Starting phenix.real_space_refine
on Wed Feb 12 00:02:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q8e_18252/02_2025/8q8e_18252.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q8e_18252/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q8e_18252/02_2025/8q8e_18252.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q8e_18252/02_2025/8q8e_18252.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q8e_18252/02_2025/8q8e_18252.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q8e_18252/02_2025/8q8e_18252.cif"
  }
  resolution = 3.81
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.63, per 1000 atoms: 0.83
  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: 1.58
  Conformation dependent library (CDL) restraints added in 974.2 milliseconds
  

  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: 1.22
  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: 1.77

  Time building geometry restraints manager: 1.84 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: 0.01
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:             3.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     20.190
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.300
-------------------------------------------------------------------------------
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= 0.790
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.95 (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
 HIS   0.013   0.004   HIS I 362 
 PHE   0.040   0.010   PHE B 346 
 TYR   0.153   0.042   TYR G 310 
 ARG   0.009   0.001   ARG K 349 

*********************** 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  : 0.800 
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: 0.7431 (ttmt)
REVERT: A  346 PHE cc_start: 0.9093 (m-10) cc_final: 0.8765 (m-10)
REVERT: A  349 ARG cc_start: 0.8143 (mtm180) cc_final: 0.7866 (mtm-85)
REVERT: A  359 ASN cc_start: 0.8475 (m-40) cc_final: 0.8226 (m110)
REVERT: C  321 LYS cc_start: 0.8286 (mttt) cc_final: 0.7602 (ttmt)
REVERT: C  349 ARG cc_start: 0.7971 (mtm180) cc_final: 0.6817 (ppt170)
REVERT: E  311 LYS cc_start: 0.7997 (mttt) cc_final: 0.7192 (mmtm)
REVERT: E  321 LYS cc_start: 0.7964 (mttt) cc_final: 0.7494 (ttmt)
REVERT: E  331 LYS cc_start: 0.8711 (mttt) cc_final: 0.8089 (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: 0.6745 (mmp-170)
REVERT: B  320 SER cc_start: 0.8655 (m) cc_final: 0.8365 (m)
REVERT: B  349 ARG cc_start: 0.7358 (mtm180) cc_final: 0.7129 (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: 0.7009 (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)
REVERT: K  374 HIS cc_start: 0.5785 (m-70) cc_final: 0.5240 (p-80)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.2583
  time to fit residues: 60.0469
Evaluate side-chains
  135 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:   40.0000
   chunk 63 optimal weight:    8.9990
   chunk 35 optimal weight:    8.9990
   chunk 21 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9990
   chunk 34 optimal weight:    8.9990
   chunk 65 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 76 optimal weight:    6.9990
   overall best weight:    2.5990

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

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

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5301 r_free = 0.5301 target = 0.377453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 143)---------------|
| r_work = 0.5326 r_free = 0.5326 target = 0.262087 restraints weight = 8929.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.5336 r_free = 0.5336 target = 0.264802 restraints weight = 6645.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.5339 r_free = 0.5339 target = 0.266261 restraints weight = 5144.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.5252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6708
moved from start:          0.5056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6918  Z= 0.287
  Angle     :  0.805   7.387   9258  Z= 0.428
  Chirality :  0.053   0.163   1044
  Planarity :  0.004   0.027   1176
  Dihedral  :  6.637  27.698    912
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 10.90 %
    Favored  : 86.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.48 (0.23), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.88 (0.17), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.002   HIS I 329 
 PHE   0.013   0.002   PHE B 378 
 TYR   0.020   0.003   TYR L 310 
 ARG   0.008   0.002   ARG J 349 

*********************** 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
  199 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 177
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  336 GLN cc_start: 0.8301 (tm-30) cc_final: 0.8061 (tm-30)
REVERT: C  351 GLN cc_start: 0.7970 (mp10) cc_final: 0.7527 (mp10)
REVERT: E  331 LYS cc_start: 0.8825 (mttt) cc_final: 0.8077 (mmmt)
REVERT: E  349 ARG cc_start: 0.7694 (mtm180) cc_final: 0.7273 (mmp-170)
REVERT: G  331 LYS cc_start: 0.8232 (mmtt) cc_final: 0.7834 (mttt)
REVERT: H  344 LEU cc_start: 0.8791 (mp) cc_final: 0.8129 (tt)
REVERT: H  345 ASP cc_start: 0.7464 (m-30) cc_final: 0.7119 (t0)
REVERT: H  349 ARG cc_start: 0.6910 (mtm180) cc_final: 0.5875 (ptt-90)
REVERT: I  322 CYS cc_start: 0.8025 (t) cc_final: 0.7724 (m)
REVERT: I  349 ARG cc_start: 0.7277 (mtm180) cc_final: 0.7051 (mmp-170)
REVERT: J  348 ASP cc_start: 0.7800 (t0) cc_final: 0.7596 (t0)
REVERT: K  348 ASP cc_start: 0.7380 (t0) cc_final: 0.6957 (t0)
REVERT: K  376 LEU cc_start: 0.5766 (pt) cc_final: 0.5554 (tt)
  outliers start: 22
  outliers final: 13
  residues processed: 189
  average time/residue: 0.2670
  time to fit residues: 61.4516
Evaluate side-chains
  147 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 134
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
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  325 LEU
Chi-restraints excluded: chain E residue  356 SER
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  322 CYS
Chi-restraints excluded: chain I residue  306 VAL
Chi-restraints excluded: chain J residue  350 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 9 optimal weight:    6.9990
   chunk 12 optimal weight:    7.9990
   chunk 22 optimal weight:   20.0000
   chunk 65 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 83 optimal weight:   10.0000
   chunk 3 optimal weight:   20.0000
   chunk 47 optimal weight:   10.0000
   chunk 48 optimal weight:    1.9990
   chunk 42 optimal weight:   10.0000
   chunk 13 optimal weight:    9.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
F 330 HIS
** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 359 ASN
J 368 ASN
K 359 ASN
K 368 ASN
L 327 ASN
L 368 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5221 r_free = 0.5221 target = 0.304405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.5128 r_free = 0.5128 target = 0.244972 restraints weight = 9477.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.5152 r_free = 0.5152 target = 0.242027 restraints weight = 12548.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.5156 r_free = 0.5156 target = 0.241310 restraints weight = 11123.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.4713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7341
moved from start:          0.7708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   6918  Z= 0.367
  Angle     :  0.899  10.029   9258  Z= 0.476
  Chirality :  0.057   0.207   1044
  Planarity :  0.005   0.047   1176
  Dihedral  :  7.237  35.257    912
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 15.51 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.68 (0.23), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.03 (0.18), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS B 330 
 PHE   0.013   0.002   PHE B 378 
 TYR   0.044   0.005   TYR I 310 
 ARG   0.006   0.001   ARG B 349 

