Starting phenix.real_space_refine
on Tue Aug  4 12:47:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/28lq_56601/08_2026/28lq_56601.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/28lq_56601/08_2026/28lq_56601.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/28lq_56601/08_2026/28lq_56601.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/28lq_56601/08_2026/28lq_56601.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/28lq_56601/08_2026/28lq_56601.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/28lq_56601/08_2026/28lq_56601.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       4      5.16       5
     C    1868      2.51       5
     N     552      2.21       5
     O     548      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 2972
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 743
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 0.42, per 1000 atoms: 0.14
  Number of scatterers: 2972
  At special positions: 0
  Unit cell: (128.544, 70.04, 39.552, 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       4     16.00
     O     548      8.00
     N     552      7.00
     C    1868      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.11
  Conformation dependent library (CDL) restraints added in 61.0 milliseconds
  

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  672

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 45.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 253 through 260
      removed outlier: 6.391A  pdb=" N   LEU B 253 " --> pdb=" O   LYS C 254 " (cutoff:3.500A)
      removed outlier: 8.307A  pdb=" N   VAL C 256 " --> pdb=" O   LEU B 253 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   ASN B 255 " --> pdb=" O   VAL C 256 " (cutoff:3.500A)
      removed outlier: 7.988A  pdb=" N   SER C 258 " --> pdb=" O   ASN B 255 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   LYS B 257 " --> pdb=" O   SER C 258 " (cutoff:3.500A)
      removed outlier: 8.265A  pdb=" N   ILE C 260 " --> pdb=" O   LYS B 257 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   LYS B 259 " --> pdb=" O   ILE C 260 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   LEU A 253 " --> pdb=" O   LYS B 254 " (cutoff:3.500A)
      removed outlier: 8.307A  pdb=" N   VAL B 256 " --> pdb=" O   LEU A 253 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   ASN A 255 " --> pdb=" O   VAL B 256 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   SER B 258 " --> pdb=" O   ASN A 255 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   LYS A 257 " --> pdb=" O   SER B 258 " (cutoff:3.500A)
      removed outlier: 8.264A  pdb=" N   ILE B 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   LYS A 259 " --> pdb=" O   ILE B 260 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 263 through 268
      removed outlier: 6.711A  pdb=" N   THR A 263 " --> pdb=" O   GLU D 264 " (cutoff:3.500A)
      removed outlier: 8.002A  pdb=" N   LEU D 266 " --> pdb=" O   THR A 263 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   ASN A 265 " --> pdb=" O   LEU D 266 " (cutoff:3.500A)
      removed outlier: 7.756A  pdb=" N   HIS D 268 " --> pdb=" O   ASN A 265 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   LYS A 267 " --> pdb=" O   HIS D 268 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 306 through 310
      removed outlier: 6.614A  pdb=" N   GLN B 307 " --> pdb=" O   ILE C 308 " (cutoff:3.500A)
      removed outlier: 7.952A  pdb=" N   TYR C 310 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   VAL B 309 " --> pdb=" O   TYR C 310 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   GLN A 307 " --> pdb=" O   ILE B 308 " (cutoff:3.500A)
      removed outlier: 7.952A  pdb=" N   TYR B 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   VAL A 309 " --> pdb=" O   TYR B 310 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 313 through 314
      removed outlier: 6.906A  pdb=" N   VAL B 313 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   VAL A 313 " --> pdb=" O   ASP B 314 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 319 through 321
      removed outlier: 6.536A  pdb=" N   PHE A 320 " --> pdb=" O   LYS D 321 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 337 through 354
      removed outlier: 9.107A  pdb=" N   VAL B 337 " --> pdb=" O   GLU C 338 " (cutoff:3.500A)
      removed outlier: 9.734A  pdb=" N   LYS C 340 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 8.840A  pdb=" N   VAL B 339 " --> pdb=" O   LYS C 340 " (cutoff:3.500A)
      removed outlier: 10.643A  pdb=" N   GLU C 342 " --> pdb=" O   VAL B 339 " (cutoff:3.500A)
      removed outlier: 9.163A  pdb=" N   SER B 341 " --> pdb=" O   GLU C 342 " (cutoff:3.500A)
      removed outlier: 9.221A  pdb=" N   LEU C 344 " --> pdb=" O   SER B 341 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   LYS B 343 " --> pdb=" O   LEU C 344 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   PHE C 346 " --> pdb=" O   LYS B 343 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ASP B 345 " --> pdb=" O   PHE C 346 " (cutoff:3.500A)
      removed outlier: 7.475A  pdb=" N   ASP C 348 " --> pdb=" O   ASP B 345 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   LYS B 347 " --> pdb=" O   ASP C 348 " (cutoff:3.500A)
      removed outlier: 8.603A  pdb=" N   VAL C 350 " --> pdb=" O   LYS B 347 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   ARG B 349 " --> pdb=" O   VAL C 350 " (cutoff:3.500A)
      removed outlier: 7.916A  pdb=" N   SER C 352 " --> pdb=" O   ARG B 349 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   GLN B 351 " --> pdb=" O   SER C 352 " (cutoff:3.500A)
