Starting phenix.real_space_refine
on Tue Mar 11 23:41:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q8e_18252/03_2025/8q8e_18252.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q8e_18252/03_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_18252/03_2025/8q8e_18252.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q8e_18252/03_2025/8q8e_18252.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q8e_18252/03_2025/8q8e_18252.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q8e_18252/03_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-5624/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: 5.40, per 1000 atoms: 0.79
  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: 1.36
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 34 sheets defined
      0.0% alpha, 38.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  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: 1.57

  Time building geometry restraints manager: 1.66 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:             3.900
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.660
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.020
  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:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.080
-------------------------------------------------------------------------------
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  : 0.712 
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: 0.2399
  time to fit residues: 55.8195
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  : 0.891 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 76 optimal weight:    6.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
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 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 329 HIS
** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 329 HIS
** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5288 r_free = 0.5288 target = 0.372478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 101)---------------|
| r_work = 0.5310 r_free = 0.5310 target = 0.257242 restraints weight = 8889.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.5325 r_free = 0.5325 target = 0.259994 restraints weight = 6035.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.5329 r_free = 0.5329 target = 0.261380 restraints weight = 4678.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.5234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6799
moved from start:          0.5326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6918  Z= 0.302
  Angle     :  0.813   7.451   9258  Z= 0.434
  Chirality :  0.054   0.162   1044
  Planarity :  0.004   0.031   1176
  Dihedral  :  6.782  29.553    912
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 11.41 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.49 (0.23), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.89 (0.17), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.002   HIS I 329 
 PHE   0.015   0.002   PHE H 378 
 TYR   0.021   0.003   TYR I 310 
 ARG   0.007   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
  206 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 185
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  336 GLN cc_start: 0.8313 (tm-30) cc_final: 0.8072 (tm-30)
REVERT: E  331 LYS cc_start: 0.8862 (mttt) cc_final: 0.8093 (mmmt)
REVERT: E  349 ARG cc_start: 0.7741 (mtm180) cc_final: 0.7082 (mmp-170)
REVERT: E  376 LEU cc_start: 0.7157 (tt) cc_final: 0.6943 (mp)
REVERT: G  331 LYS cc_start: 0.8337 (mmtt) cc_final: 0.7909 (mttt)
REVERT: G  362 HIS cc_start: 0.8442 (t70) cc_final: 0.8193 (t-90)
REVERT: H  344 LEU cc_start: 0.8784 (mp) cc_final: 0.8112 (tt)
REVERT: H  345 ASP cc_start: 0.7425 (m-30) cc_final: 0.7165 (t0)
REVERT: H  349 ARG cc_start: 0.7042 (mtm180) cc_final: 0.5832 (ptt-90)
REVERT: I  322 CYS cc_start: 0.8086 (t) cc_final: 0.7530 (m)
REVERT: I  349 ARG cc_start: 0.7328 (mtm180) cc_final: 0.7003 (mmp-170)
REVERT: J  348 ASP cc_start: 0.7920 (t0) cc_final: 0.7708 (t0)
REVERT: K  348 ASP cc_start: 0.7532 (t0) cc_final: 0.7135 (t0)
REVERT: K  376 LEU cc_start: 0.5889 (pt) cc_final: 0.5554 (tt)
REVERT: L  360 ILE cc_start: 0.6900 (tt) cc_final: 0.6686 (mp)
  outliers start: 21
  outliers final: 12
  residues processed: 198
  average time/residue: 0.2668
  time to fit residues: 64.6730
Evaluate side-chains
  158 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 146
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain 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:   10.0000
   chunk 22 optimal weight:   20.0000
   chunk 65 optimal weight:   10.0000
   chunk 10 optimal weight:   20.0000
   chunk 83 optimal weight:    9.9990
   chunk 3 optimal weight:   20.0000
   chunk 47 optimal weight:    9.9990
   chunk 48 optimal weight:    4.9990
   chunk 42 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   overall best weight:    6.9990

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5147 r_free = 0.5147 target = 0.295009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.5048 r_free = 0.5048 target = 0.237891 restraints weight = 9604.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 96)----------------|
