutoff:3.500A)
      removed outlier: 8.329A  pdb=" N   THR K 373 " --> pdb=" O   LYS J 370 " (cutoff:3.500A)
      removed outlier: 7.470A  pdb=" N   GLU J 372 " --> pdb=" O   THR K 373 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   LYS J 369 " --> pdb=" O   LYS L 370 " (cutoff:3.500A)
      removed outlier: 7.996A  pdb=" N   GLU L 372 " --> pdb=" O   LYS J 369 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   ILE J 371 " --> pdb=" O   GLU L 372 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD6
    Processing sheet with id=AD7, first strand: chain 'K' and resid 376 through 377
      removed outlier: 6.742A  pdb=" N   LEU J 376 " --> pdb=" O   THR K 377 " (cutoff:3.500A)

    136 hydrogen bonds defined for protein.
    408 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: 0.70

  Time building geometry restraints manager: 0.49 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1827
        1.33 -     1.45: 955
        1.45 -     1.57: 4124
        1.57 -     1.69: 0
        1.69 -     1.81: 12
  Bond restraints: 6918
  Sorted by residual:
  bond pdb=" N   LYS H 370 "
       pdb=" CA  LYS H 370 "
    ideal  model  delta    sigma   weight residual
    1.456  1.496 -0.040 1.21e-02 6.83e+03 1.07e+01
  bond pdb=" N   LYS C 370 "
       pdb=" CA  LYS C 370 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.039 1.21e-02 6.83e+03 1.04e+01
  bond pdb=" CZ  ARG K 349 "
       pdb=" NH2 ARG K 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.289  0.041 1.30e-02 5.92e+03 1.01e+01
  bond pdb=" CZ  ARG D 349 "
       pdb=" NH2 ARG D 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.289  0.041 1.30e-02 5.92e+03 9.92e+00
  bond pdb=" CZ  ARG B 349 "
       pdb=" NH2 ARG B 349 "
    ideal  model  delta    sigma   weight residual
    1.330  1.291  0.039 1.30e-02 5.92e+03 8.88e+00
  ... (remaining 6913 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.32: 7088
        2.32 -     4.63: 1927
        4.63 -     6.94: 225
        6.94 -     9.26: 14
        9.26 -    11.57: 4
  Bond angle restraints: 9258
  Sorted by residual:
  angle pdb=" O   SER E 352 "
        pdb=" C   SER E 352 "
        pdb=" N   LYS E 353 "
      ideal   model   delta    sigma   weight residual
     123.24  111.67   11.57 1.32e+00 5.74e-01 7.69e+01
  angle pdb=" O   SER I 352 "
        pdb=" C   SER I 352 "
        pdb=" N   LYS I 353 "
      ideal   model   delta    sigma   weight residual
     123.24  111.68   11.56 1.32e+00 5.74e-01 7.67e+01
  angle pdb=" CA  ASP B 358 "
        pdb=" CB  ASP B 358 "
        pdb=" CG  ASP B 358 "
      ideal   model   delta    sigma   weight residual
     112.60  119.08   -6.48 1.00e+00 1.00e+00 4.20e+01
  angle pdb=" CA  ASP J 358 "
        pdb=" CB  ASP J 358 "
        pdb=" CG  ASP J 358 "
      ideal   model   delta    sigma   weight residual
     112.60  119.08   -6.48 1.00e+00 1.00e+00 4.20e+01
  angle pdb=" CA  PHE J 346 "
        pdb=" CB  PHE J 346 "
        pdb=" CG  PHE J 346 "
      ideal   model   delta    sigma   weight residual
     113.80  119.89   -6.09 1.00e+00 1.00e+00 3.71e+01
  ... (remaining 9253 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.69: 3845
       14.69 -    29.38: 291
       29.38 -    44.07: 46
       44.07 -    58.76: 20
       58.76 -    73.45: 4
  Dihedral angle restraints: 4206
    sinusoidal: 1752
      harmonic: 2454
  Sorted by residual:
  dihedral pdb=" CA  LYS C 343 "
           pdb=" C   LYS C 343 "
           pdb=" N   LEU C 344 "
           pdb=" CA  LEU C 344 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.92   29.08     0      5.00e+00 4.00e-02 3.38e+01
  dihedral pdb=" CA  LYS H 343 "
           pdb=" C   LYS H 343 "
           pdb=" N   LEU H 344 "
           pdb=" CA  LEU H 344 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.93   29.07     0      5.00e+00 4.00e-02 3.38e+01
  dihedral pdb=" CA  SER F 341 "
           pdb=" C   SER F 341 "
           pdb=" N   GLU F 342 "
           pdb=" CA  GLU F 342 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.23   28.77     0      5.00e+00 4.00e-02 3.31e+01
  ... (remaining 4203 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.100: 716
       0.100 -    0.199: 263
       0.199 -    0.299: 47
       0.299 -    0.398: 8
       0.398 -    0.498: 10
  Chirality restraints: 1044
  Sorted by residual:
  chirality pdb=" CA  LYS B 347 "
            pdb=" N   LYS B 347 "
            pdb=" C   LYS B 347 "
            pdb=" CB  LYS B 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.01    0.50 2.00e-01 2.50e+01 6.19e+00
  chirality pdb=" CA  LYS J 347 "
            pdb=" N   LYS J 347 "
            pdb=" C   LYS J 347 "
            pdb=" CB  LYS J 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.02    0.49 2.00e-01 2.50e+01 6.09e+00
  chirality pdb=" CA  LYS D 311 "
            pdb=" N   LYS D 311 "
            pdb=" C   LYS D 311 "
            pdb=" CB  LYS D 311 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 5.10e+00
  ... (remaining 1041 not shown)

  Planarity restraints: 1176
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 310 "    0.153 2.00e-02 2.50e+03   8.17e-02 1.34e+02
        pdb=" CG  TYR A 310 "   -0.063 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 310 "   -0.054 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 310 "   -0.071 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 310 "   -0.045 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 310 "   -0.036 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 310 "   -0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR A 310 "    0.121 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR G 310 "    0.153 2.00e-02 2.50e+03   8.17e-02 1.34e+02
        pdb=" CG  TYR G 310 "   -0.063 2.00e-02 2.50e+03
        pdb=" CD1 TYR G 310 "   -0.054 2.00e-02 2.50e+03
        pdb=" CD2 TYR G 310 "   -0.071 2.00e-02 2.50e+03
        pdb=" CE1 TYR G 310 "   -0.045 2.00e-02 2.50e+03
        pdb=" CE2 TYR G 310 "   -0.036 2.00e-02 2.50e+03
        pdb=" CZ  TYR G 310 "   -0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR G 310 "    0.121 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER E 352 "   -0.055 2.00e-02 2.50e+03   1.04e-01 1.08e+02
        pdb=" C   SER E 352 "    0.180 2.00e-02 2.50e+03
        pdb=" O   SER E 352 "   -0.066 2.00e-02 2.50e+03
        pdb=" N   LYS E 353 "   -0.058 2.00e-02 2.50e+03
  ... (remaining 1173 not shown)