      removed outlier: 8.359A  pdb=" N   ILE C 354 " --> pdb=" O   GLN B 351 " (cutoff:3.500A)
      removed outlier: 6.063A  pdb=" N   LYS B 353 " --> pdb=" O   ILE C 354 " (cutoff:3.500A)
      removed outlier: 9.107A  pdb=" N   VAL A 337 " --> pdb=" O   GLU B 338 " (cutoff:3.500A)
      removed outlier: 9.734A  pdb=" N   LYS B 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 8.839A  pdb=" N   VAL A 339 " --> pdb=" O   LYS B 340 " (cutoff:3.500A)
      removed outlier: 10.643A  pdb=" N   GLU B 342 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 9.162A  pdb=" N   SER A 341 " --> pdb=" O   GLU B 342 " (cutoff:3.500A)
      removed outlier: 9.221A  pdb=" N   LEU B 344 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   LYS A 343 " --> pdb=" O   LEU B 344 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   PHE B 346 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ASP A 345 " --> pdb=" O   PHE B 346 " (cutoff:3.500A)
      removed outlier: 7.475A  pdb=" N   ASP B 348 " --> pdb=" O   ASP A 345 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   LYS A 347 " --> pdb=" O   ASP B 348 " (cutoff:3.500A)
      removed outlier: 8.603A  pdb=" N   VAL B 350 " --> pdb=" O   LYS A 347 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   ARG A 349 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
      removed outlier: 7.916A  pdb=" N   SER B 352 " --> pdb=" O   ARG A 349 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   GLN A 351 " --> pdb=" O   SER B 352 " (cutoff:3.500A)
      removed outlier: 8.358A  pdb=" N   ILE B 354 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 6.063A  pdb=" N   LYS A 353 " --> pdb=" O   ILE B 354 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   GLU A 338 " --> pdb=" O   VAL D 337 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   VAL D 339 " --> pdb=" O   GLU A 338 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   LYS A 340 " --> pdb=" O   VAL D 339 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   SER D 341 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   GLU A 342 " --> pdb=" O   SER D 341 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   LYS D 343 " --> pdb=" O   GLU A 342 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 360 through 362
      removed outlier: 6.891A  pdb=" N   ILE A 360 " --> pdb=" O   THR D 361 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 372 through 378
      removed outlier: 6.220A  pdb=" N   THR B 373 " --> pdb=" O   HIS C 374 " (cutoff:3.500A)
      removed outlier: 7.824A  pdb=" N   LEU C 376 " --> pdb=" O   THR B 373 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   LYS B 375 " --> pdb=" O   LEU C 376 " (cutoff:3.500A)
      removed outlier: 8.065A  pdb=" N   PHE C 378 " --> pdb=" O   LYS B 375 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   THR B 377 " --> pdb=" O   PHE C 378 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   THR A 373 " --> pdb=" O   HIS B 374 " (cutoff:3.500A)
      removed outlier: 7.824A  pdb=" N   LEU B 376 " --> pdb=" O   THR A 373 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   LYS A 375 " --> pdb=" O   LEU B 376 " (cutoff:3.500A)
      removed outlier: 8.065A  pdb=" N   PHE B 378 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   THR A 377 " --> pdb=" O   PHE B 378 " (cutoff:3.500A)

    47 hydrogen bonds defined for protein.
    141 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.42

  Time building geometry restraints manager: 0.16 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: 711
        1.33 -     1.45: 690
        1.45 -     1.57: 1615
        1.57 -     1.69: 0
        1.69 -     1.82: 4
  Bond restraints: 3020
  Sorted by residual:
  bond pdb=" CB  HIS C 362 "
       pdb=" CG  HIS C 362 "
    ideal  model  delta    sigma   weight residual
    1.497  1.449  0.048 1.40e-02 5.10e+03 1.19e+01
  bond pdb=" CB  HIS D 362 "
       pdb=" CG  HIS D 362 "
    ideal  model  delta    sigma   weight residual
    1.497  1.449  0.048 1.40e-02 5.10e+03 1.17e+01
  bond pdb=" CB  HIS A 362 "
       pdb=" CG  HIS A 362 "
    ideal  model  delta    sigma   weight residual
    1.497  1.449  0.048 1.40e-02 5.10e+03 1.17e+01
  bond pdb=" CB  HIS B 362 "
       pdb=" CG  HIS B 362 "
    ideal  model  delta    sigma   weight residual
    1.497  1.449  0.048 1.40e-02 5.10e+03 1.16e+01
  bond pdb=" CG  HIS C 362 "
       pdb=" CD2 HIS C 362 "
    ideal  model  delta    sigma   weight residual
    1.354  1.319  0.035 1.10e-02 8.26e+03 9.92e+00
  ... (remaining 3015 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 3128
        2.09 -     4.18: 700
        4.18 -     6.27: 164
        6.27 -     8.36: 36
        8.36 -    10.45: 4
  Bond angle restraints: 4032
  Sorted by residual:
  angle pdb=" C   GLU D 372 "
        pdb=" CA  GLU D 372 "
        pdb=" CB  GLU D 372 "
      ideal   model   delta    sigma   weight residual
     110.24  120.69  -10.45 1.46e+00 4.69e-01 5.12e+01
  angle pdb=" C   GLU A 372 "
        pdb=" CA  GLU A 372 "
        pdb=" CB  GLU A 372 "
      ideal   model   delta    sigma   weight residual
     110.24  120.68  -10.44 1.46e+00 4.69e-01 5.11e+01
  angle pdb=" C   GLU B 372 "
        pdb=" CA  GLU B 372 "
        pdb=" CB  GLU B 372 "
      ideal   model   delta    sigma   weight residual
     110.24  120.65  -10.41 1.46e+00 4.69e-01 5.08e+01
  angle pdb=" C   GLU C 372 "
        pdb=" CA  GLU C 372 "
        pdb=" CB  GLU C 372 "
      ideal   model   delta    sigma   weight residual