| r_work = 0.5079 r_free = 0.5079 target = 0.234295 restraints weight = 12561.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 75)----------------|
| r_work = 0.5080 r_free = 0.5080 target = 0.232804 restraints weight = 12810.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.4653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.8633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   6918  Z= 0.436
  Angle     :  1.032  13.173   9258  Z= 0.547
  Chirality :  0.060   0.252   1044
  Planarity :  0.006   0.053   1176
  Dihedral  :  7.986  38.856    912
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.70 %
    Favored  : 92.30 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 15.38 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.24 %

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: -2.91 (0.23), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.21 (0.17), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.011   0.002   HIS B 330 
 PHE   0.017   0.003   PHE J 346 
 TYR   0.043   0.006   TYR I 310 
 ARG   0.008   0.001   ARG K 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
  208 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 178
  time to evaluate  : 0.712 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.8346 (mtpt) cc_final: 0.8093 (mtpt)
REVERT: A  379 ARG cc_start: 0.7582 (mtt180) cc_final: 0.7289 (ttm110)
REVERT: C  336 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7888 (tm-30)
REVERT: C  345 ASP cc_start: 0.7402 (m-30) cc_final: 0.7084 (t0)
REVERT: C  349 ARG cc_start: 0.8148 (mtt90) cc_final: 0.6716 (ptt90)
REVERT: E  336 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8140 (tm-30)
REVERT: E  349 ARG cc_start: 0.7991 (mtm180) cc_final: 0.6925 (mmp-170)
REVERT: E  351 GLN cc_start: 0.7154 (mp10) cc_final: 0.6909 (mp10)
REVERT: E  379 ARG cc_start: 0.7745 (mtt180) cc_final: 0.7346 (ttm110)
REVERT: D  347 LYS cc_start: 0.8609 (ptmt) cc_final: 0.8224 (ttmm)
REVERT: D  348 ASP cc_start: 0.8415 (t0) cc_final: 0.8109 (t0)
REVERT: F  347 LYS cc_start: 0.9151 (mtpp) cc_final: 0.8690 (ttmm)
REVERT: G  345 ASP cc_start: 0.8032 (t0) cc_final: 0.7684 (m-30)
REVERT: G  375 LYS cc_start: 0.8495 (mtpt) cc_final: 0.8237 (ttmt)
REVERT: H  311 LYS cc_start: 0.7978 (pttm) cc_final: 0.7673 (mtpt)
REVERT: H  349 ARG cc_start: 0.7993 (mtm180) cc_final: 0.6260 (ptt-90)
REVERT: I  310 TYR cc_start: 0.5940 (OUTLIER) cc_final: 0.4650 (t80)
REVERT: I  349 ARG cc_start: 0.7884 (mtm180) cc_final: 0.7277 (mmp-170)
REVERT: I  362 HIS cc_start: 0.8944 (t-90) cc_final: 0.8717 (t-90)
REVERT: I  375 LYS cc_start: 0.8314 (mmtm) cc_final: 0.7610 (tppt)
REVERT: J  374 HIS cc_start: 0.5986 (m90) cc_final: 0.5366 (m-70)
REVERT: K  346 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8299 (m-10)
REVERT: K  348 ASP cc_start: 0.8436 (t0) cc_final: 0.8218 (t0)
REVERT: K  349 ARG cc_start: 0.8293 (mtm180) cc_final: 0.7861 (mtm-85)
REVERT: K  351 GLN cc_start: 0.8371 (mp10) cc_final: 0.8125 (mp10)
REVERT: K  376 LEU cc_start: 0.6163 (pt) cc_final: 0.5767 (tt)
REVERT: L  347 LYS cc_start: 0.8821 (ptmt) cc_final: 0.8441 (ttmm)
REVERT: L  348 ASP cc_start: 0.7942 (t0) cc_final: 0.6822 (p0)
REVERT: L  374 HIS cc_start: 0.6201 (m-70) cc_final: 0.5955 (m90)
  outliers start: 30
  outliers final: 21
  residues processed: 194
  average time/residue: 0.2579
  time to fit residues: 61.1964
Evaluate side-chains
  164 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 141
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
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  310 TYR
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  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 G residue  376 LEU
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain I residue  306 VAL
Chi-restraints excluded: chain I residue  310 TYR
Chi-restraints excluded: chain I residue  315 LEU
Chi-restraints excluded: chain J residue  350 VAL
Chi-restraints excluded: chain J residue  360 ILE
Chi-restraints excluded: chain K residue  346 PHE
Chi-restraints excluded: chain K residue  360 ILE
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:    5.9990
   chunk 60 optimal weight:   10.0000
   chunk 51 optimal weight:    9.9990
   chunk 72 optimal weight:    1.9990
   chunk 76 optimal weight:   10.0000
   chunk 56 optimal weight:    0.0030
   chunk 25 optimal weight:   10.0000
   chunk 41 optimal weight:    8.9990
   chunk 62 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9990
   chunk 6 optimal weight:    6.9990
   overall best weight:    2.7998

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
A 362 HIS
F 330 HIS
F 368 ASN
G 362 HIS
I 351 GLN
I 374 HIS
J 368 ASN
** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 327 ASN
L 368 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5065 r_free = 0.5065 target = 0.324163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.5099 r_free = 0.5099 target = 0.217731 restraints weight = 8812.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.5114 r_free = 0.5114 target = 0.220515 restraints weight = 5199.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.5144 r_free = 0.5144 target = 0.222555 restraints weight = 3818.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.5005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.8999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6918  Z= 0.221