*********************** 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
  202 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 178
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
REVERT: A  347 LYS cc_start: 0.8475 (mmtm) cc_final: 0.8212 (mmtm)
REVERT: A  353 LYS cc_start: 0.8816 (tttt) cc_final: 0.8191 (tttt)
REVERT: A  379 ARG cc_start: 0.7409 (mtt180) cc_final: 0.7130 (ttm110)
REVERT: C  336 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7941 (tm-30)
REVERT: C  351 GLN cc_start: 0.7850 (mp10) cc_final: 0.7495 (mp10)
REVERT: E  349 ARG cc_start: 0.7954 (mtm180) cc_final: 0.6983 (mmp-170)
REVERT: E  351 GLN cc_start: 0.7162 (mp10) cc_final: 0.6944 (mp10)
REVERT: E  379 ARG cc_start: 0.7750 (mtt180) cc_final: 0.7335 (ttm110)
REVERT: B  315 LEU cc_start: 0.9056 (mm) cc_final: 0.8635 (mm)
REVERT: B  347 LYS cc_start: 0.8573 (ptmt) cc_final: 0.8313 (ttmm)
REVERT: D  347 LYS cc_start: 0.8169 (ptmt) cc_final: 0.7721 (ttmm)
REVERT: D  348 ASP cc_start: 0.8381 (t0) cc_final: 0.7885 (t0)
REVERT: D  349 ARG cc_start: 0.8132 (mtm180) cc_final: 0.7931 (mtm-85)
REVERT: F  347 LYS cc_start: 0.9088 (mtpp) cc_final: 0.8714 (ttmm)
REVERT: F  348 ASP cc_start: 0.8301 (t0) cc_final: 0.8038 (t0)
REVERT: H  311 LYS cc_start: 0.7694 (pttp) cc_final: 0.7469 (mtpt)
REVERT: H  349 ARG cc_start: 0.7919 (mtm180) cc_final: 0.6239 (ptt-90)
REVERT: I  349 ARG cc_start: 0.7676 (mtm180) cc_final: 0.7196 (mmp-170)
REVERT: I  375 LYS cc_start: 0.8167 (mmtm) cc_final: 0.7746 (mptt)
REVERT: J  348 ASP cc_start: 0.8391 (t0) cc_final: 0.8128 (t0)
REVERT: J  374 HIS cc_start: 0.5898 (m90) cc_final: 0.5471 (m-70)
REVERT: K  317 LYS cc_start: 0.7862 (pttt) cc_final: 0.7473 (mmmt)
REVERT: K  349 ARG cc_start: 0.8328 (mtm180) cc_final: 0.8038 (mtm-85)
REVERT: K  371 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8037 (mp)
REVERT: K  376 LEU cc_start: 0.6126 (pt) cc_final: 0.5543 (tt)
REVERT: L  348 ASP cc_start: 0.7676 (t0) cc_final: 0.6762 (p0)
  outliers start: 24
  outliers final: 17
  residues processed: 191
  average time/residue: 0.3140
  time to fit residues: 72.3372
Evaluate side-chains
  165 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 147
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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 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 J residue  350 VAL
Chi-restraints excluded: chain K residue  360 ILE
Chi-restraints excluded: chain K residue  371 ILE
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 37 optimal weight:   10.0000
   chunk 60 optimal weight:    8.9990
   chunk 51 optimal weight:   10.0000
   chunk 72 optimal weight:    0.9990
   chunk 76 optimal weight:   20.0000
   chunk 56 optimal weight:    0.0270
   chunk 25 optimal weight:   10.0000
   chunk 41 optimal weight:   20.0000
   chunk 62 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 6 optimal weight:    9.9990
   overall best weight:    3.8046