  Histogram of nonbonded interaction distances:
        1.52 -     2.20: 7
        2.20 -     2.87: 2010
        2.87 -     3.55: 8455
        3.55 -     4.22: 14788
        4.22 -     4.90: 25944
  Nonbonded interactions: 51204
  Sorted by model distance:
  nonbonded pdb=" CG  GLN F 336 "
            pdb=" CB  GLN L 336 "
     model   vdw
     1.524 3.840
  nonbonded pdb=" NZ  LYS F 340 "
            pdb=" NZ  LYS L 331 "
     model   vdw
     1.609 3.200
  nonbonded pdb=" CE  LYS F 340 "
            pdb=" NZ  LYS L 331 "
     model   vdw
     1.729 3.520
  nonbonded pdb=" CG  GLN F 336 "
            pdb=" CG  GLN L 336 "
     model   vdw
     1.852 3.840
  nonbonded pdb=" CG  GLN B 336 "
            pdb=" CB  GLN J 336 "
     model   vdw
     1.943 3.840
  ... (remaining 51199 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 306 through 378)
  selection = chain 'B'
  selection = (chain 'C' and resid 306 through 378)
  selection = chain 'D'
  selection = (chain 'E' and resid 306 through 378)
  selection = chain 'F'
  selection = (chain 'G' and resid 306 through 378)
  selection = (chain 'H' and resid 306 through 378)
  selection = (chain 'I' and resid 306 through 378)
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.310
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.000
  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:             0.010
  Load rotamer database and sin/cos tables:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5163
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      :  0.012   0.041   6918  Z= 0.731
  Angle     :  2.007  11.574   9258  Z= 1.324
  Chirality :  0.109   0.498   1044
  Planarity :  0.012   0.104   1176
  Dihedral  : 11.636  73.452   2646
  Min Nonbonded Distance : 1.524

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.97 %
    Favored  : 91.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Cbeta Deviations :  0.77 %
  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: -2.95 (0.23), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.24 (0.17), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG K 349 
 TYR   0.153   0.042   TYR G 310 
 PHE   0.040   0.010   PHE B 346 
 HIS   0.013   0.004   HIS I 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.01164 ( 6918)
  covalent geometry    : angle       2.00723 ( 9258)
  hydrogen bonds       : bond        0.13671 (  136)
  hydrogen bonds       : angle       7.94282 (  408)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  321 LYS cc_start: 0.7960 (mttt) cc_final: 0.7430 (ttmt)
REVERT: A  346 PHE cc_start: 0.9093 (m-10) cc_final: 0.8771 (m-10)
REVERT: A  349 ARG cc_start: 0.8143 (mtm180) cc_final: 0.7865 (mtm-85)
REVERT: A  359 ASN cc_start: 0.8475 (m-40) cc_final: 0.8225 (m110)
REVERT: C  321 LYS cc_start: 0.8286 (mttt) cc_final: 0.7600 (ttmt)
REVERT: C  349 ARG cc_start: 0.7971 (mtm180) cc_final: 0.6958 (ppt170)
REVERT: E  311 LYS cc_start: 0.7997 (mttt) cc_final: 0.7191 (mmtm)
REVERT: E  321 LYS cc_start: 0.7964 (mttt) cc_final: 0.7493 (ttmt)
REVERT: E  331 LYS cc_start: 0.8711 (mttt) cc_final: 0.8090 (mmtt)
REVERT: E  347 LYS cc_start: 0.8392 (mttp) cc_final: 0.8104 (ttmm)
REVERT: E  349 ARG cc_start: 0.7824 (mtm180) cc_final: 0.6743 (mmp-170)
REVERT: B  320 SER cc_start: 0.8655 (m) cc_final: 0.8368 (m)
REVERT: B  348 ASP cc_start: 0.7799 (t0) cc_final: 0.7536 (t0)
REVERT: B  349 ARG cc_start: 0.7358 (mtm180) cc_final: 0.7096 (mtm-85)
REVERT: B  369 LYS cc_start: 0.8037 (mtpt) cc_final: 0.7622 (mptt)
REVERT: D  349 ARG cc_start: 0.7475 (mtm180) cc_final: 0.7150 (mtm-85)
REVERT: D  369 LYS cc_start: 0.8023 (mtpt) cc_final: 0.7596 (mptt)
REVERT: H  346 PHE cc_start: 0.8255 (m-10) cc_final: 0.7885 (m-80)
REVERT: I  349 ARG cc_start: 0.7113 (mtm180) cc_final: 0.6572 (mmp80)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.0992
  time to fit residues: 23.2379
Evaluate side-chains
  134 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:    7.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
B 327 ASN
B 330 HIS
B 362 HIS
D 327 ASN
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 359 ASN
D 362 HIS
F 327 ASN
** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 362 HIS
** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 329 HIS
** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5245 r_free = 0.5245 target = 0.365450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.5260 r_free = 0.5260 target = 0.247987 restraints weight = 8945.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.5278 r_free = 0.5278 target = 0.251257 restraints weight = 5584.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.5284 r_free = 0.5284 target = 0.252974 restraints weight = 4195.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.5301 r_free = 0.5301 target = 0.254312 restraints weight = 3552.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.5303 r_free = 0.5303 target = 0.254941 restraints weight = 3210.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.5198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6923
moved from start:          0.5526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   6918  Z= 0.232
  Angle     :  0.856   8.206   9258  Z= 0.457
  Chirality :  0.055   0.180   1044
  Planarity :  0.004   0.034   1176
  Dihedral  :  7.035  31.973    912
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  :  9.87 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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: -2.52 (0.23), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.91 (0.18), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG J 349 
 TYR   0.030   0.005   TYR I 310 
 PHE   0.017   0.002   PHE G 346 
 HIS   0.011   0.002   HIS K 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 ( 6918)
  covalent geometry    : angle       0.85582 ( 9258)
  hydrogen bonds       : bond        0.04047 (  136)
  hydrogen bonds       : angle       6.69213 (  408)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 178
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
REVERT: A  353 LYS cc_start: 0.8967 (tttt) cc_final: 0.8693 (tttt)
REVERT: C  336 GLN cc_start: 0.8306 (tm-30) cc_final: 0.8050 (tm-30)
REVERT: C  349 ARG cc_start: 0.8062 (mtm180) cc_final: 0.7042 (ptt90)
REVERT: E  311 LYS cc_start: 0.7618 (mttt) cc_final: 0.7385 (mmtt)
REVERT: E  331 LYS cc_start: 0.8891 (mttt) cc_final: 0.8094 (mmmt)
REVERT: E  376 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6984 (mp)
REVERT: B  363 VAL cc_start: 0.8784 (t) cc_final: 0.8438 (t)
REVERT: D  348 ASP cc_start: 0.7862 (t0) cc_final: 0.7561 (t0)
REVERT: F  322 CYS cc_start: 0.7671 (p) cc_final: 0.7460 (p)
REVERT: G  331 LYS cc_start: 0.8402 (mmtt) cc_final: 0.7916 (mttt)
REVERT: G  369 LYS cc_start: 0.8824 (ptpp) cc_final: 0.8476 (ptpp)
REVERT: H  344 LEU cc_start: 0.8813 (mp) cc_final: 0.8530 (tt)
REVERT: H  346 PHE cc_start: 0.8296 (m-10) cc_final: 0.8008 (m-80)
REVERT: H  349 ARG cc_start: 0.7317 (mtm180) cc_final: 0.5958 (ptt-90)
REVERT: I  329 HIS cc_start: 0.0307 (m-70) cc_final: -0.0169 (m-70)
REVERT: I  349 ARG cc_start: 0.7435 (mtm180) cc_final: 0.6924 (mmp-170)
REVERT: K  317 LYS cc_start: 0.7319 (pttt) cc_final: 0.7105 (mmmt)
REVERT: K  348 ASP cc_start: 0.7885 (t0) cc_final: 0.7356 (t0)
REVERT: K  371 ILE cc_start: 0.8029 (tt) cc_final: 0.7535 (mp)
REVERT: K  376 LEU cc_start: 0.6126 (pt) cc_final: 0.5848 (tt)
  outliers start: 27
  outliers final: 17
  residues processed: 195
  average time/residue: 0.1097
  time to fit residues: 26.0173
Evaluate side-chains
  158 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain E residue  376 LEU
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain F residue  313 VAL
Chi-restraints excluded: chain G residue  306 VAL
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  319 THR
Chi-restraints excluded: chain H residue  322 CYS
Chi-restraints excluded: chain H residue  376 LEU
Chi-restraints excluded: chain I residue  306 VAL
Chi-restraints excluded: chain J residue  350 VAL
Chi-restraints excluded: chain L residue  337 VAL
Chi-restraints excluded: chain L residue  350 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 61 optimal weight:    9.9990
   chunk 79 optimal weight:    4.9990
   chunk 8 optimal weight:    7.9990
   chunk 83 optimal weight:   30.0000
   chunk 39 optimal weight:    0.0050
   chunk 26 optimal weight:    9.9990
   chunk 53 optimal weight:    9.9990
   chunk 59 optimal weight:    9.9990
   chunk 45 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 82 optimal weight:    0.3980
   overall best weight:    3.0800