  Angle     :  0.736   8.589   9258  Z= 0.378
  Chirality :  0.050   0.140   1044
  Planarity :  0.005   0.052   1176
  Dihedral  :  6.539  24.997    912
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 18.08 %
    Favored  : 77.69 %
  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: -2.84 (0.23), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.15 (0.18), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B 330 
 PHE   0.020   0.002   PHE F 378 
 TYR   0.020   0.003   TYR I 310 
 ARG   0.006   0.001   ARG D 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
  181 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 148
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
REVERT: C  349 ARG cc_start: 0.7909 (mtt90) cc_final: 0.6725 (ptt90)
REVERT: C  379 ARG cc_start: 0.6976 (mtt180) cc_final: 0.6555 (ttm110)
REVERT: E  349 ARG cc_start: 0.7818 (mtm180) cc_final: 0.7278 (mmp-170)
REVERT: E  351 GLN cc_start: 0.7643 (mp10) cc_final: 0.7427 (mp10)
REVERT: B  348 ASP cc_start: 0.8081 (t0) cc_final: 0.7651 (t0)
REVERT: B  360 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8451 (mt)
REVERT: F  347 LYS cc_start: 0.8805 (mtpp) cc_final: 0.8459 (ttmm)
REVERT: H  349 ARG cc_start: 0.7909 (mtm180) cc_final: 0.6441 (ptt-90)
REVERT: I  331 LYS cc_start: 0.5055 (mmtm) cc_final: 0.4753 (mmtm)
REVERT: I  349 ARG cc_start: 0.7921 (mtm180) cc_final: 0.7579 (mmp-170)
REVERT: J  348 ASP cc_start: 0.7799 (t0) cc_final: 0.7479 (t0)
REVERT: J  349 ARG cc_start: 0.7872 (mtm-85) cc_final: 0.7526 (mtm-85)
REVERT: K  349 ARG cc_start: 0.7925 (mtm180) cc_final: 0.7666 (mtm-85)
REVERT: L  348 ASP cc_start: 0.7417 (t0) cc_final: 0.6614 (p0)
  outliers start: 33
  outliers final: 23
  residues processed: 170
  average time/residue: 0.2690
  time to fit residues: 55.5945
Evaluate side-chains
  155 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 131
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
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  350 VAL
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  321 LYS
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  322 CYS
Chi-restraints excluded: chain G residue  306 VAL
Chi-restraints excluded: chain G residue  351 GLN
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain I residue  306 VAL
Chi-restraints excluded: chain J residue  322 CYS
Chi-restraints excluded: chain J residue  350 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  337 VAL
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:    1.9990
   chunk 2 optimal weight:   10.0000
   chunk 42 optimal weight:   20.0000
   chunk 77 optimal weight:    8.9990
   chunk 65 optimal weight:   10.0000
   chunk 64 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   chunk 55 optimal weight:   10.0000
   chunk 11 optimal weight:    6.9990
   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
** J 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 327 ASN ** 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 = 0.4821 r_free = 0.4821 target = 0.179059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.145119 restraints weight = 9157.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.147993 restraints weight = 4696.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.149599 restraints weight = 3166.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.4474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.9987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   6918  Z= 0.388
  Angle     :  0.861   9.799   9258  Z= 0.458
  Chirality :  0.055   0.194   1044
  Planarity :  0.006   0.065   1176
  Dihedral  :  7.321  32.372    912
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.39 %
    Favored  : 91.61 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 18.21 %
    Favored  : 76.28 %
  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: -3.22 (0.22), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.44 (0.17), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS I 374 
 PHE   0.018   0.003   PHE F 378 
 TYR   0.038   0.005   TYR I 310 
 ARG   0.012   0.001   ARG G 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
  199 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 156
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 LYS cc_start: 0.8558 (mmtm) cc_final: 0.8321 (mmtm)
REVERT: C  336 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8014 (tm-30)
REVERT: C  349 ARG cc_start: 0.8108 (mtt90) cc_final: 0.6437 (ptt90)
REVERT: C  379 ARG cc_start: 0.7067 (mtt180) cc_final: 0.6728 (ttm110)
REVERT: E  349 ARG cc_start: 0.8095 (mtm180) cc_final: 0.6858 (mmp-170)
REVERT: E  351 GLN cc_start: 0.7133 (mp10) cc_final: 0.6828 (mp10)
REVERT: B  360 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8240 (mt)
REVERT: D  347 LYS cc_start: 0.8636 (ptmt) cc_final: 0.8221 (ttmm)
REVERT: D  375 LYS cc_start: 0.7363 (tptt) cc_final: 0.6899 (tptp)
REVERT: F  314 ASP cc_start: 0.6426 (p0) cc_final: 0.6140 (p0)
REVERT: F  347 LYS cc_start: 0.9165 (mtpp) cc_final: 0.8673 (ttmm)