     110.24  120.64  -10.40 1.46e+00 4.69e-01 5.08e+01
  angle pdb=" CA  ASP B 252 "
        pdb=" CB  ASP B 252 "
        pdb=" CG  ASP B 252 "
      ideal   model   delta    sigma   weight residual
     112.60  117.42   -4.82 1.00e+00 1.00e+00 2.33e+01
  ... (remaining 4027 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    12.79: 1611
       12.79 -    25.58: 173
       25.58 -    38.37: 32
       38.37 -    51.16: 16
       51.16 -    63.94: 12
  Dihedral angle restraints: 1844
    sinusoidal: 784
      harmonic: 1060
  Sorted by residual:
  dihedral pdb=" C   GLU D 372 "
           pdb=" N   GLU D 372 "
           pdb=" CA  GLU D 372 "
           pdb=" CB  GLU D 372 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.38   10.78     0      2.50e+00 1.60e-01 1.86e+01
  dihedral pdb=" C   GLU A 372 "
           pdb=" N   GLU A 372 "
           pdb=" CA  GLU A 372 "
           pdb=" CB  GLU A 372 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.36   10.76     0      2.50e+00 1.60e-01 1.85e+01
  dihedral pdb=" C   GLU C 372 "
           pdb=" N   GLU C 372 "
           pdb=" CA  GLU C 372 "
           pdb=" CB  GLU C 372 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.35   10.75     0      2.50e+00 1.60e-01 1.85e+01
  ... (remaining 1841 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.074: 236
       0.074 -    0.146: 124
       0.146 -    0.219: 50
       0.219 -    0.292: 18
       0.292 -    0.365: 16
  Chirality restraints: 444
  Sorted by residual:
  chirality pdb=" CA  GLN D 351 "
            pdb=" N   GLN D 351 "
            pdb=" C   GLN D 351 "
            pdb=" CB  GLN D 351 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.33e+00
  chirality pdb=" CA  GLN C 351 "
            pdb=" N   GLN C 351 "
            pdb=" C   GLN C 351 "
            pdb=" CB  GLN C 351 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.33e+00
  chirality pdb=" CA  GLN A 351 "
            pdb=" N   GLN A 351 "
            pdb=" C   GLN A 351 "
            pdb=" CB  GLN A 351 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.33e+00
  ... (remaining 441 not shown)

  Planarity restraints: 516
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 310 "    0.035 2.00e-02 2.50e+03   1.79e-02 6.40e+00
        pdb=" CG  TYR D 310 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 310 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 310 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 310 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 310 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 310 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR D 310 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 310 "    0.035 2.00e-02 2.50e+03   1.79e-02 6.39e+00
        pdb=" CG  TYR A 310 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 310 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 310 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 310 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 310 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 310 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR A 310 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 310 "    0.035 2.00e-02 2.50e+03   1.78e-02 6.37e+00
        pdb=" CG  TYR C 310 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 310 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 310 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 310 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 310 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 310 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR C 310 "    0.018 2.00e-02 2.50e+03
  ... (remaining 513 not shown)

  Histogram of nonbonded interaction distances:
        2.55 -     3.02: 1538
        3.02 -     3.49: 2955
        3.49 -     3.96: 4526
        3.96 -     4.43: 4974
        4.43 -     4.90: 9905
  Nonbonded interactions: 23898
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D 263 "
            pdb=" OG  SER D 352 "
     model   vdw
     2.554 3.040
  nonbonded pdb=" OG1 THR B 263 "
            pdb=" OG  SER B 352 "
     model   vdw
     2.554 3.040
  nonbonded pdb=" OG1 THR C 263 "
            pdb=" OG  SER C 352 "
     model   vdw
     2.554 3.040
  nonbonded pdb=" OG1 THR A 263 "
            pdb=" OG  SER A 352 "
     model   vdw
     2.554 3.040
  nonbonded pdb=" NZ  LYS A 254 "
            pdb=" O   PRO B 364 "
     model   vdw
     2.563 3.120
  ... (remaining 23893 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'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     3.350
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:5.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
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      :  0.011   0.048   3020  Z= 0.731
  Angle     :  1.951  10.445   4032  Z= 1.222
  Chirality :  0.118   0.365    444
  Planarity :  0.009   0.032    516
  Dihedral  : 12.913  63.944   1172
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.42 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  :  4.76 %
    Favored  : 86.90 %
  Cbeta Deviations :  1.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.57 (0.23), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.48 (0.18), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG D 379 
 TYR   0.035   0.014   TYR A 310 
 PHE   0.017   0.006   PHE C 320 
 HIS   0.013   0.005   HIS D 362 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01136 /  0.73 ( 3020)
  covalent geometry    : angle       1.95085 /  1.22 ( 4032)
  hydrogen bonds       : bond        0.19483 / 11.35 (   47)