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

Flipped N/Q/H residues before XYZ refinement:
A 362 HIS
C 362 HIS
B 330 HIS
F 330 HIS
** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 329 HIS
H 336 GLN
H 368 ASN
I 351 GLN
J 368 ASN
K 359 ASN
K 368 ASN
L 327 ASN
L 368 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5132 r_free = 0.5132 target = 0.341502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 100)---------------|
| r_work = 0.5208 r_free = 0.5208 target = 0.235092 restraints weight = 8621.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.5226 r_free = 0.5226 target = 0.237957 restraints weight = 5429.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.5233 r_free = 0.5233 target = 0.239513 restraints weight = 4102.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.5256 r_free = 0.5256 target = 0.240779 restraints weight = 3502.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.5258 r_free = 0.5258 target = 0.241383 restraints weight = 3169.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.4925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7157
moved from start:          0.7396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6918  Z= 0.170
  Angle     :  0.793   8.772   9258  Z= 0.413
  Chirality :  0.052   0.177   1044
  Planarity :  0.004   0.038   1176
  Dihedral  :  6.519  25.605    912
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 13.59 %
    Favored  : 83.21 %
  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: -2.49 (0.24), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.89 (0.18), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG K 349 
 TYR   0.026   0.004   TYR G 310 
 PHE   0.015   0.002   PHE B 378 
 HIS   0.009   0.001   HIS I 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 6918)
  covalent geometry    : angle       0.79292 ( 9258)
  hydrogen bonds       : bond        0.03197 (  136)
  hydrogen bonds       : angle       6.30948 (  408)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 174
  time to evaluate  : 0.279 
Fit side-chains
REVERT: A  353 LYS cc_start: 0.8702 (tttt) cc_final: 0.8461 (tttt)
REVERT: A  379 ARG cc_start: 0.7600 (mtt180) cc_final: 0.7255 (ttm110)
REVERT: C  345 ASP cc_start: 0.7526 (m-30) cc_final: 0.7243 (t0)
REVERT: E  336 GLN cc_start: 0.8513 (tm-30) cc_final: 0.8036 (tm-30)
REVERT: E  376 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7310 (mp)
REVERT: E  379 ARG cc_start: 0.7789 (mtt180) cc_final: 0.7348 (ttm110)
REVERT: B  315 LEU cc_start: 0.9024 (mm) cc_final: 0.8581 (mm)
REVERT: D  349 ARG cc_start: 0.8096 (mtm180) cc_final: 0.7861 (mtm-85)
REVERT: F  347 LYS cc_start: 0.8932 (mtpp) cc_final: 0.8445 (ttmm)
REVERT: F  348 ASP cc_start: 0.8274 (t0) cc_final: 0.7200 (p0)
REVERT: G  318 VAL cc_start: 0.7108 (t) cc_final: 0.6627 (t)
REVERT: G  321 LYS cc_start: 0.8458 (tttm) cc_final: 0.7919 (tmtt)
REVERT: G  351 GLN cc_start: 0.6830 (OUTLIER) cc_final: 0.6495 (pm20)
REVERT: H  349 ARG cc_start: 0.7616 (mtm180) cc_final: 0.5830 (ptt-90)
REVERT: I  311 LYS cc_start: 0.7293 (ptmm) cc_final: 0.6298 (tptp)
REVERT: I  349 ARG cc_start: 0.7531 (mtm180) cc_final: 0.7038 (mmp-170)
REVERT: I  375 LYS cc_start: 0.7938 (mmtm) cc_final: 0.7439 (mptt)
REVERT: J  343 LYS cc_start: 0.6955 (ttmt) cc_final: 0.6664 (tttt)
REVERT: J  374 HIS cc_start: 0.6176 (m90) cc_final: 0.5602 (m-70)
REVERT: K  317 LYS cc_start: 0.7794 (pttt) cc_final: 0.7502 (mmtt)
REVERT: K  322 CYS cc_start: 0.7134 (p) cc_final: 0.6886 (p)
REVERT: K  348 ASP cc_start: 0.8240 (t0) cc_final: 0.7871 (t0)
REVERT: K  349 ARG cc_start: 0.8317 (mtm180) cc_final: 0.8102 (mtm180)
REVERT: K  371 ILE cc_start: 0.8069 (tt) cc_final: 0.7655 (mp)
REVERT: K  376 LEU cc_start: 0.6443 (pt) cc_final: 0.5621 (tt)
REVERT: L  330 HIS cc_start: 0.6924 (OUTLIER) cc_final: 0.6720 (m170)
REVERT: L  349 ARG cc_start: 0.7192 (mtm110) cc_final: 0.6696 (mtm-85)
  outliers start: 25
  outliers final: 15
  residues processed: 184
  average time/residue: 0.1179
  time to fit residues: 26.4106
Evaluate side-chains
  166 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 148
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  376 LEU
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain G residue  306 VAL
Chi-restraints excluded: chain G residue  351 GLN
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  319 THR
Chi-restraints excluded: chain I residue  306 VAL
Chi-restraints excluded: chain J residue  350 VAL
Chi-restraints excluded: chain K residue  360 ILE
Chi-restraints excluded: chain L residue  330 HIS
Chi-restraints excluded: chain L residue  337 VAL
Chi-restraints excluded: chain L residue  350 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 45 optimal weight:    9.9990
   chunk 18 optimal weight:    5.9990
   chunk 23 optimal weight:    7.9990
   chunk 21 optimal weight:   30.0000
   chunk 32 optimal weight:    1.9990
   chunk 33 optimal weight:   10.0000
   chunk 82 optimal weight:    9.9990
   chunk 79 optimal weight:    9.9990
   chunk 37 optimal weight:    4.9990
   chunk 69 optimal weight:   20.0000
   chunk 38 optimal weight:    9.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
C 368 ASN
B 330 HIS
F 368 ASN
G 368 ASN
** J 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 362 HIS
** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 362 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5014 r_free = 0.5014 target = 0.324883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 105)---------------|
| r_work = 0.5063 r_free = 0.5063 target = 0.213566 restraints weight = 8649.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.5073 r_free = 0.5073 target = 0.215427 restraints weight = 5602.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.5091 r_free = 0.5091 target = 0.216819 restraints weight = 4337.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.5095 r_free = 0.5095 target = 0.217472 restraints weight = 3726.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.5100 r_free = 0.5100 target = 0.218051 restraints weight = 3418.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.4639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.9332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   6918  Z= 0.275
  Angle     :  0.913  13.970   9258  Z= 0.485
  Chirality :  0.056   0.215   1044
  Planarity :  0.006   0.055   1176
  Dihedral  :  7.353  35.952    912
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 16.54 %
    Favored  : 78.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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: -3.06 (0.23), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.32 (0.17), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG J 349 
 TYR   0.036   0.005   TYR I 310 
 PHE   0.018   0.003   PHE F 346 
 HIS   0.009   0.002   HIS B 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00595 ( 6918)
  covalent geometry    : angle       0.91339 ( 9258)
  hydrogen bonds       : bond        0.04269 (  136)
  hydrogen bonds       : angle       7.83037 (  408)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 161
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A  353 LYS cc_start: 0.9194 (tttt) cc_final: 0.8859 (tttt)
REVERT: A  379 ARG cc_start: 0.7600 (mtt180) cc_final: 0.7393 (ttm110)
REVERT: C  311 LYS cc_start: 0.8569 (mtpt) cc_final: 0.8347 (mtpt)
REVERT: C  379 ARG cc_start: 0.7126 (mtt180) cc_final: 0.6755 (ttm110)
REVERT: E  336 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8129 (tm-30)
REVERT: E  349 ARG cc_start: 0.8575 (mtp85) cc_final: 0.7296 (mmp-170)
REVERT: D  347 LYS cc_start: 0.8468 (ptmt) cc_final: 0.8204 (ttmm)
REVERT: D  348 ASP cc_start: 0.8076 (t0) cc_final: 0.7862 (t0)
REVERT: F  347 LYS cc_start: 0.9150 (mtpp) cc_final: 0.8639 (ttmm)
REVERT: G  345 ASP cc_start: 0.7924 (t0) cc_final: 0.7454 (m-30)
REVERT: H  311 LYS cc_start: 0.7891 (pttm) cc_final: 0.7617 (mtpt)
REVERT: H  349 ARG cc_start: 0.7891 (mtm180) cc_final: 0.6250 (ptt-90)
REVERT: I  310 TYR cc_start: 0.5999 (OUTLIER) cc_final: 0.4558 (t80)
REVERT: I  349 ARG cc_start: 0.7991 (mtm180) cc_final: 0.7285 (mmp-170)
REVERT: I  375 LYS cc_start: 0.8399 (mmtm) cc_final: 0.7675 (tppt)
REVERT: J  347 LYS cc_start: 0.8623 (ptmt) cc_final: 0.8296 (ttmm)
REVERT: J  374 HIS cc_start: 0.5941 (m90) cc_final: 0.5356 (m-70)
REVERT: K  349 ARG cc_start: 0.8136 (mtm180) cc_final: 0.7898 (mtm-85)
REVERT: K  376 LEU cc_start: 0.6656 (pt) cc_final: 0.5919 (tt)
REVERT: L  347 LYS cc_start: 0.8732 (ptmt) cc_final: 0.8433 (ttmm)
REVERT: L  349 ARG cc_start: 0.7468 (mtm110) cc_final: 0.7187 (mtm-85)
REVERT: L  374 HIS cc_start: 0.6335 (m-70) cc_final: 0.5827 (m90)
  outliers start: 36
  outliers final: 24
  residues processed: 184
  average time/residue: 0.1055
  time to fit residues: 23.9423
Evaluate side-chains
  161 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 136
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain F residue  322 CYS
Chi-restraints excluded: chain F residue  341 SER
Chi-restraints excluded: chain G residue  306 VAL
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  319 THR
Chi-restraints excluded: chain I residue  306 VAL
Chi-restraints excluded: chain I residue  310 TYR
Chi-restraints excluded: chain I residue  315 LEU
Chi-restraints excluded: chain I residue  320 SER
Chi-restraints excluded: chain I residue  327 ASN
Chi-restraints excluded: chain J residue  322 CYS
Chi-restraints excluded: chain J residue  350 VAL
Chi-restraints excluded: chain K residue  360 ILE
Chi-restraints excluded: chain L residue  337 VAL
Chi-restraints excluded: chain L residue  350 VAL
Chi-restraints excluded: chain L residue  362 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 25 optimal weight:    9.9990
   chunk 78 optimal weight:    9.9990
   chunk 37 optimal weight:    8.9990
   chunk 20 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 16 optimal weight:   10.0000
   chunk 57 optimal weight:    9.9990
   chunk 31 optimal weight:    7.9990
   chunk 81 optimal weight:    3.9990
   chunk 77 optimal weight:   20.0000
   overall best weight:    4.7588