REVERT: F  348 ASP cc_start: 0.8377 (t0) cc_final: 0.8141 (t0)
REVERT: G  376 LEU cc_start: 0.8106 (mt) cc_final: 0.6503 (mt)
REVERT: H  349 ARG cc_start: 0.8057 (mtm180) cc_final: 0.6276 (ptt-90)
REVERT: I  310 TYR cc_start: 0.6106 (OUTLIER) cc_final: 0.4444 (t80)
REVERT: I  349 ARG cc_start: 0.8052 (mtm180) cc_final: 0.7212 (mmp-170)
REVERT: J  348 ASP cc_start: 0.8433 (t0) cc_final: 0.8097 (t0)
REVERT: K  314 ASP cc_start: 0.5781 (p0) cc_final: 0.5574 (p0)
REVERT: K  348 ASP cc_start: 0.8377 (t0) cc_final: 0.8169 (t0)
REVERT: L  347 LYS cc_start: 0.8878 (ptmm) cc_final: 0.8305 (ttmm)
REVERT: L  348 ASP cc_start: 0.8154 (t0) cc_final: 0.6825 (p0)
REVERT: L  349 ARG cc_start: 0.8003 (mpp80) cc_final: 0.7713 (mpp80)
REVERT: L  369 LYS cc_start: 0.5310 (ttmm) cc_final: 0.4964 (mtmm)
  outliers start: 43
  outliers final: 36
  residues processed: 184
  average time/residue: 0.2437
  time to fit residues: 55.6795
Evaluate side-chains
  177 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 139
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
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  350 VAL
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  321 LYS
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  337 VAL
Chi-restraints excluded: chain G residue  351 GLN
Chi-restraints excluded: chain H residue  306 VAL
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  320 SER
Chi-restraints excluded: chain I residue  356 SER
Chi-restraints excluded: chain J residue  322 CYS
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 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:    9.9990
   chunk 39 optimal weight:    7.9990
   chunk 77 optimal weight:   10.0000
   chunk 46 optimal weight:    9.9990
   chunk 70 optimal weight:    0.3980
   chunk 0 optimal weight:   10.0000
   chunk 63 optimal weight:    6.9990
   chunk 72 optimal weight:    0.7980
   chunk 16 optimal weight:    9.9990
   chunk 18 optimal weight:    5.9990
   chunk 50 optimal weight:    9.9990
   overall best weight:    4.4386

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

Flipped N/Q/H residues before XYZ refinement:
I 368 ASN
J 327 ASN
J 362 HIS
K 327 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4934 r_free = 0.4934 target = 0.298422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 93)----------------|
| r_work = 0.4968 r_free = 0.4968 target = 0.202247 restraints weight = 9092.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4982 r_free = 0.4982 target = 0.204532 restraints weight = 5524.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.5000 r_free = 0.5000 target = 0.205991 restraints weight = 4146.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.4570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          1.0213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6918  Z= 0.282
  Angle     :  0.747   7.883   9258  Z= 0.391
  Chirality :  0.052   0.162   1044
  Planarity :  0.005   0.063   1176
  Dihedral  :  6.691  27.309    912
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 19.36 %
    Favored  : 75.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.26 (0.22), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.47 (0.17), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS I 330 
 PHE   0.019   0.002   PHE I 378 
 TYR   0.026   0.004   TYR I 310 
 ARG   0.009   0.001   ARG F 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
  194 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 154
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  349 ARG cc_start: 0.8030 (mtt90) cc_final: 0.6475 (ptt90)
REVERT: C  379 ARG cc_start: 0.7008 (mtt180) cc_final: 0.6765 (ttm110)
REVERT: E  349 ARG cc_start: 0.8012 (mtm180) cc_final: 0.7085 (mmp-170)
REVERT: E  351 GLN cc_start: 0.7354 (mp10) cc_final: 0.7094 (mp10)
REVERT: B  360 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8278 (mt)
REVERT: D  347 LYS cc_start: 0.8131 (ptmt) cc_final: 0.7752 (ttmm)
REVERT: D  375 LYS cc_start: 0.7509 (tptt) cc_final: 0.7167 (tptp)
REVERT: F  347 LYS cc_start: 0.9017 (mtpp) cc_final: 0.8554 (ttmm)
REVERT: G  340 LYS cc_start: 0.7357 (tptp) cc_final: 0.6068 (mttm)
REVERT: G  342 GLU cc_start: 0.8413 (mp0) cc_final: 0.8186 (mp0)
REVERT: G  345 ASP cc_start: 0.7961 (t0) cc_final: 0.7456 (m-30)
REVERT: G  350 VAL cc_start: 0.8781 (OUTLIER) cc_final: 0.8503 (p)
REVERT: H  349 ARG cc_start: 0.8102 (mtm180) cc_final: 0.6374 (ptt-90)
REVERT: I  349 ARG cc_start: 0.7997 (mtm180) cc_final: 0.7181 (mmp-170)
REVERT: J  347 LYS cc_start: 0.8797 (mtpp) cc_final: 0.8250 (ttmm)
REVERT: K  349 ARG cc_start: 0.7872 (mtm-85) cc_final: 0.7638 (mtm-85)
REVERT: L  347 LYS cc_start: 0.8666 (ptmm) cc_final: 0.8191 (ttmm)
REVERT: L  348 ASP cc_start: 0.7884 (t0) cc_final: 0.6594 (p0)
  outliers start: 40
  outliers final: 36
  residues processed: 179
  average time/residue: 0.2418
  time to fit residues: 53.4385
Evaluate side-chains
  178 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 140
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
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  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  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  337 VAL