  hydrogen bonds       : angle       7.32347 /  4.86 (  141)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 66
  time to evaluate  : 0.072 
Fit side-chains
   revert: symmetry clash
REVERT: A  331 LYS cc_start: 0.7344 (OUTLIER) cc_final: 0.7094 (mttt)
REVERT: A  347 LYS cc_start: 0.7819 (ttmt) cc_final: 0.7541 (mttp)
REVERT: B  266 LEU cc_start: 0.8662 (mt) cc_final: 0.8435 (tt)
REVERT: B  331 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.7037 (mttt)
REVERT: B  347 LYS cc_start: 0.7751 (ttmt) cc_final: 0.7482 (mttp)
REVERT: C  266 LEU cc_start: 0.8800 (mt) cc_final: 0.8534 (tt)
REVERT: C  347 LYS cc_start: 0.7994 (ttmt) cc_final: 0.7770 (mttp)
REVERT: C  379 ARG cc_start: 0.5916 (tpt170) cc_final: 0.5517 (tmm160)
REVERT: D  345 ASP cc_start: 0.8140 (t0) cc_final: 0.7908 (t0)
REVERT: D  347 LYS cc_start: 0.7882 (ttmt) cc_final: 0.7639 (mttt)
  outliers start: 28
  outliers final: 2
  residues processed: 86
  average time/residue: 0.4172
  time to fit residues: 36.7002
Evaluate side-chains
  51 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 SER
Chi-restraints excluded: chain A residue  331 LYS
Chi-restraints excluded: chain B residue  331 LYS
Chi-restraints excluded: chain D residue  262 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:   10.0000
   chunk 13 optimal weight:    7.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 307 GLN
B 307 GLN
C 307 GLN
** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 307 GLN
** D 368 ASN ** 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 = 0.4712 r_free = 0.4712 target = 0.150314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.126295 restraints weight = 3540.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.4497 rms_B_bonded: 2.92
r_work: 0.4361 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.4361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.2885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3020  Z= 0.175
  Angle     :  0.667   6.158   4032  Z= 0.354
  Chirality :  0.050   0.147    444
  Planarity :  0.004   0.021    516
  Dihedral  :  5.543  38.614    406
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 12.20 %
    Favored  : 84.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.89 (0.27), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.96 (0.20), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 349 
 TYR   0.004   0.001   TYR D 310 
 PHE   0.032   0.003   PHE B 320 
 HIS   0.003   0.001   HIS A 362 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00380 /  0.18 ( 3020)
  covalent geometry    : angle       0.66664 /  0.35 ( 4032)
  hydrogen bonds       : bond        0.03016 /  1.79 (   47)
  hydrogen bonds       : angle       6.81268 /  4.43 (  141)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
REVERT: A  265 ASN cc_start: 0.7813 (t0) cc_final: 0.7501 (t0)
REVERT: A  331 LYS cc_start: 0.7121 (OUTLIER) cc_final: 0.6908 (mttp)
REVERT: A  347 LYS cc_start: 0.7272 (ttmt) cc_final: 0.7018 (mttp)
REVERT: A  369 LYS cc_start: 0.7721 (ttpt) cc_final: 0.7200 (tmtt)
REVERT: B  266 LEU cc_start: 0.8250 (mt) cc_final: 0.7733 (tt)
REVERT: B  331 LYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6794 (mttp)
REVERT: B  343 LYS cc_start: 0.7453 (mttp) cc_final: 0.7245 (mppt)
REVERT: B  352 SER cc_start: 0.8572 (p) cc_final: 0.8252 (m)
REVERT: B  369 LYS cc_start: 0.7853 (ttpt) cc_final: 0.7359 (tmtt)
REVERT: C  266 LEU cc_start: 0.8585 (mt) cc_final: 0.8145 (tt)
REVERT: C  313 VAL cc_start: 0.8008 (m) cc_final: 0.7767 (t)
REVERT: C  343 LYS cc_start: 0.7875 (mttp) cc_final: 0.7590 (mptt)
REVERT: C  348 ASP cc_start: 0.8147 (p0) cc_final: 0.7847 (p0)
  outliers start: 12
  outliers final: 6
  residues processed: 64
  average time/residue: 0.4870
  time to fit residues: 31.9607
Evaluate side-chains
  55 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  331 LYS
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  331 LYS
Chi-restraints excluded: chain B residue  349 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   chunk 13 optimal weight:    8.9990
   chunk 24 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    2.1588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 329 HIS
A 374 HIS
B 265 ASN
B 329 HIS
C 374 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4682 r_free = 0.4682 target = 0.147354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.123177 restraints weight = 3772.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.4473 rms_B_bonded: 3.07
r_work: 0.4340 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.4340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.4022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   3020  Z= 0.250
  Angle     :  0.734   8.455   4032  Z= 0.393
  Chirality :  0.053   0.154    444
  Planarity :  0.004   0.024    516
  Dihedral  :  5.350  38.776    404
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 12.50 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.65 (0.29), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.77 (0.22), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 379 
 TYR   0.006   0.002   TYR D 310 
 PHE   0.029   0.003   PHE B 320 
 HIS   0.005   0.002   HIS C 362 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00516 /  0.25 ( 3020)
  covalent geometry    : angle       0.73389 /  0.39 ( 4032)
  hydrogen bonds       : bond        0.03303 /  1.99 (   47)
  hydrogen bonds       : angle       6.46716 /  4.17 (  141)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 43
  time to evaluate  : 0.093 
Fit side-chains