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

Flipped N/Q/H residues before XYZ refinement:
** I 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 327 ASN
** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 327 ASN
L 362 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4860 r_free = 0.4860 target = 0.182773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4462 r_free = 0.4462 target = 0.148011 restraints weight = 9457.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.150894 restraints weight = 5003.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.152667 restraints weight = 3427.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.153485 restraints weight = 2758.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4534 r_free = 0.4534 target = 0.153935 restraints weight = 2481.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.4555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.9719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6918  Z= 0.206
  Angle     :  0.770   8.889   9258  Z= 0.405
  Chirality :  0.052   0.175   1044
  Planarity :  0.005   0.053   1176
  Dihedral  :  6.664  29.895    912
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 18.33 %
    Favored  : 76.03 %
  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: -3.15 (0.23), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.39 (0.17), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 349 
 TYR   0.024   0.004   TYR I 310 
 PHE   0.018   0.002   PHE F 378 
 HIS   0.032   0.002   HIS L 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 6918)
  covalent geometry    : angle       0.77005 ( 9258)
  hydrogen bonds       : bond        0.02937 (  136)
  hydrogen bonds       : angle       7.17689 (  408)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 149
  time to evaluate  : 0.246 
Fit side-chains
REVERT: C  349 ARG cc_start: 0.7992 (mtt90) cc_final: 0.6254 (ppt170)
REVERT: C  379 ARG cc_start: 0.7076 (mtt180) cc_final: 0.6741 (ttm110)
REVERT: E  336 GLN cc_start: 0.8575 (tm-30) cc_final: 0.8092 (tm-30)
REVERT: E  349 ARG cc_start: 0.8571 (mtp85) cc_final: 0.7184 (mmp-170)
REVERT: E  351 GLN cc_start: 0.7297 (mp10) cc_final: 0.6867 (mp10)
REVERT: B  360 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8218 (mt)
REVERT: D  347 LYS cc_start: 0.8153 (ptmt) cc_final: 0.7765 (ttmm)
REVERT: D  348 ASP cc_start: 0.8005 (t0) cc_final: 0.7694 (t0)
REVERT: D  375 LYS cc_start: 0.7242 (tptt) cc_final: 0.6797 (tptp)
REVERT: F  347 LYS cc_start: 0.9089 (mtpp) cc_final: 0.8490 (ttmm)
REVERT: G  340 LYS cc_start: 0.7422 (tptp) cc_final: 0.6039 (mttm)
REVERT: G  342 GLU cc_start: 0.8509 (mp0) cc_final: 0.8160 (mp0)
REVERT: G  345 ASP cc_start: 0.7867 (t0) cc_final: 0.7411 (m-30)
REVERT: G  350 VAL cc_start: 0.8771 (OUTLIER) cc_final: 0.8554 (p)
REVERT: H  311 LYS cc_start: 0.7798 (pttm) cc_final: 0.7477 (mtpt)
REVERT: H  349 ARG cc_start: 0.8041 (mtm180) cc_final: 0.6227 (ptt90)
REVERT: I  310 TYR cc_start: 0.5722 (OUTLIER) cc_final: 0.4164 (t80)
REVERT: I  349 ARG cc_start: 0.8064 (mtm180) cc_final: 0.7293 (mmp-170)
REVERT: I  375 LYS cc_start: 0.8376 (mmtm) cc_final: 0.7689 (tppt)
REVERT: J  347 LYS cc_start: 0.8290 (ptmt) cc_final: 0.7935 (ptmm)
REVERT: J  374 HIS cc_start: 0.6017 (m90) cc_final: 0.5602 (m-70)
REVERT: K  314 ASP cc_start: 0.5770 (p0) cc_final: 0.4774 (t70)
REVERT: K  376 LEU cc_start: 0.6673 (pt) cc_final: 0.5876 (tt)
REVERT: L  347 LYS cc_start: 0.8664 (ptmt) cc_final: 0.8241 (ttmm)
REVERT: L  349 ARG cc_start: 0.7620 (mtm110) cc_final: 0.7287 (mtm-85)
REVERT: L  369 LYS cc_start: 0.5129 (mtpp) cc_final: 0.4846 (mtmm)
REVERT: L  374 HIS cc_start: 0.6486 (m-70) cc_final: 0.5975 (m90)
  outliers start: 44
  outliers final: 34
  residues processed: 179
  average time/residue: 0.0870
  time to fit residues: 19.6769
Evaluate side-chains
  174 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 137
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain D residue  327 ASN
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  341 SER
Chi-restraints excluded: chain G residue  306 VAL
Chi-restraints excluded: chain G residue  315 LEU
Chi-restraints excluded: chain G residue  316 SER
Chi-restraints excluded: chain G residue  337 VAL
Chi-restraints excluded: chain G residue  350 VAL
Chi-restraints excluded: chain G residue  351 GLN
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  319 THR
Chi-restraints excluded: chain I residue  306 VAL
Chi-restraints excluded: chain I residue  310 TYR
Chi-restraints excluded: chain I residue  319 THR
Chi-restraints excluded: chain I residue  320 SER
Chi-restraints excluded: chain J residue  313 VAL
Chi-restraints excluded: chain J residue  322 CYS
Chi-restraints excluded: chain J residue  341 SER
Chi-restraints excluded: chain J residue  350 VAL
Chi-restraints excluded: chain J residue  360 ILE
Chi-restraints excluded: chain K residue  322 CYS
Chi-restraints excluded: chain K residue  341 SER
Chi-restraints excluded: chain K residue  360 ILE
Chi-restraints excluded: chain L residue  316 SER
Chi-restraints excluded: chain L residue  337 VAL
Chi-restraints excluded: chain L residue  350 VAL
Chi-restraints excluded: chain L residue  362 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 9 optimal weight:    4.9990
   chunk 7 optimal weight:    0.4980
   chunk 1 optimal weight:    7.9990
   chunk 59 optimal weight:    9.9990
   chunk 69 optimal weight:   20.0000
   chunk 49 optimal weight:   20.0000
   chunk 81 optimal weight:    4.9990
   chunk 32 optimal weight:    9.9990
   chunk 71 optimal weight:   20.0000
   chunk 53 optimal weight:    5.9990
   overall best weight:    3.4986