Chi-restraints excluded: chain G residue  350 VAL
Chi-restraints excluded: chain G residue  351 GLN
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  363 VAL
Chi-restraints excluded: chain I residue  306 VAL
Chi-restraints excluded: chain I residue  319 THR
Chi-restraints excluded: chain I residue  320 SER
Chi-restraints excluded: chain I residue  356 SER
Chi-restraints excluded: chain J residue  313 VAL
Chi-restraints excluded: chain J residue  322 CYS
Chi-restraints excluded: chain J residue  350 VAL
Chi-restraints excluded: chain K residue  318 VAL
Chi-restraints excluded: chain K residue  322 CYS
Chi-restraints excluded: chain K residue  360 ILE
Chi-restraints excluded: chain L residue  319 THR
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:   10.0000
   chunk 64 optimal weight:   30.0000
   chunk 6 optimal weight:    9.9990
   chunk 53 optimal weight:    9.9990
   chunk 3 optimal weight:   40.0000
   chunk 43 optimal weight:   10.0000
   chunk 5 optimal weight:    9.9990
   chunk 66 optimal weight:    9.9990
   chunk 21 optimal weight:   40.0000
   chunk 40 optimal weight:    3.9990
   chunk 50 optimal weight:    9.9990
   overall best weight:    8.7990

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

Flipped N/Q/H residues before XYZ refinement:
J 368 ASN
K 329 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4744 r_free = 0.4744 target = 0.168661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.136554 restraints weight = 9462.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.139218 restraints weight = 4810.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.140850 restraints weight = 3220.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.4382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          1.0962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.054   6918  Z= 0.498
  Angle     :  0.939  10.688   9258  Z= 0.499
  Chirality :  0.059   0.214   1044
  Planarity :  0.007   0.071   1176
  Dihedral  :  7.657  29.131    912
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 14.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.84 %
    Favored  : 88.16 %
  Rotamer:
    Outliers :  6.28 %
    Allowed  : 19.87 %
    Favored  : 73.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.73 (0.22), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.84 (0.17), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS C 374 
 PHE   0.020   0.003   PHE F 378 
 TYR   0.040   0.005   TYR I 310 
 ARG   0.007   0.001   ARG A 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
  209 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 160
  time to evaluate  : 0.769 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 LYS cc_start: 0.8617 (mmtm) cc_final: 0.8374 (mmtm)
REVERT: C  336 GLN cc_start: 0.8378 (tm-30) cc_final: 0.8001 (tm-30)
REVERT: E  349 ARG cc_start: 0.8100 (mtm180) cc_final: 0.6950 (mmp-170)
REVERT: E  351 GLN cc_start: 0.7189 (mp10) cc_final: 0.6944 (mp10)
REVERT: B  348 ASP cc_start: 0.8385 (t0) cc_final: 0.7942 (t0)
REVERT: B  360 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8184 (mt)
REVERT: D  347 LYS cc_start: 0.8786 (ptmt) cc_final: 0.8289 (ttmm)
REVERT: D  357 LEU cc_start: 0.8816 (mp) cc_final: 0.8616 (mp)
REVERT: F  347 LYS cc_start: 0.9224 (mtpp) cc_final: 0.8720 (ttmm)
REVERT: G  340 LYS cc_start: 0.7215 (tptp) cc_final: 0.5954 (mtmt)
REVERT: G  350 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8503 (p)
REVERT: H  349 ARG cc_start: 0.8226 (mtm180) cc_final: 0.6414 (ptt-90)
REVERT: I  310 TYR cc_start: 0.6309 (OUTLIER) cc_final: 0.4556 (t80)
REVERT: I  349 ARG cc_start: 0.8090 (mtm180) cc_final: 0.7323 (mmp-170)
REVERT: I  378 PHE cc_start: 0.6321 (t80) cc_final: 0.4958 (p90)
REVERT: J  347 LYS cc_start: 0.9172 (mtpp) cc_final: 0.8676 (ttmm)
REVERT: L  347 LYS cc_start: 0.8984 (ptmm) cc_final: 0.8465 (ttmm)
  outliers start: 49
  outliers final: 40
  residues processed: 189
  average time/residue: 0.2316
  time to fit residues: 54.5307
Evaluate side-chains
  191 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 148
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
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  325 LEU
Chi-restraints excluded: chain E residue  347 LYS
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain D residue  322 CYS
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  322 CYS
Chi-restraints excluded: chain F residue  341 SER
Chi-restraints excluded: chain G residue  306 VAL
Chi-restraints excluded: chain G residue  316 SER
Chi-restraints excluded: chain G residue  331 LYS
Chi-restraints excluded: chain G residue  337 VAL
Chi-restraints excluded: chain G residue  350 VAL
Chi-restraints excluded: chain G residue  351 GLN
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  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 I residue  356 SER
Chi-restraints excluded: chain J residue  322 CYS
Chi-restraints excluded: chain J residue  350 VAL
Chi-restraints excluded: chain J residue  360 ILE
Chi-restraints excluded: chain K residue  318 VAL
Chi-restraints excluded: chain K residue  360 ILE
Chi-restraints excluded: chain L residue  316 SER
Chi-restraints excluded: chain L residue  319 THR