REVERT: A  264 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6308 (tm-30)
REVERT: A  265 ASN cc_start: 0.7997 (t0) cc_final: 0.7736 (t0)
REVERT: A  343 LYS cc_start: 0.7695 (mttp) cc_final: 0.7410 (mptt)
REVERT: A  352 SER cc_start: 0.8461 (p) cc_final: 0.8088 (m)
REVERT: B  343 LYS cc_start: 0.7543 (mttp) cc_final: 0.7259 (mppt)
REVERT: B  348 ASP cc_start: 0.8279 (p0) cc_final: 0.7898 (p0)
REVERT: C  255 ASN cc_start: 0.7399 (p0) cc_final: 0.7159 (p0)
REVERT: C  265 ASN cc_start: 0.7986 (t0) cc_final: 0.7774 (t0)
REVERT: C  343 LYS cc_start: 0.7930 (mttp) cc_final: 0.7679 (mptt)
REVERT: C  372 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7132 (pm20)
REVERT: D  264 GLU cc_start: 0.7814 (pt0) cc_final: 0.6953 (pp20)
REVERT: D  265 ASN cc_start: 0.8221 (t0) cc_final: 0.7929 (t0)
REVERT: D  343 LYS cc_start: 0.7497 (mttp) cc_final: 0.7295 (mppt)
  outliers start: 17
  outliers final: 7
  residues processed: 55
  average time/residue: 0.4148
  time to fit residues: 23.4322
Evaluate side-chains
  48 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  349 ARG
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  349 ARG
Chi-restraints excluded: chain C residue  253 LEU
Chi-restraints excluded: chain C residue  349 ARG
Chi-restraints excluded: chain C residue  372 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 1 optimal weight:    7.9990
   chunk 29 optimal weight:    7.9990
   chunk 20 optimal weight:    0.4980
   chunk 30 optimal weight:    4.9990
   chunk 22 optimal weight:    9.9990
   chunk 32 optimal weight:    5.9990
   chunk 14 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   overall best weight:    2.4988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 265 ASN
B 374 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4660 r_free = 0.4660 target = 0.147048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.122229 restraints weight = 3440.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.4445 rms_B_bonded: 2.99
r_work: 0.4295 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.4295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.4763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   3020  Z= 0.264
  Angle     :  0.717   7.426   4032  Z= 0.382
  Chirality :  0.052   0.156    444
  Planarity :  0.004   0.027    516
  Dihedral  :  4.257  12.147    396
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 16.07 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.72 (0.30), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.83 (0.23), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 349 
 TYR   0.007   0.003   TYR A 310 
 PHE   0.028   0.003   PHE B 320 
 HIS   0.007   0.002   HIS A 329 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00545 /  0.26 ( 3020)
  covalent geometry    : angle       0.71726 /  0.38 ( 4032)
  hydrogen bonds       : bond        0.03202 /  1.97 (   47)
  hydrogen bonds       : angle       6.26253 /  4.01 (  141)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 36
  time to evaluate  : 0.066 
Fit side-chains
REVERT: A  264 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6326 (tm-30)
REVERT: A  347 LYS cc_start: 0.7283 (ttmt) cc_final: 0.7002 (mttp)
REVERT: A  352 SER cc_start: 0.8342 (p) cc_final: 0.7994 (m)
REVERT: B  348 ASP cc_start: 0.8353 (p0) cc_final: 0.7977 (p0)
REVERT: B  351 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.7176 (tt0)
REVERT: C  372 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7185 (pm20)
REVERT: C  379 ARG cc_start: 0.6676 (mpt180) cc_final: 0.5675 (tmm160)
REVERT: D  264 GLU cc_start: 0.7894 (pt0) cc_final: 0.7019 (pp20)
REVERT: D  343 LYS cc_start: 0.7533 (mttp) cc_final: 0.7274 (mppt)
REVERT: D  348 ASP cc_start: 0.8088 (p0) cc_final: 0.7666 (p0)
  outliers start: 16
  outliers final: 9
  residues processed: 48
  average time/residue: 0.4865
  time to fit residues: 23.9829
Evaluate side-chains
  45 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 33
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  349 ARG
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  349 ARG
Chi-restraints excluded: chain B residue  351 GLN
Chi-restraints excluded: chain C residue  253 LEU
Chi-restraints excluded: chain C residue  349 ARG
Chi-restraints excluded: chain C residue  372 GLU
Chi-restraints excluded: chain D residue  258 SER
Chi-restraints excluded: chain D residue  370 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 17 optimal weight:    0.0370
   chunk 21 optimal weight:    5.9990
   chunk 11 optimal weight:    8.9990
   chunk 16 optimal weight:    2.9990
   chunk 13 optimal weight:    6.9990
   chunk 6 optimal weight:    7.9990
   chunk 18 optimal weight:    7.9990
   chunk 24 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 29 optimal weight:    0.4980
   chunk 4 optimal weight:    3.9990
   overall best weight:    1.7064

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 265 ASN
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 265 ASN
B 329 HIS
C 265 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4667 r_free = 0.4667 target = 0.147449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4460 r_free = 0.4460 target = 0.123479 restraints weight = 3463.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.4480 rms_B_bonded: 2.95
r_work: 0.4330 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.4330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.5164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3020  Z= 0.184
  Angle     :  0.621   7.441   4032  Z= 0.324
  Chirality :  0.049   0.143    444
  Planarity :  0.004   0.028    516