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

Flipped N/Q/H residues before XYZ refinement:
** I 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 327 ASN
L 362 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4878 r_free = 0.4878 target = 0.183447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.148811 restraints weight = 9317.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.151680 restraints weight = 4867.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.153451 restraints weight = 3331.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4541 r_free = 0.4541 target = 0.154349 restraints weight = 2698.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.154642 restraints weight = 2414.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.4530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          1.0001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   6918  Z= 0.164
  Angle     :  0.712   8.055   9258  Z= 0.373
  Chirality :  0.051   0.165   1044
  Planarity :  0.005   0.055   1176
  Dihedral  :  6.300  29.843    912
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 19.62 %
    Favored  : 75.13 %
  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 (0.22), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.37 (0.17), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 349 
 TYR   0.020   0.003   TYR I 310 
 PHE   0.019   0.002   PHE H 378 
 HIS   0.007   0.001   HIS L 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 6918)
  covalent geometry    : angle       0.71163 ( 9258)
  hydrogen bonds       : bond        0.02685 (  136)
  hydrogen bonds       : angle       6.84191 (  408)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 144
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
REVERT: C  379 ARG cc_start: 0.6974 (mtt180) cc_final: 0.6768 (ttm110)
REVERT: E  336 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8102 (tm-30)
REVERT: E  349 ARG cc_start: 0.8587 (mtp85) cc_final: 0.7220 (mmp-170)
REVERT: B  360 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8172 (mt)
REVERT: D  375 LYS cc_start: 0.7382 (tptt) cc_final: 0.6990 (tptp)
REVERT: F  314 ASP cc_start: 0.6390 (p0) cc_final: 0.6152 (p0)
REVERT: F  347 LYS cc_start: 0.9018 (mtpp) cc_final: 0.8453 (ttmm)
REVERT: G  321 LYS cc_start: 0.8597 (tttm) cc_final: 0.8212 (tmtt)
REVERT: G  340 LYS cc_start: 0.7122 (tptp) cc_final: 0.6080 (mttm)
REVERT: G  342 GLU cc_start: 0.8453 (mp0) cc_final: 0.8131 (mp0)
REVERT: G  345 ASP cc_start: 0.7845 (t0) cc_final: 0.7350 (m-30)
REVERT: G  353 LYS cc_start: 0.8036 (mtpt) cc_final: 0.7710 (tttt)
REVERT: H  311 LYS cc_start: 0.7831 (pttm) cc_final: 0.7521 (mtpt)
REVERT: H  321 LYS cc_start: 0.8585 (ttmt) cc_final: 0.8365 (ttmt)
REVERT: H  349 ARG cc_start: 0.8056 (mtm180) cc_final: 0.6180 (ptt-90)
REVERT: I  349 ARG cc_start: 0.8011 (mtm180) cc_final: 0.7247 (mmp-170)
REVERT: J  347 LYS cc_start: 0.8268 (ptmt) cc_final: 0.7874 (ttmm)
REVERT: J  374 HIS cc_start: 0.6144 (m90) cc_final: 0.5839 (m-70)
REVERT: K  314 ASP cc_start: 0.5786 (p0) cc_final: 0.4834 (t70)
REVERT: K  375 LYS cc_start: 0.7764 (tptt) cc_final: 0.7509 (tptt)
REVERT: K  376 LEU cc_start: 0.6856 (pt) cc_final: 0.6499 (tt)
REVERT: L  347 LYS cc_start: 0.8692 (ptmt) cc_final: 0.8237 (ttmm)
REVERT: L  348 ASP cc_start: 0.8059 (t0) cc_final: 0.6860 (p0)
REVERT: L  349 ARG cc_start: 0.7588 (mtm110) cc_final: 0.7085 (mtm-85)
  outliers start: 41
  outliers final: 39
  residues processed: 170
  average time/residue: 0.0900
  time to fit residues: 19.1356
Evaluate side-chains
  179 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 139
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain D residue  322 CYS
Chi-restraints excluded: chain D residue  327 ASN
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  341 SER
Chi-restraints excluded: chain G residue  306 VAL
Chi-restraints excluded: chain G residue  315 LEU
Chi-restraints excluded: chain G residue  316 SER
Chi-restraints excluded: chain G residue  331 LYS
Chi-restraints excluded: chain G residue  337 VAL
Chi-restraints excluded: chain G residue  350 VAL
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  319 THR
Chi-restraints excluded: chain I residue  306 VAL
Chi-restraints excluded: chain I residue  319 THR
Chi-restraints excluded: chain I residue  320 SER
Chi-restraints excluded: chain I residue  356 SER
Chi-restraints excluded: chain I residue  371 ILE
Chi-restraints excluded: chain J residue  313 VAL
Chi-restraints excluded: chain J residue  322 CYS
Chi-restraints excluded: chain J residue  341 SER
Chi-restraints excluded: chain J residue  350 VAL
Chi-restraints excluded: chain J residue  360 ILE
Chi-restraints excluded: chain K residue  322 CYS
Chi-restraints excluded: chain K residue  341 SER
Chi-restraints excluded: chain K residue  360 ILE
Chi-restraints excluded: chain L residue  327 ASN
Chi-restraints excluded: chain L residue  330 HIS
Chi-restraints excluded: chain L residue  337 VAL
Chi-restraints excluded: chain L residue  350 VAL
Chi-restraints excluded: chain L residue  362 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 51 optimal weight:    9.9990
   chunk 50 optimal weight:    9.9990
   chunk 6 optimal weight:    9.9990
   chunk 4 optimal weight:   20.0000
   chunk 30 optimal weight:    9.9990
   chunk 37 optimal weight:    0.0980
   chunk 40 optimal weight:    9.9990
   chunk 27 optimal weight:    3.9990
   chunk 53 optimal weight:    6.9990
   chunk 43 optimal weight:    8.9990
   chunk 32 optimal weight:    0.0770
   overall best weight:    4.0344