Chi-restraints excluded: chain L residue  330 HIS
Chi-restraints excluded: chain L residue  337 VAL
Chi-restraints excluded: chain L residue  341 SER
Chi-restraints excluded: chain L residue  350 VAL
Chi-restraints excluded: chain L residue  360 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 75 optimal weight:    0.0970
   chunk 14 optimal weight:    7.9990
   chunk 39 optimal weight:    0.6980
   chunk 18 optimal weight:   20.0000
   chunk 0 optimal weight:    9.9990
   chunk 26 optimal weight:    6.9990
   chunk 63 optimal weight:    9.9990
   chunk 5 optimal weight:    6.9990
   chunk 79 optimal weight:    9.9990
   chunk 64 optimal weight:   10.0000
   overall best weight:    3.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
I 351 GLN
K 336 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4904 r_free = 0.4904 target = 0.293214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 92)----------------|
| r_work = 0.4937 r_free = 0.4937 target = 0.198304 restraints weight = 8995.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4952 r_free = 0.4952 target = 0.200493 restraints weight = 5464.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4963 r_free = 0.4963 target = 0.201760 restraints weight = 4110.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.4490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          1.1018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6918  Z= 0.264
  Angle     :  0.764   7.925   9258  Z= 0.399
  Chirality :  0.052   0.170   1044
  Planarity :  0.006   0.071   1176
  Dihedral  :  6.706  22.410    912
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 20.51 %
    Favored  : 73.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.22), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.74 (0.17), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS I 330 
 PHE   0.024   0.002   PHE E 378 
 TYR   0.022   0.003   TYR I 310 
 ARG   0.008   0.001   ARG A 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
  195 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 152
  time to evaluate  : 0.808 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 LYS cc_start: 0.8523 (mmtm) cc_final: 0.8210 (mmtm)
REVERT: C  336 GLN cc_start: 0.8431 (tm-30) cc_final: 0.8094 (tm-30)
REVERT: C  351 GLN cc_start: 0.7737 (mp10) cc_final: 0.7430 (mp10)
REVERT: E  349 ARG cc_start: 0.8075 (mtm180) cc_final: 0.7102 (mmp-170)
REVERT: E  351 GLN cc_start: 0.7214 (mp10) cc_final: 0.6997 (mp10)
REVERT: B  348 ASP cc_start: 0.8181 (t0) cc_final: 0.7793 (t0)
REVERT: B  349 ARG cc_start: 0.8124 (mtm180) cc_final: 0.7839 (mtm180)
REVERT: B  360 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8234 (mt)
REVERT: D  347 LYS cc_start: 0.8268 (ptmt) cc_final: 0.7734 (ttmm)
REVERT: D  360 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.7744 (mt)
REVERT: F  347 LYS cc_start: 0.8973 (mtpp) cc_final: 0.8416 (ttmm)
REVERT: G  350 VAL cc_start: 0.8664 (OUTLIER) cc_final: 0.8411 (p)
REVERT: H  349 ARG cc_start: 0.8131 (mtm180) cc_final: 0.6401 (ptt90)
REVERT: I  349 ARG cc_start: 0.7978 (mtm180) cc_final: 0.7052 (mmp-170)
REVERT: I  378 PHE cc_start: 0.6462 (t80) cc_final: 0.5763 (m-80)
REVERT: J  311 LYS cc_start: 0.7175 (ptpp) cc_final: 0.6132 (mmtm)
REVERT: J  347 LYS cc_start: 0.8810 (mtpp) cc_final: 0.8274 (ttmm)
REVERT: L  347 LYS cc_start: 0.8696 (ptmm) cc_final: 0.8122 (ttmm)
REVERT: L  348 ASP cc_start: 0.8040 (t0) cc_final: 0.6692 (p0)
REVERT: L  349 ARG cc_start: 0.8000 (mpp80) cc_final: 0.7794 (mpp80)
  outliers start: 43
  outliers final: 38
  residues processed: 172
  average time/residue: 0.2215
  time to fit residues: 48.3350
Evaluate side-chains
  187 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 146
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
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  325 LEU
Chi-restraints excluded: chain E residue  347 LYS
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  337 VAL
Chi-restraints excluded: chain G residue  350 VAL
Chi-restraints excluded: chain G residue  351 GLN
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  363 VAL
Chi-restraints excluded: chain I residue  306 VAL
Chi-restraints excluded: chain I residue  319 THR
Chi-restraints excluded: chain I residue  320 SER
Chi-restraints excluded: chain I residue  356 SER
Chi-restraints excluded: chain J residue  322 CYS
Chi-restraints excluded: chain J residue  350 VAL
Chi-restraints excluded: chain K residue  319 THR
Chi-restraints excluded: chain K residue  360 ILE
Chi-restraints excluded: chain K residue  376 LEU
Chi-restraints excluded: chain L residue  316 SER
Chi-restraints excluded: chain L residue  319 THR
Chi-restraints excluded: chain L residue  330 HIS
Chi-restraints excluded: chain L residue  337 VAL
Chi-restraints excluded: chain L residue  341 SER
Chi-restraints excluded: chain L residue  350 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 22 optimal weight:    8.9990
   chunk 17 optimal weight:   30.0000
   chunk 54 optimal weight:    9.9990
   chunk 42 optimal weight:   20.0000
   chunk 25 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 43 optimal weight:   10.0000
   chunk 58 optimal weight:    7.9990