  Dihedral  :  3.845  11.304    396
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 18.75 %
    Favored  : 77.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.74 (0.30), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.84 (0.23), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 379 
 TYR   0.006   0.002   TYR B 310 
 PHE   0.030   0.003   PHE B 320 
 HIS   0.003   0.001   HIS D 362 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00384 /  0.18 ( 3020)
  covalent geometry    : angle       0.62071 /  0.32 ( 4032)
  hydrogen bonds       : bond        0.02631 /  1.63 (   47)
  hydrogen bonds       : angle       6.16650 /  4.02 (  141)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 33
  time to evaluate  : 0.085 
Fit side-chains
REVERT: A  264 GLU cc_start: 0.7311 (pt0) cc_final: 0.6340 (tm-30)
REVERT: B  255 ASN cc_start: 0.7070 (p0) cc_final: 0.6584 (t0)
REVERT: B  348 ASP cc_start: 0.8343 (p0) cc_final: 0.7986 (p0)
REVERT: C  372 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6818 (mp0)
REVERT: C  379 ARG cc_start: 0.6761 (mpt180) cc_final: 0.5716 (tmm160)
REVERT: D  343 LYS cc_start: 0.7514 (mttp) cc_final: 0.7280 (mppt)
  outliers start: 14
  outliers final: 7
  residues processed: 44
  average time/residue: 0.5155
  time to fit residues: 23.2776
Evaluate side-chains
  37 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 29
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  349 ARG
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  349 ARG
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  349 ARG
Chi-restraints excluded: chain C residue  372 GLU
Chi-restraints excluded: chain D residue  258 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 35 optimal weight:    0.0470
   chunk 30 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 4 optimal weight:   10.0000
   chunk 6 optimal weight:    8.9990
   chunk 8 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 26 optimal weight:    0.0050
   overall best weight:    2.0098

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 265 ASN
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 265 ASN
B 329 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4651 r_free = 0.4651 target = 0.146456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.122074 restraints weight = 3469.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.4453 rms_B_bonded: 2.98
r_work: 0.4300 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.4300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.5494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   3020  Z= 0.217
  Angle     :  0.657   7.356   4032  Z= 0.347
  Chirality :  0.049   0.147    444
  Planarity :  0.004   0.029    516
  Dihedral  :  3.957  11.997    396
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 19.94 %
    Favored  : 75.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.87 (0.30), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.94 (0.23), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG D 349 
 TYR   0.006   0.002   TYR A 310 
 PHE   0.028   0.003   PHE B 320 
 HIS   0.004   0.001   HIS D 362 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00450 /  0.22 ( 3020)
  covalent geometry    : angle       0.65735 /  0.35 ( 4032)
  hydrogen bonds       : bond        0.02630 /  1.59 (   47)
  hydrogen bonds       : angle       6.08305 /  3.97 (  141)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 28
  time to evaluate  : 0.128 
Fit side-chains
REVERT: A  264 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6335 (tm-30)
REVERT: A  352 SER cc_start: 0.8271 (p) cc_final: 0.7986 (m)
REVERT: B  255 ASN cc_start: 0.7174 (p0) cc_final: 0.6963 (p0)
REVERT: B  265 ASN cc_start: 0.7757 (t0) cc_final: 0.7526 (t0)
REVERT: C  372 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6782 (mp0)
REVERT: C  379 ARG cc_start: 0.6829 (mpt180) cc_final: 0.5767 (tmm160)
REVERT: D  265 ASN cc_start: 0.8207 (t0) cc_final: 0.7957 (t0)
REVERT: D  343 LYS cc_start: 0.7584 (mttp) cc_final: 0.7336 (mppt)
  outliers start: 16
  outliers final: 6
  residues processed: 41
  average time/residue: 0.5144
  time to fit residues: 21.6346
Evaluate side-chains
  37 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 29
  time to evaluate  : 0.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  349 ARG
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  349 ARG
Chi-restraints excluded: chain C residue  349 ARG
Chi-restraints excluded: chain C residue  372 GLU
Chi-restraints excluded: chain D residue  258 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 25 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 27 optimal weight:   10.0000
   chunk 22 optimal weight:    7.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9990
   chunk 18 optimal weight:    8.9990
   overall best weight:    2.1586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 374 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4645 r_free = 0.4645 target = 0.145690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.121145 restraints weight = 3539.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.4439 rms_B_bonded: 3.02
r_work: 0.4286 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.4286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.5796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   3020  Z= 0.223
  Angle     :  0.672   8.879   4032  Z= 0.353
  Chirality :  0.050   0.145    444
  Planarity :  0.004   0.029    516
  Dihedral  :  3.986  12.117    396
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 20.54 %