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

Flipped N/Q/H residues before XYZ refinement:
** I 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 368 ASN
** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 329 HIS
** L 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4864 r_free = 0.4864 target = 0.181328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4460 r_free = 0.4460 target = 0.147474 restraints weight = 9216.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.150255 restraints weight = 4843.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.151929 restraints weight = 3311.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.152733 restraints weight = 2680.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4533 r_free = 0.4533 target = 0.153310 restraints weight = 2412.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.4521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          1.0226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6918  Z= 0.177
  Angle     :  0.716   7.971   9258  Z= 0.374
  Chirality :  0.051   0.170   1044
  Planarity :  0.005   0.056   1176
  Dihedral  :  6.248  28.916    912
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.82 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 19.62 %
    Favored  : 73.97 %
  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: -3.16 (0.23), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.40 (0.17), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 349 
 TYR   0.024   0.003   TYR I 310 
 PHE   0.015   0.002   PHE F 378 
 HIS   0.006   0.001   HIS I 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 6918)
  covalent geometry    : angle       0.71575 ( 9258)
  hydrogen bonds       : bond        0.02695 (  136)
  hydrogen bonds       : angle       6.87729 (  408)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 137
  time to evaluate  : 0.278 
Fit side-chains
REVERT: C  379 ARG cc_start: 0.6984 (mtt180) cc_final: 0.6774 (ttm110)
REVERT: E  336 GLN cc_start: 0.8594 (tm-30) cc_final: 0.8108 (tm-30)
REVERT: E  349 ARG cc_start: 0.8597 (mtp85) cc_final: 0.7234 (mmp-170)
REVERT: B  360 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8150 (mt)
REVERT: D  375 LYS cc_start: 0.7234 (tptt) cc_final: 0.6971 (tptp)
REVERT: F  314 ASP cc_start: 0.6414 (p0) cc_final: 0.6170 (p0)
REVERT: F  347 LYS cc_start: 0.9051 (mtpp) cc_final: 0.8479 (ttmm)
REVERT: G  321 LYS cc_start: 0.8588 (tttm) cc_final: 0.7870 (tmtt)
REVERT: G  340 LYS cc_start: 0.7202 (tptp) cc_final: 0.6120 (mttm)
REVERT: G  342 GLU cc_start: 0.8390 (mp0) cc_final: 0.8089 (mp0)
REVERT: G  345 ASP cc_start: 0.7835 (t0) cc_final: 0.7362 (m-30)
REVERT: G  350 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8477 (p)
REVERT: H  311 LYS cc_start: 0.7869 (pttm) cc_final: 0.7542 (mtpt)
REVERT: H  349 ARG cc_start: 0.8115 (mtm180) cc_final: 0.6246 (ptt-90)
REVERT: I  310 TYR cc_start: 0.5743 (OUTLIER) cc_final: 0.4168 (t80)
REVERT: I  349 ARG cc_start: 0.7972 (mtm180) cc_final: 0.7434 (mmp-170)
REVERT: J  347 LYS cc_start: 0.8373 (ptmt) cc_final: 0.7930 (ttmm)
REVERT: J  374 HIS cc_start: 0.6062 (m90) cc_final: 0.5762 (m-70)
REVERT: K  314 ASP cc_start: 0.5863 (p0) cc_final: 0.5554 (p0)
REVERT: K  348 ASP cc_start: 0.8187 (t0) cc_final: 0.7890 (t0)
REVERT: K  375 LYS cc_start: 0.7721 (tptt) cc_final: 0.7380 (tptp)
REVERT: K  376 LEU cc_start: 0.6779 (pt) cc_final: 0.6470 (tt)
REVERT: L  347 LYS cc_start: 0.8750 (ptmt) cc_final: 0.8285 (ttmm)
REVERT: L  348 ASP cc_start: 0.8051 (t0) cc_final: 0.6906 (p0)
REVERT: L  349 ARG cc_start: 0.7578 (mtm110) cc_final: 0.7085 (mtm-85)
  outliers start: 50
  outliers final: 42
  residues processed: 169
  average time/residue: 0.0974
  time to fit residues: 20.8247
Evaluate side-chains
  178 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 133
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain D residue  322 CYS
Chi-restraints excluded: chain D residue  327 ASN
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  322 CYS
Chi-restraints excluded: chain F residue  327 ASN
Chi-restraints excluded: chain F residue  341 SER
Chi-restraints excluded: chain G residue  306 VAL
Chi-restraints excluded: chain G residue  315 LEU
Chi-restraints excluded: chain G residue  316 SER
Chi-restraints excluded: chain G residue  331 LYS
Chi-restraints excluded: chain G residue  337 VAL
Chi-restraints excluded: chain G residue  350 VAL
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  319 THR
Chi-restraints excluded: chain I residue  306 VAL
Chi-restraints excluded: chain I residue  310 TYR
Chi-restraints excluded: chain I residue  319 THR
Chi-restraints excluded: chain I residue  320 SER
Chi-restraints excluded: chain I residue  356 SER
Chi-restraints excluded: chain I residue  371 ILE
Chi-restraints excluded: chain J residue  313 VAL
Chi-restraints excluded: chain J residue  322 CYS
Chi-restraints excluded: chain J residue  341 SER
Chi-restraints excluded: chain J residue  350 VAL
Chi-restraints excluded: chain J residue  360 ILE
Chi-restraints excluded: chain K residue  322 CYS
Chi-restraints excluded: chain K residue  341 SER
Chi-restraints excluded: chain K residue  360 ILE
Chi-restraints excluded: chain L residue  327 ASN
Chi-restraints excluded: chain L residue  330 HIS
Chi-restraints excluded: chain L residue  337 VAL
Chi-restraints excluded: chain L residue  341 SER
Chi-restraints excluded: chain L residue  350 VAL
Chi-restraints excluded: chain L residue  362 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 81 optimal weight:    0.0770
   chunk 48 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   chunk 30 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 56 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 79 optimal weight:   10.0000
   chunk 51 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   overall best weight:    2.9944