   chunk 3 optimal weight:   20.0000
   chunk 76 optimal weight:   20.0000
   chunk 40 optimal weight:    7.9990
   overall best weight:    8.9992

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
I 351 GLN
** J 368 ASN ** 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 = 0.4713 r_free = 0.4713 target = 0.166038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.134786 restraints weight = 9605.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.137404 restraints weight = 4862.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.139048 restraints weight = 3226.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.4354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          1.1395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.055   6918  Z= 0.507
  Angle     :  0.933  10.331   9258  Z= 0.495
  Chirality :  0.058   0.220   1044
  Planarity :  0.007   0.074   1176
  Dihedral  :  7.482  27.179    912
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 14.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.22 %
    Favored  : 86.78 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 20.77 %
    Favored  : 73.33 %
  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: -3.89 (0.22), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.95 (0.17), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS L 362 
 PHE   0.020   0.003   PHE D 378 
 TYR   0.045   0.005   TYR I 310 
 ARG   0.009   0.001   ARG A 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
  203 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 157
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 LYS cc_start: 0.8616 (mmtm) cc_final: 0.8338 (mmtm)
REVERT: C  336 GLN cc_start: 0.8409 (tm-30) cc_final: 0.8069 (tm-30)
REVERT: C  351 GLN cc_start: 0.7767 (mp10) cc_final: 0.7435 (mp10)
REVERT: E  349 ARG cc_start: 0.8102 (mtm180) cc_final: 0.6967 (mmp-170)
REVERT: E  351 GLN cc_start: 0.7204 (mp10) cc_final: 0.6962 (mp10)
REVERT: B  348 ASP cc_start: 0.8350 (t0) cc_final: 0.8149 (t0)
REVERT: B  360 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8234 (mt)
REVERT: D  347 LYS cc_start: 0.8745 (ptmt) cc_final: 0.8264 (ttmm)
REVERT: F  347 LYS cc_start: 0.9155 (mtpp) cc_final: 0.8617 (ttmm)
REVERT: G  350 VAL cc_start: 0.8764 (OUTLIER) cc_final: 0.8491 (p)
REVERT: H  349 ARG cc_start: 0.8237 (mtm180) cc_final: 0.6520 (ptt-90)
REVERT: I  351 GLN cc_start: 0.7366 (tt0) cc_final: 0.6653 (mt0)
REVERT: I  378 PHE cc_start: 0.6697 (t80) cc_final: 0.6087 (m-80)
REVERT: J  311 LYS cc_start: 0.7202 (ptpp) cc_final: 0.6496 (mmmt)
REVERT: J  347 LYS cc_start: 0.9097 (mtpp) cc_final: 0.8612 (ttmm)
REVERT: L  347 LYS cc_start: 0.8950 (ptmm) cc_final: 0.8476 (ttmm)
  outliers start: 46
  outliers final: 42
  residues processed: 182
  average time/residue: 0.2487
  time to fit residues: 56.6447
Evaluate side-chains
  194 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 150
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
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  325 LEU
Chi-restraints excluded: chain E residue  347 LYS
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain D residue  322 CYS
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain F residue  319 THR
Chi-restraints excluded: chain F residue  322 CYS
Chi-restraints excluded: chain F residue  341 SER
Chi-restraints excluded: chain G residue  306 VAL
Chi-restraints excluded: chain G residue  310 TYR
Chi-restraints excluded: chain G residue  316 SER
Chi-restraints excluded: chain G residue  331 LYS
Chi-restraints excluded: chain G residue  337 VAL
Chi-restraints excluded: chain G residue  350 VAL
Chi-restraints excluded: chain G residue  351 GLN
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  363 VAL
Chi-restraints excluded: chain I residue  306 VAL
Chi-restraints excluded: chain I residue  319 THR
Chi-restraints excluded: chain I residue  320 SER
Chi-restraints excluded: chain I residue  356 SER
Chi-restraints excluded: chain J residue  322 CYS
Chi-restraints excluded: chain J residue  350 VAL
Chi-restraints excluded: chain K residue  308 ILE
Chi-restraints excluded: chain K residue  318 VAL
Chi-restraints excluded: chain K residue  319 THR
Chi-restraints excluded: chain K residue  327 ASN
Chi-restraints excluded: chain K residue  328 ILE
Chi-restraints excluded: chain K residue  360 ILE
Chi-restraints excluded: chain K residue  376 LEU
Chi-restraints excluded: chain L residue  316 SER
Chi-restraints excluded: chain L residue  319 THR
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:    8.9990
   chunk 75 optimal weight:    0.0170
   chunk 37 optimal weight:    8.9990
   chunk 21 optimal weight:   10.0000
   chunk 31 optimal weight:    0.3980
   chunk 54 optimal weight:    0.3980
   chunk 6 optimal weight:    3.9990
   chunk 33 optimal weight:    8.9990
   chunk 34 optimal weight:    5.9990
   chunk 72 optimal weight:    4.9990
   chunk 24 optimal weight:   10.0000
   overall best weight:    1.9622

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