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

Flipped N/Q/H residues before XYZ refinement:
A 362 HIS
C 336 GLN
** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 336 GLN
** J 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 = 0.5044 r_free = 0.5044 target = 0.307613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.5105 r_free = 0.5105 target = 0.217833 restraints weight = 9041.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.5099 r_free = 0.5099 target = 0.218932 restraints weight = 7120.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.5095 r_free = 0.5095 target = 0.219609 restraints weight = 6036.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.4687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.8636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6918  Z= 0.270
  Angle     :  0.763   9.380   9258  Z= 0.396
  Chirality :  0.052   0.167   1044
  Planarity :  0.005   0.052   1176
  Dihedral  :  6.541  27.232    912
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 16.67 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.79 (0.23), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.12 (0.18), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS B 374 
 PHE   0.020   0.002   PHE F 378 
 TYR   0.031   0.005   TYR A 310 
 ARG   0.009   0.001   ARG J 349 

*********************** 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
  189 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 156
  time to evaluate  : 0.845 
Fit side-chains
   revert: symmetry clash
REVERT: C  336 GLN cc_start: 0.8405 (tm130) cc_final: 0.8157 (tm-30)
REVERT: C  351 GLN cc_start: 0.7878 (mp10) cc_final: 0.7571 (mp10)
REVERT: C  379 ARG cc_start: 0.7010 (mtt180) cc_final: 0.6605 (ttm170)
REVERT: E  349 ARG cc_start: 0.7928 (mtm180) cc_final: 0.7226 (mmp-170)
REVERT: E  351 GLN cc_start: 0.7542 (mp10) cc_final: 0.7298 (mp10)
REVERT: E  379 ARG cc_start: 0.7532 (mtt180) cc_final: 0.7253 (ttm110)
REVERT: D  347 LYS cc_start: 0.7772 (ptmt) cc_final: 0.7469 (ttmm)
REVERT: D  348 ASP cc_start: 0.8043 (t0) cc_final: 0.7772 (t0)
REVERT: F  347 LYS cc_start: 0.8982 (mtpp) cc_final: 0.8542 (ttmm)
REVERT: F  348 ASP cc_start: 0.8083 (t0) cc_final: 0.7841 (t0)
REVERT: G  320 SER cc_start: 0.8704 (p) cc_final: 0.8442 (p)
REVERT: G  376 LEU cc_start: 0.7952 (mt) cc_final: 0.6558 (mt)
REVERT: H  311 LYS cc_start: 0.7786 (pttp) cc_final: 0.7414 (mtpt)
REVERT: H  349 ARG cc_start: 0.7972 (mtm180) cc_final: 0.6423 (ptt-90)
REVERT: I  310 TYR cc_start: 0.5311 (OUTLIER) cc_final: 0.3985 (t80)
REVERT: I  349 ARG cc_start: 0.7901 (mtm180) cc_final: 0.7352 (mmp-170)
REVERT: I  375 LYS cc_start: 0.8168 (mmtm) cc_final: 0.7624 (tppt)
REVERT: J  348 ASP cc_start: 0.8156 (t0) cc_final: 0.7869 (t0)
REVERT: J  349 ARG cc_start: 0.8091 (mtm-85) cc_final: 0.7585 (mtm-85)
REVERT: K  317 LYS cc_start: 0.8022 (pttt) cc_final: 0.7611 (mmmt)
REVERT: K  349 ARG cc_start: 0.8073 (mtm180) cc_final: 0.7810 (mtm-85)
REVERT: K  371 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8071 (mp)
REVERT: K  376 LEU cc_start: 0.6272 (pt) cc_final: 0.5591 (tt)
REVERT: L  348 ASP cc_start: 0.7605 (t0) cc_final: 0.6556 (p0)
  outliers start: 33
  outliers final: 26
  residues processed: 178
  average time/residue: 0.2720
  time to fit residues: 59.6237
Evaluate side-chains
  162 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 134
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
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 C residue  320 SER
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  347 LYS
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  319 THR
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 J residue  322 CYS
Chi-restraints excluded: chain J residue  341 SER
Chi-restraints excluded: chain J residue  350 VAL
Chi-restraints excluded: chain K residue  322 CYS
Chi-restraints excluded: chain K residue  360 ILE
Chi-restraints excluded: chain K residue  371 ILE
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 12 optimal weight:   20.0000
   chunk 4 optimal weight:   20.0000
   chunk 78 optimal weight:    0.9980
   chunk 2 optimal weight:   10.0000
   chunk 42 optimal weight:   20.0000
   chunk 77 optimal weight:    7.9990
   chunk 65 optimal weight:    9.9990
   chunk 64 optimal weight:    5.9990
   chunk 18 optimal weight:    8.9990
   chunk 55 optimal weight:    9.9990
   chunk 11 optimal weight:    9.9990
   overall best weight:    6.7988