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

Flipped N/Q/H residues before XYZ refinement:
** I 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 374 HIS
L 329 HIS
L 374 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4892 r_free = 0.4892 target = 0.183997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4487 r_free = 0.4487 target = 0.149520 restraints weight = 9242.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.152332 restraints weight = 4804.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.154048 restraints weight = 3266.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.154895 restraints weight = 2643.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4558 r_free = 0.4558 target = 0.155489 restraints weight = 2370.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.4545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          1.0356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6918  Z= 0.147
  Angle     :  0.683   7.480   9258  Z= 0.354
  Chirality :  0.050   0.158   1044
  Planarity :  0.005   0.056   1176
  Dihedral  :  6.023  26.454    912
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.55 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 20.38 %
    Favored  : 73.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.17 (0.23), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.41 (0.17), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG K 349 
 TYR   0.018   0.003   TYR I 310 
 PHE   0.021   0.002   PHE H 378 
 HIS   0.005   0.001   HIS I 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 6918)
  covalent geometry    : angle       0.68275 ( 9258)
  hydrogen bonds       : bond        0.02551 (  136)
  hydrogen bonds       : angle       6.61297 (  408)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 140
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A  336 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8185 (tm-30)
REVERT: C  336 GLN cc_start: 0.8406 (tm-30) cc_final: 0.8110 (tm-30)
REVERT: E  336 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8153 (tm-30)
REVERT: E  349 ARG cc_start: 0.8599 (mtp85) cc_final: 0.7269 (mmp-170)
REVERT: B  360 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8185 (mt)
REVERT: D  360 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.7721 (mt)
REVERT: D  375 LYS cc_start: 0.7157 (tptt) cc_final: 0.6854 (tptp)
REVERT: F  347 LYS cc_start: 0.9004 (mtpp) cc_final: 0.8446 (ttmm)
REVERT: G  321 LYS cc_start: 0.8562 (tttm) cc_final: 0.7851 (tmtt)
REVERT: G  340 LYS cc_start: 0.7217 (tptp) cc_final: 0.6159 (mtmt)
REVERT: G  342 GLU cc_start: 0.8368 (mp0) cc_final: 0.8051 (mp0)
REVERT: G  345 ASP cc_start: 0.7768 (t0) cc_final: 0.7299 (m-30)
REVERT: G  350 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8385 (p)
REVERT: G  351 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6918 (pm20)
REVERT: H  311 LYS cc_start: 0.7852 (pttm) cc_final: 0.7554 (mtpt)
REVERT: H  349 ARG cc_start: 0.8102 (mtm180) cc_final: 0.6241 (ptt-90)
REVERT: I  310 TYR cc_start: 0.5587 (OUTLIER) cc_final: 0.3997 (t80)
REVERT: J  347 LYS cc_start: 0.8250 (ptmt) cc_final: 0.7903 (ttmm)
REVERT: K  314 ASP cc_start: 0.5523 (p0) cc_final: 0.5243 (p0)
REVERT: K  375 LYS cc_start: 0.7635 (tptt) cc_final: 0.7258 (tptp)
REVERT: K  376 LEU cc_start: 0.6567 (pt) cc_final: 0.6277 (tt)
REVERT: L  347 LYS cc_start: 0.8724 (ptmt) cc_final: 0.8289 (ttmm)
REVERT: L  348 ASP cc_start: 0.8004 (t0) cc_final: 0.6776 (p0)
REVERT: L  349 ARG cc_start: 0.7554 (mtm110) cc_final: 0.7098 (mtm-85)
  outliers start: 45
  outliers final: 40
  residues processed: 167
  average time/residue: 0.1068
  time to fit residues: 22.2161
Evaluate side-chains
  180 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 135
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain D residue  322 CYS
Chi-restraints excluded: chain D residue  327 ASN
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  322 CYS
Chi-restraints excluded: chain F residue  327 ASN
Chi-restraints excluded: chain F residue  341 SER
Chi-restraints excluded: chain G residue  306 VAL
Chi-restraints excluded: chain G residue  315 LEU
Chi-restraints excluded: chain G residue  316 SER
Chi-restraints excluded: chain G residue  331 LYS
Chi-restraints excluded: chain G residue  337 VAL
Chi-restraints excluded: chain G residue  350 VAL
Chi-restraints excluded: chain G residue  351 GLN
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  319 THR
Chi-restraints excluded: chain I residue  306 VAL
Chi-restraints excluded: chain I residue  310 TYR
Chi-restraints excluded: chain I residue  315 LEU
Chi-restraints excluded: chain I residue  320 SER
Chi-restraints excluded: chain I residue  356 SER
Chi-restraints excluded: chain I residue  371 ILE
Chi-restraints excluded: chain J residue  311 LYS
Chi-restraints excluded: chain J residue  313 VAL
Chi-restraints excluded: chain J residue  322 CYS
Chi-restraints excluded: chain J residue  341 SER
Chi-restraints excluded: chain J residue  350 VAL
Chi-restraints excluded: chain J residue  360 ILE
Chi-restraints excluded: chain K residue  318 VAL
Chi-restraints excluded: chain K residue  322 CYS
Chi-restraints excluded: chain K residue  341 SER
Chi-restraints excluded: chain K residue  360 ILE
Chi-restraints excluded: chain L residue  330 HIS
Chi-restraints excluded: chain L residue  337 VAL
Chi-restraints excluded: chain L residue  350 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 45 optimal weight:   20.0000
   chunk 25 optimal weight:   10.0000
   chunk 77 optimal weight:    8.9990
   chunk 50 optimal weight:   20.0000
   chunk 64 optimal weight:   30.0000
   chunk 35 optimal weight:    0.5980
   chunk 78 optimal weight:    6.9990
   chunk 38 optimal weight:    9.9990
   chunk 12 optimal weight:    7.9990
   chunk 54 optimal weight:   10.0000
   chunk 71 optimal weight:    5.9990
   overall best weight:    6.1188

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

Flipped N/Q/H residues before XYZ refinement:
** I 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 329 HIS
L 329 HIS
L 362 HIS
** L 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4786 r_free = 0.4786 target = 0.172660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.139510 restraints weight = 9646.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.142131 restraints weight = 5013.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.143719 restraints weight = 3407.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.144450 restraints weight = 2751.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.144846 restraints weight = 2480.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.4428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          1.0855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   6918  Z= 0.247
  Angle     :  0.805   8.494   9258  Z= 0.424
  Chirality :  0.053   0.201   1044
  Planarity :  0.006   0.062   1176
  Dihedral  :  6.750  29.043    912
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.54 %
    Favored  : 90.46 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 19.74 %
    Favored  : 73.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.39 (0.23), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.18), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG K 349 
 TYR   0.031   0.004   TYR I 310 
 PHE   0.020   0.002   PHE I 346 
 HIS   0.005   0.001   HIS G 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 ( 6918)
  covalent geometry    : angle       0.80522 ( 9258)
  hydrogen bonds       : bond        0.03397 (  136)
  hydrogen bonds       : angle       7.49662 (  408)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 139
  time to evaluate  : 0.275 
Fit side-chains
REVERT: C  336 GLN cc_start: 0.8435 (tm-30) cc_final: 0.8110 (tm-30)
REVERT: E  336 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8128 (tm-30)
REVERT: E  349 ARG cc_start: 0.8614 (mtp85) cc_final: 0.7218 (mmp-170)
REVERT: B  360 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8176 (mt)
REVERT: D  347 LYS cc_start: 0.8452 (ptmt) cc_final: 0.8058 (ttmm)
REVERT: F  347 LYS cc_start: 0.9120 (mtpp) cc_final: 0.8644 (ttmm)
REVERT: G  342 GLU cc_start: 0.8334 (mp0) cc_final: 0.8001 (mp0)
REVERT: G  345 ASP cc_start: 0.7802 (t0) cc_final: 0.7443 (m-30)
REVERT: H  311 LYS cc_start: 0.7854 (pttm) cc_final: 0.7500 (mtpp)
REVERT: H  349 ARG cc_start: 0.8169 (mtm180) cc_final: 0.6568 (ptt90)
REVERT: I  310 TYR cc_start: 0.6100 (OUTLIER) cc_final: 0.4635 (t80)
REVERT: I  378 PHE cc_start: 0.6382 (t80) cc_final: 0.5196 (p90)
REVERT: J  347 LYS cc_start: 0.8589 (ptmt) cc_final: 0.8185 (ttmm)
REVERT: K  375 LYS cc_start: 0.7619 (tptt) cc_final: 0.7273 (tptp)
REVERT: K  376 LEU cc_start: 0.6575 (pt) cc_final: 0.6265 (tt)
REVERT: L  347 LYS cc_start: 0.8981 (ptmt) cc_final: 0.8455 (ttmm)
REVERT: L  349 ARG cc_start: 0.7655 (mtm110) cc_final: 0.7445 (mtm-85)
  outliers start: 50
  outliers final: 44
  residues processed: 171
  average time/residue: 0.0947
  time to fit residues: 20.8833
Evaluate side-chains
  174 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 128
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain D residue  322 CYS
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  322 CYS
Chi-restraints excluded: chain F residue  341 SER
Chi-restraints excluded: chain G residue  306 VAL
Chi-restraints excluded: chain G residue  315 LEU
Chi-restraints excluded: chain G residue  316 SER
Chi-restraints excluded: chain G residue  331 LYS
Chi-restraints excluded: chain G residue  337 VAL
Chi-restraints excluded: chain G residue  350 VAL
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  319 THR
Chi-restraints excluded: chain I residue  306 VAL
Chi-restraints excluded: chain I residue  310 TYR
Chi-restraints excluded: chain I residue  319 THR
Chi-restraints excluded: chain I residue  320 SER
Chi-restraints excluded: chain I residue  356 SER
Chi-restraints excluded: chain I residue  371 ILE
Chi-restraints excluded: chain J residue  311 LYS
Chi-restraints excluded: chain J residue  313 VAL
Chi-restraints excluded: chain J residue  322 CYS
Chi-restraints excluded: chain J residue  341 SER
Chi-restraints excluded: chain J residue  350 VAL
Chi-restraints excluded: chain J residue  360 ILE
Chi-restraints excluded: chain K residue  318 VAL
Chi-restraints excluded: chain K residue  322 CYS
Chi-restraints excluded: chain K residue  341 SER
Chi-restraints excluded: chain K residue  360 ILE
Chi-restraints excluded: chain L residue  327 ASN
Chi-restraints excluded: chain L residue  330 HIS
Chi-restraints excluded: chain L residue  337 VAL
Chi-restraints excluded: chain L residue  341 SER
Chi-restraints excluded: chain L residue  350 VAL
Chi-restraints excluded: chain L residue  362 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 57 optimal weight:   10.0000
   chunk 14 optimal weight:    0.3980
   chunk 68 optimal weight:    9.9990
   chunk 81 optimal weight:    2.9990
   chunk 69 optimal weight:    8.9990
   chunk 34 optimal weight:   20.0000
   chunk 37 optimal weight:    3.9990
   chunk 60 optimal weight:   20.0000
   chunk 41 optimal weight:   20.0000
   chunk 42 optimal weight:   20.0000
   chunk 77 optimal weight:    0.0040
   overall best weight:    3.2798