** J 368 ASN ** 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 = 0.5082 r_free = 0.5082 target = 0.291829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.5012 r_free = 0.5012 target = 0.231247 restraints weight = 9782.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 77)----------------|
| r_work = 0.5038 r_free = 0.5038 target = 0.229439 restraints weight = 13842.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 66)----------------|
| r_work = 0.5046 r_free = 0.5046 target = 0.228330 restraints weight = 12352.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.4609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          1.1368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6918  Z= 0.203
  Angle     :  0.744   8.485   9258  Z= 0.381
  Chirality :  0.052   0.214   1044
  Planarity :  0.006   0.072   1176
  Dihedral  :  6.439  21.962    912
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 22.82 %
    Favored  : 72.56 %
  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: -3.64 (0.22), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.76 (0.17), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS K 362 
 PHE   0.022   0.001   PHE D 378 
 TYR   0.019   0.002   TYR C 310 
 ARG   0.009   0.001   ARG K 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
  179 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 143
  time to evaluate  : 0.815 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 LYS cc_start: 0.8600 (mmtm) cc_final: 0.8324 (mmtm)
REVERT: C  336 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8109 (tm-30)
REVERT: C  351 GLN cc_start: 0.7863 (mp10) cc_final: 0.7604 (mp10)
REVERT: E  349 ARG cc_start: 0.8012 (mtm180) cc_final: 0.7457 (mmp-170)
REVERT: B  348 ASP cc_start: 0.8032 (t0) cc_final: 0.7815 (t0)
REVERT: B  360 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8232 (mt)
REVERT: G  350 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8412 (p)
REVERT: H  349 ARG cc_start: 0.8166 (mtm180) cc_final: 0.6547 (ptt-90)
REVERT: I  349 ARG cc_start: 0.8130 (mtp180) cc_final: 0.7276 (mmp-170)
REVERT: I  351 GLN cc_start: 0.7496 (tt0) cc_final: 0.6790 (mt0)
REVERT: J  311 LYS cc_start: 0.6826 (ptpp) cc_final: 0.6328 (mmmt)
REVERT: K  360 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.7954 (mt)
REVERT: L  348 ASP cc_start: 0.7908 (t0) cc_final: 0.6325 (p0)
REVERT: L  349 ARG cc_start: 0.7878 (mpp80) cc_final: 0.6821 (ppt170)
  outliers start: 36
  outliers final: 30
  residues processed: 159
  average time/residue: 0.2098
  time to fit residues: 42.9022
Evaluate side-chains
  170 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 137
  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  350 VAL
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  347 LYS
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain D residue  327 ASN
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain F residue  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 G residue  350 VAL
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  363 VAL
Chi-restraints excluded: chain I residue  306 VAL
Chi-restraints excluded: chain I residue  319 THR
Chi-restraints excluded: chain I residue  320 SER
Chi-restraints excluded: chain I residue  356 SER
Chi-restraints excluded: chain J residue  350 VAL
Chi-restraints excluded: chain K residue  318 VAL
Chi-restraints excluded: chain K residue  360 ILE
Chi-restraints excluded: chain K residue  375 LYS
Chi-restraints excluded: chain K residue  376 LEU
Chi-restraints excluded: chain L residue  319 THR
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:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 69 optimal weight:   30.0000
   chunk 48 optimal weight:    8.9990
   chunk 24 optimal weight:    7.9990
   chunk 17 optimal weight:   30.0000
   chunk 31 optimal weight:    2.9990
   chunk 52 optimal weight:   20.0000
   chunk 61 optimal weight:   10.0000
   chunk 37 optimal weight:   10.0000
   chunk 10 optimal weight:   10.0000
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
** J 368 ASN ** 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 = 0.4887 r_free = 0.4887 target = 0.291646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4921 r_free = 0.4921 target = 0.196003 restraints weight = 9084.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4937 r_free = 0.4937 target = 0.198254 restraints weight = 5219.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4956 r_free = 0.4956 target = 0.199634 restraints weight = 3869.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.4467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          1.1485

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     :  0.783  10.659   9258  Z= 0.404
  Chirality :  0.053   0.235   1044
  Planarity :  0.006   0.074   1176
  Dihedral  :  6.518  21.792    912
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.89 %
    Favored  : 90.11 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 23.59 %
    Favored  : 71.79 %
  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: -3.67 (0.22), residues: 870
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.79 (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   0.028   0.003   TYR I 310 
 ARG   0.009   0.001   ARG K 349 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2736.88 seconds
wall clock time: 48 minutes 27.38 seconds (2907.38 seconds total)