    Favored  : 74.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.03 (0.29), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.06 (0.22), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 379 
 TYR   0.006   0.002   TYR A 310 
 PHE   0.027   0.003   PHE B 320 
 HIS   0.004   0.001   HIS D 362 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00470 /  0.22 ( 3020)
  covalent geometry    : angle       0.67182 /  0.35 ( 4032)
  hydrogen bonds       : bond        0.02668 /  1.63 (   47)
  hydrogen bonds       : angle       6.06201 /  3.95 (  141)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 27
  time to evaluate  : 0.120 
Fit side-chains
REVERT: A  264 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6302 (tm-30)
REVERT: A  352 SER cc_start: 0.8263 (p) cc_final: 0.7961 (m)
REVERT: B  351 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.7178 (tt0)
REVERT: C  264 GLU cc_start: 0.7850 (pt0) cc_final: 0.7502 (pt0)
REVERT: C  379 ARG cc_start: 0.6817 (mpt180) cc_final: 0.5849 (tmm160)
REVERT: D  264 GLU cc_start: 0.7879 (pt0) cc_final: 0.7112 (pp20)
REVERT: D  265 ASN cc_start: 0.8182 (t0) cc_final: 0.7954 (t0)
REVERT: D  343 LYS cc_start: 0.7580 (mttp) cc_final: 0.7331 (mppt)
  outliers start: 16
  outliers final: 5
  residues processed: 40
  average time/residue: 0.4786
  time to fit residues: 19.6352
Evaluate side-chains
  34 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 27
  time to evaluate  : 0.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  349 ARG
Chi-restraints excluded: chain B residue  351 GLN
Chi-restraints excluded: chain C residue  349 ARG
Chi-restraints excluded: chain D residue  258 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 0 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0770
   chunk 1 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    1.6146

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 265 ASN
B 329 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4656 r_free = 0.4656 target = 0.146627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.122330 restraints weight = 3618.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.4457 rms_B_bonded: 3.02
r_work: 0.4304 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.4304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.5924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3020  Z= 0.181
  Angle     :  0.651   8.164   4032  Z= 0.335
  Chirality :  0.048   0.142    444
  Planarity :  0.004   0.041    516
  Dihedral  :  3.921  11.824    396
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 23.21 %
    Favored  : 73.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.07 (0.29), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.10 (0.22), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 379 
 TYR   0.006   0.002   TYR A 310 
 PHE   0.042   0.003   PHE B 320 
 HIS   0.004   0.001   HIS D 362 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00384 /  0.18 ( 3020)
  covalent geometry    : angle       0.65058 /  0.34 ( 4032)
  hydrogen bonds       : bond        0.02518 /  1.54 (   47)
  hydrogen bonds       : angle       5.90462 /  3.76 (  141)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 28
  time to evaluate  : 0.082 
Fit side-chains
REVERT: A  264 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6400 (tm-30)
REVERT: A  342 GLU cc_start: 0.8088 (tt0) cc_final: 0.7441 (tm-30)
REVERT: A  352 SER cc_start: 0.8215 (p) cc_final: 0.7992 (m)
REVERT: C  264 GLU cc_start: 0.7780 (pt0) cc_final: 0.7444 (pt0)
REVERT: C  379 ARG cc_start: 0.6863 (mpt180) cc_final: 0.5886 (tmm160)
REVERT: D  265 ASN cc_start: 0.8204 (t0) cc_final: 0.7970 (t0)
REVERT: D  343 LYS cc_start: 0.7551 (mttp) cc_final: 0.7307 (mppt)
  outliers start: 11
  outliers final: 5
  residues processed: 37
  average time/residue: 0.4481
  time to fit residues: 16.9951
Evaluate side-chains
  32 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 26
  time to evaluate  : 0.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  349 ARG
Chi-restraints excluded: chain C residue  349 ARG
Chi-restraints excluded: chain D residue  258 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 35 optimal weight:    0.0010
   chunk 33 optimal weight:    0.0370
   chunk 25 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   chunk 5 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 17 optimal weight:    0.0020
   chunk 20 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.3874

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 265 ASN
B 368 ASN
** D 329 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 = 0.4715 r_free = 0.4715 target = 0.150670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.126151 restraints weight = 3569.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.4512 rms_B_bonded: 3.06
r_work: 0.4366 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.4366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.6074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   3020  Z= 0.101
  Angle     :  0.563   7.745   4032  Z= 0.283
  Chirality :  0.046   0.119    444
  Planarity :  0.004   0.043    516
  Dihedral  :  3.699  12.172    396
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 24.70 %
    Favored  : 72.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.03 (0.29), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.07 (0.22), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 379 
 TYR   0.006   0.001   TYR B 310 
 PHE   0.041   0.003   PHE B 320 
 HIS   0.002   0.000   HIS D 362 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00220 /  0.10 ( 3020)