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

Flipped N/Q/H residues before XYZ refinement:
** I 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 329 HIS
L 329 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4857 r_free = 0.4857 target = 0.179136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.145883 restraints weight = 9324.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.148628 restraints weight = 4827.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.150335 restraints weight = 3272.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.151194 restraints weight = 2633.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.151473 restraints weight = 2357.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.4507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          1.0904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6918  Z= 0.158
  Angle     :  0.722   7.364   9258  Z= 0.375
  Chirality :  0.051   0.162   1044
  Planarity :  0.006   0.069   1176
  Dihedral  :  6.281  23.327    912
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 20.77 %
    Favored  : 73.46 %
  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: -3.37 (0.23), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.56 (0.17), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 349 
 TYR   0.020   0.003   TYR I 310 
 PHE   0.021   0.002   PHE H 378 
 HIS   0.009   0.001   HIS L 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 6918)
  covalent geometry    : angle       0.72225 ( 9258)
  hydrogen bonds       : bond        0.02667 (  136)
  hydrogen bonds       : angle       6.96287 (  408)

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 134
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
REVERT: A  336 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8200 (tm-30)
REVERT: C  336 GLN cc_start: 0.8467 (tm-30) cc_final: 0.8178 (tm-30)
REVERT: C  351 GLN cc_start: 0.7772 (mp10) cc_final: 0.7459 (mp10)
REVERT: E  336 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8181 (tm-30)
REVERT: E  349 ARG cc_start: 0.8616 (mtp85) cc_final: 0.7284 (mmp-170)
REVERT: B  360 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8206 (mt)
REVERT: D  360 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.7721 (mt)
REVERT: F  348 ASP cc_start: 0.8151 (t0) cc_final: 0.7853 (t0)
REVERT: F  349 ARG cc_start: 0.7941 (mpp80) cc_final: 0.7072 (ptt90)
REVERT: G  342 GLU cc_start: 0.8316 (mp0) cc_final: 0.7983 (mp0)
REVERT: G  345 ASP cc_start: 0.7681 (t0) cc_final: 0.7368 (m-30)
REVERT: G  350 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8242 (p)
REVERT: H  311 LYS cc_start: 0.7798 (pttm) cc_final: 0.7472 (mtpp)
REVERT: H  349 ARG cc_start: 0.8124 (mtm180) cc_final: 0.6236 (ptt-90)
REVERT: I  310 TYR cc_start: 0.5756 (OUTLIER) cc_final: 0.4329 (t80)
REVERT: I  378 PHE cc_start: 0.6351 (t80) cc_final: 0.5056 (p90)
REVERT: J  347 LYS cc_start: 0.8311 (ptmt) cc_final: 0.7891 (ttmm)
REVERT: K  347 LYS cc_start: 0.8365 (mtpp) cc_final: 0.8095 (ttmm)
REVERT: K  375 LYS cc_start: 0.7567 (tptt) cc_final: 0.7256 (tptp)
REVERT: L  347 LYS cc_start: 0.8781 (ptmt) cc_final: 0.8257 (ttmm)
REVERT: L  348 ASP cc_start: 0.8059 (t0) cc_final: 0.6807 (p0)
REVERT: L  349 ARG cc_start: 0.7603 (mtm110) cc_final: 0.7154 (mtm-85)
  outliers start: 45
  outliers final: 40
  residues processed: 161
  average time/residue: 0.0921
  time to fit residues: 19.1928
Evaluate side-chains
  175 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 131
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain D residue  322 CYS
Chi-restraints excluded: chain D residue  327 ASN
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  322 CYS
Chi-restraints excluded: chain F residue  341 SER
Chi-restraints excluded: chain G residue  306 VAL
Chi-restraints excluded: chain G residue  315 LEU
Chi-restraints excluded: chain G residue  316 SER
Chi-restraints excluded: chain G residue  331 LYS
Chi-restraints excluded: chain G residue  337 VAL
Chi-restraints excluded: chain G residue  350 VAL
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  314 ASP
Chi-restraints excluded: chain H residue  319 THR
Chi-restraints excluded: chain I residue  306 VAL
Chi-restraints excluded: chain I residue  310 TYR
Chi-restraints excluded: chain I residue  320 SER
Chi-restraints excluded: chain I residue  356 SER
Chi-restraints excluded: chain I residue  371 ILE
Chi-restraints excluded: chain J residue  311 LYS
Chi-restraints excluded: chain J residue  322 CYS
Chi-restraints excluded: chain J residue  341 SER
Chi-restraints excluded: chain J residue  350 VAL
Chi-restraints excluded: chain J residue  360 ILE
Chi-restraints excluded: chain K residue  318 VAL
Chi-restraints excluded: chain K residue  322 CYS
Chi-restraints excluded: chain K residue  341 SER
Chi-restraints excluded: chain K residue  360 ILE
Chi-restraints excluded: chain L residue  330 HIS
Chi-restraints excluded: chain L residue  337 VAL
Chi-restraints excluded: chain L residue  341 SER
Chi-restraints excluded: chain L residue  350 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 39 optimal weight:   10.0000
   chunk 11 optimal weight:   10.0000
   chunk 81 optimal weight:    0.5980
   chunk 37 optimal weight:    6.9990
   chunk 74 optimal weight:    4.9990
   chunk 61 optimal weight:    9.9990
   chunk 23 optimal weight:    0.5980
   chunk 22 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9990
   chunk 41 optimal weight:    0.2980
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
I 329 HIS
K 329 HIS
L 329 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5032 r_free = 0.5032 target = 0.303798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.5019 r_free = 0.5019 target = 0.206107 restraints weight = 8967.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.5039 r_free = 0.5039 target = 0.208684 restraints weight = 5462.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.5049 r_free = 0.5049 target = 0.209948 restraints weight = 4073.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.5058 r_free = 0.5058 target = 0.210928 restraints weight = 3518.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.5074 r_free = 0.5074 target = 0.211603 restraints weight = 3208.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.4628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          1.0951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6918  Z= 0.113
  Angle     :  0.657   7.183   9258  Z= 0.337
  Chirality :  0.049   0.136   1044
  Planarity :  0.005   0.064   1176
  Dihedral  :  5.595  17.428    912
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 22.05 %
    Favored  : 73.97 %
  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: -3.26 (0.23), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.48 (0.18), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 349 
 TYR   0.012   0.002   TYR F 310 
 PHE   0.015   0.001   PHE I 378 
 HIS   0.006   0.001   HIS I 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 6918)
  covalent geometry    : angle       0.65750 ( 9258)
  hydrogen bonds       : bond        0.02165 (  136)
  hydrogen bonds       : angle       6.20754 (  408)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1373.27 seconds
wall clock time: 24 minutes 38.16 seconds (1478.16 seconds total)