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

Flipped N/Q/H residues before XYZ refinement:
F 368 ASN
** I 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 327 ASN
K 327 ASN
** 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 = 0.4855 r_free = 0.4855 target = 0.179969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.146444 restraints weight = 9202.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.149133 restraints weight = 4939.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.150521 restraints weight = 3461.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.4468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.9956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   6918  Z= 0.405
  Angle     :  0.871   9.761   9258  Z= 0.465
  Chirality :  0.055   0.200   1044
  Planarity :  0.006   0.064   1176
  Dihedral  :  7.418  32.263    912
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 14.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.16 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 18.21 %
    Favored  : 76.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.24 (0.23), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.46 (0.17), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS I 329 
 PHE   0.018   0.003   PHE J 346 
 TYR   0.034   0.005   TYR I 310 
 ARG   0.008   0.001   ARG D 349 

*********************** 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
  201 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 156
  time to evaluate  : 0.872 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  336 GLN cc_start: 0.8346 (tm130) cc_final: 0.8044 (tm-30)
REVERT: C  379 ARG cc_start: 0.7087 (mtt180) cc_final: 0.6772 (ttm110)
REVERT: E  349 ARG cc_start: 0.8071 (mtm180) cc_final: 0.6882 (mmp-170)
REVERT: E  351 GLN cc_start: 0.7270 (mp10) cc_final: 0.6991 (mp10)
REVERT: B  360 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8241 (mt)
REVERT: D  347 LYS cc_start: 0.8620 (ptmt) cc_final: 0.8181 (ttmm)
REVERT: F  314 ASP cc_start: 0.6429 (p0) cc_final: 0.6170 (p0)
REVERT: F  347 LYS cc_start: 0.9137 (mtpp) cc_final: 0.8664 (ttmm)
REVERT: G  345 ASP cc_start: 0.7968 (t0) cc_final: 0.7496 (m-30)
REVERT: G  348 ASP cc_start: 0.8453 (t0) cc_final: 0.8225 (t0)
REVERT: G  376 LEU cc_start: 0.8186 (mt) cc_final: 0.7036 (mt)
REVERT: H  311 LYS cc_start: 0.7874 (pttp) cc_final: 0.7405 (mtpt)
REVERT: H  349 ARG cc_start: 0.8048 (mtm180) cc_final: 0.6250 (ptt-90)
REVERT: I  310 TYR cc_start: 0.6062 (OUTLIER) cc_final: 0.4528 (t80)
REVERT: I  349 ARG cc_start: 0.8338 (mtm180) cc_final: 0.7425 (mmp-170)
REVERT: I  375 LYS cc_start: 0.8512 (mmtm) cc_final: 0.8008 (tppt)
REVERT: J  347 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8652 (mtpp)
REVERT: K  348 ASP cc_start: 0.8483 (t0) cc_final: 0.8194 (t0)
REVERT: K  371 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8188 (mp)
REVERT: K  375 LYS cc_start: 0.7830 (tptp) cc_final: 0.7467 (tptp)
REVERT: K  376 LEU cc_start: 0.6685 (pt) cc_final: 0.6028 (tt)
REVERT: L  347 LYS cc_start: 0.8914 (ptmt) cc_final: 0.8511 (ttmm)
  outliers start: 45
  outliers final: 38
  residues processed: 183
  average time/residue: 0.2552
  time to fit residues: 57.8307
Evaluate side-chains
  183 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 141
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 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 C residue  350 VAL
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  347 LYS
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  316 SER
Chi-restraints excluded: chain G residue  331 LYS
Chi-restraints excluded: chain G residue  337 VAL
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  319 THR
Chi-restraints excluded: chain I residue  306 VAL
Chi-restraints excluded: chain I residue  310 TYR
Chi-restraints excluded: chain I residue  320 SER
Chi-restraints excluded: chain J residue  322 CYS
Chi-restraints excluded: chain J residue  341 SER
Chi-restraints excluded: chain J residue  347 LYS
Chi-restraints excluded: chain J residue  350 VAL
Chi-restraints excluded: chain J residue  353 LYS
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 K residue  371 ILE
Chi-restraints excluded: chain L residue  316 SER
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 30 optimal weight:   10.0000
   chunk 39 optimal weight:    0.0570
   chunk 77 optimal weight:    8.9990
   chunk 46 optimal weight:   10.0000
   chunk 70 optimal weight:   20.0000
   chunk 0 optimal weight:   10.0000
   chunk 63 optimal weight:    8.9990
   chunk 72 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   chunk 18 optimal weight:   10.0000
   chunk 50 optimal weight:    8.9990
   overall best weight:    6.2106

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

Flipped N/Q/H residues before XYZ refinement:
** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 374 HIS
** L 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4909 r_free = 0.4909 target = 0.290785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 87)----------------|
| r_work = 0.4925 r_free = 0.4925 target = 0.196717 restraints weight = 9095.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4940 r_free = 0.4940 target = 0.198938 restraints weight = 5408.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4966 r_free = 0.4966 target = 0.200502 restraints weight = 4054.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.4499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          1.0386

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= 0.368
  Angle     :  0.817   8.453   9258  Z= 0.432
  Chirality :  0.054   0.187   1044
  Planarity :  0.006   0.066   1176
  Dihedral  :  7.021  28.634    912
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 19.62 %
    Favored  : 74.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.38 (0.23), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.17), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS J 374 
 PHE   0.014   0.002   PHE F 378 
 TYR   0.030   0.004   TYR I 310 
 ARG   0.008   0.001   ARG A 349 