  covalent geometry    : angle       0.56303 /  0.28 ( 4032)
  hydrogen bonds       : bond        0.02200 /  1.37 (   47)
  hydrogen bonds       : angle       5.78277 /  3.67 (  141)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 34
  time to evaluate  : 0.070 
Fit side-chains
REVERT: A  264 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6340 (tm-30)
REVERT: A  343 LYS cc_start: 0.7577 (mttp) cc_final: 0.7224 (mppt)
REVERT: A  347 LYS cc_start: 0.7350 (ttmt) cc_final: 0.7071 (mttp)
REVERT: B  264 GLU cc_start: 0.7642 (pt0) cc_final: 0.7147 (tm-30)
REVERT: B  343 LYS cc_start: 0.7525 (mttp) cc_final: 0.7229 (mppt)
REVERT: B  372 GLU cc_start: 0.7543 (pt0) cc_final: 0.7280 (pm20)
REVERT: C  264 GLU cc_start: 0.7604 (pt0) cc_final: 0.7313 (pt0)
REVERT: C  379 ARG cc_start: 0.6809 (mpt180) cc_final: 0.5834 (tmm160)
REVERT: D  343 LYS cc_start: 0.7458 (mttp) cc_final: 0.7237 (mppt)
  outliers start: 8
  outliers final: 3
  residues processed: 40
  average time/residue: 0.5215
  time to fit residues: 21.3680
Evaluate side-chains
  37 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain B residue  349 ARG
Chi-restraints excluded: chain C residue  349 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 31 optimal weight:    8.9990
   chunk 20 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 13 optimal weight:    5.9990
   chunk 22 optimal weight:    8.9990
   chunk 7 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   overall best weight:    2.5586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 265 ASN
** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 265 ASN
** D 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 359 ASN ** 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 = 0.4632 r_free = 0.4632 target = 0.143887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.120597 restraints weight = 3600.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.4439 rms_B_bonded: 2.90
r_work: 0.4288 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.4288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.6195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   3020  Z= 0.250
  Angle     :  0.725  10.317   4032  Z= 0.380
  Chirality :  0.050   0.144    444
  Planarity :  0.004   0.028    516
  Dihedral  :  4.127  19.982    396
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 25.30 %
    Favored  : 72.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.10 (0.29), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.12 (0.22), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 379 
 TYR   0.006   0.003   TYR A 310 
 PHE   0.036   0.003   PHE B 320 
 HIS   0.006   0.002   HIS D 362 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00530 /  0.25 ( 3020)
  covalent geometry    : angle       0.72496 /  0.38 ( 4032)
  hydrogen bonds       : bond        0.02916 /  1.79 (   47)
  hydrogen bonds       : angle       5.71818 /  3.60 (  141)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 33
  time to evaluate  : 0.076 
Fit side-chains
REVERT: A  264 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6495 (tm-30)
REVERT: A  352 SER cc_start: 0.8247 (p) cc_final: 0.8003 (m)
REVERT: B  265 ASN cc_start: 0.7751 (t0) cc_final: 0.7547 (t0)
REVERT: B  327 ASN cc_start: 0.6778 (OUTLIER) cc_final: 0.6444 (p0)
REVERT: C  264 GLU cc_start: 0.7858 (pt0) cc_final: 0.7517 (pt0)
REVERT: C  379 ARG cc_start: 0.6954 (mpt180) cc_final: 0.6098 (tmm160)
REVERT: D  264 GLU cc_start: 0.7902 (pt0) cc_final: 0.7171 (pp20)
REVERT: D  343 LYS cc_start: 0.7679 (mttp) cc_final: 0.7471 (mppt)
  outliers start: 8
  outliers final: 2
  residues processed: 39
  average time/residue: 0.4007
  time to fit residues: 16.0564
Evaluate side-chains
  33 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 29
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain B residue  327 ASN
Chi-restraints excluded: chain B residue  349 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 13 optimal weight:    7.9990
   chunk 14 optimal weight:    0.7980
   chunk 30 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    1.5586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 329 HIS
** D 329 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 = 0.4658 r_free = 0.4658 target = 0.145008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.121905 restraints weight = 3534.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.4468 rms_B_bonded: 2.93
r_work: 0.4320 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.4320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.6287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3020  Z= 0.172
  Angle     :  0.655   9.958   4032  Z= 0.334
  Chirality :  0.048   0.132    444
  Planarity :  0.004   0.037    516
  Dihedral  :  3.969  15.812    396
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 26.19 %
    Favored  : 71.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.12 (0.29), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.13 (0.22), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 379 
 TYR   0.005   0.002   TYR A 310 
 PHE   0.037   0.003   PHE B 320 
 HIS   0.003   0.001   HIS A 362 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00372 /  0.17 ( 3020)
  covalent geometry    : angle       0.65452 /  0.33 ( 4032)
  hydrogen bonds       : bond        0.02467 /  1.55 (   47)
  hydrogen bonds       : angle       5.68562 /  3.58 (  141)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1132.38 seconds
wall clock time: 20 minutes 7.51 seconds (1207.51 seconds total)