*********************** 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
  198 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 150
  time to evaluate  : 1.256 
Fit side-chains
   revert: symmetry clash
REVERT: C  336 GLN cc_start: 0.8369 (tm130) cc_final: 0.8044 (tm-30)
REVERT: C  351 GLN cc_start: 0.7842 (mp10) cc_final: 0.7461 (mp10)
REVERT: E  336 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8091 (tm-30)
REVERT: E  349 ARG cc_start: 0.8034 (mtm180) cc_final: 0.6916 (mmp-170)
REVERT: E  351 GLN cc_start: 0.7278 (mp10) cc_final: 0.7040 (mp10)
REVERT: B  360 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8216 (mt)
REVERT: D  347 LYS cc_start: 0.8393 (ptmt) cc_final: 0.7905 (ttmm)
REVERT: F  347 LYS cc_start: 0.9095 (mtpp) cc_final: 0.8648 (ttmm)
REVERT: G  340 LYS cc_start: 0.7172 (tptp) cc_final: 0.5859 (mttm)
REVERT: G  345 ASP cc_start: 0.7917 (t0) cc_final: 0.7374 (m-30)
REVERT: G  348 ASP cc_start: 0.8504 (t0) cc_final: 0.8247 (t0)
REVERT: G  376 LEU cc_start: 0.8135 (mt) cc_final: 0.6400 (mt)
REVERT: H  311 LYS cc_start: 0.7701 (pttp) cc_final: 0.7230 (mtpt)
REVERT: H  349 ARG cc_start: 0.8142 (mtm180) cc_final: 0.6381 (ptt90)
REVERT: I  310 TYR cc_start: 0.5891 (OUTLIER) cc_final: 0.4311 (t80)
REVERT: I  375 LYS cc_start: 0.8540 (mmtm) cc_final: 0.8023 (tppt)
REVERT: K  348 ASP cc_start: 0.8333 (t0) cc_final: 0.8019 (t0)
REVERT: K  375 LYS cc_start: 0.7927 (tptp) cc_final: 0.7690 (tptp)
REVERT: K  376 LEU cc_start: 0.6848 (pt) cc_final: 0.6391 (tt)
REVERT: L  369 LYS cc_start: 0.5104 (ttmm) cc_final: 0.4841 (mtmm)
REVERT: L  370 LYS cc_start: 0.6198 (tptt) cc_final: 0.5915 (tppt)
  outliers start: 48
  outliers final: 43
  residues processed: 178
  average time/residue: 0.2635
  time to fit residues: 58.3914
Evaluate side-chains
  183 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 138
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 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 C residue  350 VAL
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  347 LYS
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  327 ASN
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  316 SER
Chi-restraints excluded: chain G residue  331 LYS
Chi-restraints excluded: chain G residue  337 VAL
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  319 THR
Chi-restraints excluded: chain 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  353 LYS
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  316 SER
Chi-restraints excluded: chain L residue  322 CYS
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 56 optimal weight:   20.0000
   chunk 64 optimal weight:   20.0000
   chunk 6 optimal weight:    0.8980
   chunk 53 optimal weight:    7.9990
   chunk 3 optimal weight:   30.0000
   chunk 43 optimal weight:    8.9990
   chunk 5 optimal weight:    9.9990
   chunk 66 optimal weight:    9.9990
   chunk 21 optimal weight:   40.0000
   chunk 40 optimal weight:   10.0000
   chunk 50 optimal weight:    6.9990
   overall best weight:    6.9788

-------------------------------------------------------------------------------
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 368 ASN
K 329 HIS
** L 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4787 r_free = 0.4787 target = 0.172300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.139536 restraints weight = 9268.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.142222 restraints weight = 4670.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.143623 restraints weight = 3143.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.4413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          1.0912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   6918  Z= 0.407
  Angle     :  0.871   9.982   9258  Z= 0.461
  Chirality :  0.056   0.198   1044
  Planarity :  0.006   0.069   1176
  Dihedral  :  7.269  27.015    912
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.69 %
    Favored  : 89.31 %
  Rotamer:
    Outliers :  6.92 %
    Allowed  : 20.00 %
    Favored  : 73.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.56 (0.23), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.71 (0.17), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS I 374 
 PHE   0.020   0.003   PHE I 378 
 TYR   0.037   0.004   TYR I 310 
 ARG   0.006   0.001   ARG F 349 

*********************** 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
  215 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 161
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  336 GLN cc_start: 0.8357 (tm130) cc_final: 0.7977 (tm-30)
REVERT: C  351 GLN cc_start: 0.7841 (mp10) cc_final: 0.7091 (mp10)
REVERT: E  336 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8066 (tm-30)
REVERT: E  349 ARG cc_start: 0.8041 (mtm180) cc_final: 0.6928 (mmp-170)
REVERT: E  351 GLN cc_start: 0.7286 (mp10) cc_final: 0.7057 (mp10)
REVERT: B  360 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8204 (mt)
REVERT: D  347 LYS cc_start: 0.8623 (ptmt) cc_final: 0.8119 (ttmm)
REVERT: F  347 LYS cc_start: 0.9133 (mtpp) cc_final: 0.8610 (ttmm)
REVERT: G  340 LYS cc_start: 0.7270 (tptp) cc_final: 0.5909 (mtmt)
REVERT: G  345 ASP cc_start: 0.7861 (t0) cc_final: 0.7376 (m-30)
REVERT: G  348 ASP cc_start: 0.8522 (t0) cc_final: 0.8304 (t0)
REVERT: G  376 LEU cc_start: 0.8172 (mt) cc_final: 0.7037 (mt)
REVERT: H  311 LYS cc_start: 0.7787 (pttp) cc_final: 0.7338 (mtpt)
REVERT: H  349 ARG cc_start: 0.8159 (mtm180) cc_final: 0.6678 (ptt90)
REVERT: I  310 TYR cc_start: 0.6218 (OUTLIER) cc_final: 0.4521 (t80)
REVERT: I  375 LYS cc_start: 0.8640 (mmtm) cc_final: 0.8169 (tppt)
REVERT: I  378 PHE cc_start: 0.6137 (t80) cc_final: 0.5581 (m-80)
REVERT: J  347 LYS cc_start: 0.8989 (mtpp) cc_final: 0.8536 (ttmm)
REVERT: K  376 LEU cc_start: 0.6747 (pt) cc_final: 0.6358 (tt)
REVERT: L  347 LYS cc_start: 0.8877 (ptmm) cc_final: 0.8334 (ttmm)
  outliers start: 54
  outliers final: 47
  residues processed: 190
  average time/residue: 0.2382
  time to fit residues: 56.9955
Evaluate side-chains
  201 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 152
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  325 LEU
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 C residue  350 VAL
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  347 LYS
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  316 SER
Chi-restraints excluded: chain G residue  331 LYS
Chi-restraints excluded: chain G residue  337 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  319 THR
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  341 SER
Chi-restraints excluded: chain J residue  350 VAL
Chi-restraints excluded: chain J residue  353 LYS
Chi-restraints excluded: chain K residue  318 VAL
Chi-restraints excluded: chain K residue  322 CYS
Chi-restraints excluded: chain K residue  328 ILE
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  322 CYS
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 32 optimal weight:    9.9990
   chunk 75 optimal weight:    9.9990
   chunk 14 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 0 optimal weight:    9.9990
   chunk 26 optimal weight:    8.9990
   chunk 63 optimal weight:   20.0000
   chunk 5 optimal weight:    7.9990
   chunk 79 optimal weight:    6.9990
   chunk 64 optimal weight:    9.9990
   overall best weight:    4.3588

-------------------------------------------------------------------------------
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 362 HIS
K 336 GLN
** L 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4916 r_free = 0.4916 target = 0.294467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.4941 r_free = 0.4941 target = 0.197396 restraints weight = 8925.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4954 r_free = 0.4954 target = 0.199584 restraints weight = 5238.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4980 r_free = 0.4980 target = 0.201099 restraints weight = 3941.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.4526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          1.1029

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= 0.281
  Angle     :  0.782   8.346   9258  Z= 0.409
  Chirality :  0.053   0.165   1044
  Planarity :  0.006   0.067   1176
  Dihedral  :  6.759  23.695    912
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 22.31 %
    Favored  : 72.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.52 (0.23), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.67 (0.17), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS I 374 
 PHE   0.021   0.002   PHE D 378 
 TYR   0.024   0.004   TYR I 310 
 ARG   0.007   0.001   ARG K 349 

*********************** 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
  192 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 149
  time to evaluate  : 0.825 
Fit side-chains
   revert: symmetry clash
REVERT: C  336 GLN cc_start: 0.8327 (tm130) cc_final: 0.7982 (tm-30)
REVERT: C  351 GLN cc_start: 0.7921 (mp10) cc_final: 0.7592 (mp10)
REVERT: E  336 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8195 (tm-30)
REVERT: E  349 ARG cc_start: 0.8038 (mtm180) cc_final: 0.7287 (mmp-170)
REVERT: B  360 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8318 (mt)
REVERT: D  347 LYS cc_start: 0.8063 (ptmt) cc_final: 0.7702 (ttmm)
REVERT: D  360 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.7962 (mt)
REVERT: D  375 LYS cc_start: 0.7584 (tptt) cc_final: 0.7258 (tptp)
REVERT: F  347 LYS cc_start: 0.8954 (mtpp) cc_final: 0.8454 (ttmm)
REVERT: G  345 ASP cc_start: 0.7750 (t0) cc_final: 0.7271 (m-30)
REVERT: G  376 LEU cc_start: 0.8165 (mt) cc_final: 0.6336 (mt)
REVERT: H  311 LYS cc_start: 0.7817 (pttp) cc_final: 0.7391 (mtpt)
REVERT: H  349 ARG cc_start: 0.8172 (mtm180) cc_final: 0.6487 (ptt-90)
REVERT: I  310 TYR cc_start: 0.5827 (OUTLIER) cc_final: 0.4374 (t80)
REVERT: I  375 LYS cc_start: 0.8523 (mmtm) cc_final: 0.8036 (tppt)
REVERT: I  378 PHE cc_start: 0.6438 (t80) cc_final: 0.5795 (m-80)
REVERT: J  347 LYS cc_start: 0.8629 (mtpp) cc_final: 0.8273 (ttmm)
REVERT: K  375 LYS cc_start: 0.8015 (tmtt) cc_final: 0.7639 (tptp)
REVERT: K  376 LEU cc_start: 0.6620 (pt) cc_final: 0.6262 (tt)
REVERT: L  370 LYS cc_start: 0.4696 (tppt) cc_final: 0.4345 (tppt)
  outliers start: 43
  outliers final: 39
  residues processed: 169
  average time/residue: 0.2187
  time to fit residues: 47.2149
Evaluate side-chains
  186 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 144
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 C residue  350 VAL
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  347 LYS
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  337 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 I residue  327 ASN
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  353 LYS
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  319 THR
Chi-restraints excluded: chain L residue  322 CYS
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 22 optimal weight:    9.9990
   chunk 17 optimal weight:    0.6980
   chunk 54 optimal weight:   10.0000
   chunk 42 optimal weight:   20.0000
   chunk 25 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 43 optimal weight:   20.0000
   chunk 58 optimal weight:    6.9990
   chunk 3 optimal weight:    5.9990
   chunk 76 optimal weight:   20.0000
   chunk 40 optimal weight:    0.9980
   overall best weight:    4.9386

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

Flipped N/Q/H residues before XYZ refinement:
C 336 GLN
** I 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 368 ASN
** L 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4833 r_free = 0.4833 target = 0.175188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.142548 restraints weight = 9174.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4451 r_free = 0.4451 target = 0.145109 restraints weight = 4922.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4468 r_free = 0.4468 target = 0.146510 restraints weight = 3413.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.4487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          1.1290

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= 0.309
  Angle     :  0.791   8.057   9258  Z= 0.416
  Chirality :  0.054   0.185   1044
  Planarity :  0.006   0.070   1176
  Dihedral  :  6.745  23.686    912
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.34 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 21.41 %
    Favored  : 72.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.59 (0.23), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.73 (0.17), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS I 374 
 PHE   0.021   0.002   PHE G 378 
 TYR   0.032   0.004   TYR I 310 
 ARG   0.007   0.001   ARG D 349 

*********************** 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
  194 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 146
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  336 GLN cc_start: 0.8456 (tm-30) cc_final: 0.8128 (tm-30)
REVERT: C  351 GLN cc_start: 0.7861 (mp10) cc_final: 0.7470 (mp10)
REVERT: E  336 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8077 (tm-30)
REVERT: E  349 ARG cc_start: 0.8082 (mtm180) cc_final: 0.7042 (mmp-170)
REVERT: B  360 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8233 (mt)
REVERT: D  347 LYS cc_start: 0.8283 (ptmt) cc_final: 0.7909 (ttmm)
REVERT: D  360 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.7764 (mt)
REVERT: D  375 LYS cc_start: 0.7453 (tptt) cc_final: 0.7213 (tptp)
REVERT: F  347 LYS cc_start: 0.9028 (mtpp) cc_final: 0.8506 (ttmm)
REVERT: G  348 ASP cc_start: 0.8284 (t0) cc_final: 0.8081 (t0)
REVERT: G  376 LEU cc_start: 0.8066 (mt) cc_final: 0.6077 (mt)
REVERT: H  311 LYS cc_start: 0.7795 (pttp) cc_final: 0.7357 (mtpp)
REVERT: H  349 ARG cc_start: 0.8214 (mtm180) cc_final: 0.6797 (ptt90)
REVERT: I  310 TYR cc_start: 0.6182 (OUTLIER) cc_final: 0.4557 (t80)
REVERT: I  375 LYS cc_start: 0.8462 (mmtm) cc_final: 0.7906 (tppt)
REVERT: J  347 LYS cc_start: 0.8749 (mtpp) cc_final: 0.8379 (ttmm)
REVERT: K  375 LYS cc_start: 0.7917 (tmtt) cc_final: 0.7506 (tptp)
REVERT: K  376 LEU cc_start: 0.6623 (pt) cc_final: 0.6321 (tt)
REVERT: L  347 LYS cc_start: 0.8674 (ptmm) cc_final: 0.8292 (ttmm)
  outliers start: 48
  outliers final: 43
  residues processed: 173
  average time/residue: 0.2058
  time to fit residues: 45.6628
Evaluate side-chains
  188 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 142
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 C residue  350 VAL
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  347 LYS
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  309 VAL
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  337 VAL
Chi-restraints excluded: chain G residue  351 GLN
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  319 THR
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  341 SER
Chi-restraints excluded: chain J residue  350 VAL
Chi-restraints excluded: chain J residue  353 LYS
Chi-restraints excluded: chain K residue  318 VAL
Chi-restraints excluded: chain K residue  322 CYS
Chi-restraints excluded: chain K residue  327 ASN
Chi-restraints excluded: chain K residue  328 ILE
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  319 THR
Chi-restraints excluded: chain L residue  322 CYS
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 8 optimal weight:    7.9990
   chunk 75 optimal weight:    7.9990
   chunk 37 optimal weight:    6.9990
   chunk 21 optimal weight:   10.0000
   chunk 31 optimal weight:   20.0000
   chunk 54 optimal weight:    8.9990
   chunk 6 optimal weight:    0.0070
   chunk 33 optimal weight:    9.9990
   chunk 34 optimal weight:    6.9990
   chunk 72 optimal weight:    0.2980
   chunk 24 optimal weight:    9.9990
   overall best weight:    4.4604

-------------------------------------------------------------------------------
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**
** L 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5063 r_free = 0.5063 target = 0.287491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 92)----------------|
| r_work = 0.4980 r_free = 0.4980 target = 0.224418 restraints weight = 9789.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 78)----------------|
| r_work = 0.5004 r_free = 0.5004 target = 0.223067 restraints weight = 14145.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 118)---------------|
| r_work = 0.5014 r_free = 0.5014 target = 0.221564 restraints weight = 13080.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.4602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          1.1424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6918  Z= 0.281
  Angle     :  0.773   7.860   9258  Z= 0.403
  Chirality :  0.053   0.181   1044
  Planarity :  0.006   0.074   1176
  Dihedral  :  6.553  23.611    912
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.85 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 21.41 %
    Favored  : 72.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.60 (0.23), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.73 (0.17), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS I 330 
 PHE   0.021   0.002   PHE D 378 
 TYR   0.025   0.003   TYR I 310 
 ARG   0.006   0.001   ARG D 349 

********************** 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
  190 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 142
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  336 GLN cc_start: 0.8446 (tm-30) cc_final: 0.8150 (tm-30)
REVERT: C  351 GLN cc_start: 0.7951 (mp10) cc_final: 0.7283 (mp10)
REVERT: E  336 GLN cc_start: 0.8681 (tm-30) cc_final: 0.8186 (tm-30)
REVERT: E  349 ARG cc_start: 0.8026 (mtm180) cc_final: 0.7340 (mmp-170)
REVERT: B  310 TYR cc_start: 0.5130 (t80) cc_final: 0.4615 (t80)
REVERT: B  360 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8220 (mt)
REVERT: D  349 ARG cc_start: 0.7868 (mtm-85) cc_final: 0.7519 (mtm-85)
REVERT: D  360 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.7681 (mt)
REVERT: G  348 ASP cc_start: 0.8476 (t0) cc_final: 0.8245 (t0)
REVERT: G  376 LEU cc_start: 0.8107 (mt) cc_final: 0.6303 (mt)
REVERT: H  311 LYS cc_start: 0.7751 (pttp) cc_final: 0.7334 (mtpp)
REVERT: H  349 ARG cc_start: 0.8208 (mtm180) cc_final: 0.6751 (ptt90)
REVERT: I  310 TYR cc_start: 0.5799 (OUTLIER) cc_final: 0.4463 (t80)
REVERT: I  375 LYS cc_start: 0.8456 (mmtm) cc_final: 0.8016 (tppt)
REVERT: I  378 PHE cc_start: 0.6684 (t80) cc_final: 0.6476 (t80)
REVERT: K  347 LYS cc_start: 0.8509 (mtpp) cc_final: 0.8197 (ttmm)
REVERT: K  375 LYS cc_start: 0.7717 (tmtt) cc_final: 0.7501 (tptp)
REVERT: L  347 LYS cc_start: 0.8594 (ptmm) cc_final: 0.8285 (ttmm)
  outliers start: 48
  outliers final: 45
  residues processed: 167
  average time/residue: 0.2020
  time to fit residues: 43.8131
Evaluate side-chains
  189 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 141
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
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 C residue  350 VAL
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  347 LYS
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  309 VAL
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  337 VAL
Chi-restraints excluded: chain G residue  351 GLN
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 H residue  363 VAL
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  327 ASN
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  353 LYS
Chi-restraints excluded: chain K residue  308 ILE
Chi-restraints excluded: chain K residue  322 CYS
Chi-restraints excluded: chain K residue  328 ILE
Chi-restraints excluded: chain K residue  341 SER
Chi-restraints excluded: chain K residue  360 ILE
Chi-restraints excluded: chain L residue  319 THR
Chi-restraints excluded: chain L residue  322 CYS
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 56 optimal weight:    9.9990
   chunk 14 optimal weight:    3.9990
   chunk 69 optimal weight:    9.9990
   chunk 48 optimal weight:    7.9990
   chunk 24 optimal weight:    6.9990
   chunk 17 optimal weight:   30.0000
   chunk 31 optimal weight:   10.0000
   chunk 52 optimal weight:    7.9990
   chunk 61 optimal weight:    7.9990
   chunk 37 optimal weight:   10.0000
   chunk 10 optimal weight:    4.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
** I 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4791 r_free = 0.4791 target = 0.171419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.139649 restraints weight = 9370.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.142162 restraints weight = 4979.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.143732 restraints weight = 3437.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.4420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          1.1569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   6918  Z= 0.372
  Angle     :  0.838   8.206   9258  Z= 0.441
  Chirality :  0.055   0.206   1044
  Planarity :  0.006   0.072   1176
  Dihedral  :  6.916  24.386    912
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.41 %
    Favored  : 87.59 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 21.15 %
    Favored  : 72.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.71 (0.23), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.82 (0.17), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS I 374 
 PHE   0.022   0.002   PHE D 378 
 TYR   0.036   0.004   TYR I 310 
 ARG   0.007   0.001   ARG D 349 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2665.81 seconds
wall clock time: 48 minutes 49.77 seconds (2929.77 seconds total)