Starting phenix.real_space_refine
on Tue Mar  3 10:48:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/22jy_68389/03_2026/22jy_68389.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/22jy_68389/03_2026/22jy_68389.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/22jy_68389/03_2026/22jy_68389.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/22jy_68389/03_2026/22jy_68389.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/22jy_68389/03_2026/22jy_68389.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/22jy_68389/03_2026/22jy_68389.cif"
  }
  resolution = 2.2
  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=   0.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      10      5.16       5
     C    1195      2.51       5
     N     345      2.21       5
     O     355      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 1905
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 381
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 381
          Classifications: {'peptide': 51}
          Link IDs: {'PTRANS': 1, 'TRANS': 49}
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 0.27, per 1000 atoms: 0.14
  Number of scatterers: 1905
  At special positions: 0
  Unit cell: (60.8731, 66.407, 38.7374, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      10     16.00
     O     355      8.00
     N     345      7.00
     C    1195      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: 0.09
  Conformation dependent library (CDL) restraints added in 68.0 milliseconds
  

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  450

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 6 sheets defined
      0.0% alpha, 60.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.05
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 280 through 287
      removed outlier: 6.710A  pdb=" N   LYS B 280 " --> pdb=" O   LYS C 281 " (cutoff:3.500A)
      removed outlier: 8.176A  pdb=" N   ASP C 283 " --> pdb=" O   LYS B 280 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   LEU B 282 " --> pdb=" O   ASP C 283 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   SER C 285 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   LEU B 284 " --> pdb=" O   SER C 285 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   VAL C 287 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.741A  pdb=" N   ASN B 286 " --> pdb=" O   VAL C 287 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   VAL A 287 " --> pdb=" O   ASN C 286 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   LYS A 280 " --> pdb=" O   LYS D 281 " (cutoff:3.500A)
      removed outlier: 8.176A  pdb=" N   ASP D 283 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   LEU A 282 " --> pdb=" O   ASP D 283 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   SER D 285 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   LEU A 284 " --> pdb=" O   SER D 285 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   VAL D 287 " --> pdb=" O   LEU A 284 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   ASN A 286 " --> pdb=" O   VAL D 287 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   LYS D 280 " --> pdb=" O   LYS E 281 " (cutoff:3.500A)
      removed outlier: 8.176A  pdb=" N   ASP E 283 " --> pdb=" O   LYS D 280 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   LEU D 282 " --> pdb=" O   ASP E 283 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   SER E 285 " --> pdb=" O   LEU D 282 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   LEU D 284 " --> pdb=" O   SER E 285 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   VAL E 287 " --> pdb=" O   LEU D 284 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   ASN D 286 " --> pdb=" O   VAL E 287 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 290 through 291
      removed outlier: 6.537A  pdb=" N   LYS B 290 " --> pdb=" O   CYS C 291 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   LYS A 290 " --> pdb=" O   CYS D 291 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   LYS D 290 " --> pdb=" O   CYS E 291 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 296 through 302
      removed outlier: 9.002A  pdb=" N   ASN B 296 " --> pdb=" O   ILE C 297 " (cutoff:3.500A)
      removed outlier: 9.929A  pdb=" N   HIS C 299 " --> pdb=" O   ASN B 296 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   LYS B 298 " --> pdb=" O   HIS C 299 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   LEU C 301 " --> pdb=" O   LYS B 298 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   VAL B 300 " --> pdb=" O   LEU C 301 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   ILE A 297 " --> pdb=" O   ASN C 296 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   LYS C 298 " --> pdb=" O   ILE A 297 " (cutoff:3.500A)
      removed outlier: 9.002A  pdb=" N   ASN A 296 " --> pdb=" O   ILE D 297 " (cutoff:3.500A)
      removed outlier: 9.928A  pdb=" N   HIS D 299 " --> pdb=" O   ASN A 296 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   LYS A 298 " --> pdb=" O   HIS D 299 " (cutoff:3.500A)
      removed outlier: 7.894A  pdb=" N   LEU D 301 " --> pdb=" O   LYS A 298 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   VAL A 300 " --> pdb=" O   LEU D 301 " (cutoff:3.500A)
      removed outlier: 9.002A  pdb=" N   ASN D 296 " --> pdb=" O   ILE E 297 " (cutoff:3.500A)
      removed outlier: 9.928A  pdb=" N   HIS E 299 " --> pdb=" O   ASN D 296 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   LYS D 298 " --> pdb=" O   HIS E 299 " (cutoff:3.500A)
      removed outlier: 7.894A  pdb=" N   LEU E 301 " --> pdb=" O   LYS D 298 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   VAL D 300 " --> pdb=" O   LEU E 301 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 305 through 310
      removed outlier: 6.608A  pdb=" N   VAL B 306 " --> pdb=" O   GLN C 307 " (cutoff:3.500A)
      removed outlier: 8.004A  pdb=" N   VAL C 309 " --> pdb=" O   VAL B 306 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   ILE B 308 " --> pdb=" O   VAL C 309 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   VAL A 306 " --> pdb=" O   GLN D 307 " (cutoff:3.500A)
      removed outlier: 8.004A  pdb=" N   VAL D 309 " --> pdb=" O   VAL A 306 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   ILE A 308 " --> pdb=" O   VAL D 309 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   VAL D 306 " --> pdb=" O   GLN E 307 " (cutoff:3.500A)
      removed outlier: 8.003A  pdb=" N   VAL E 309 " --> pdb=" O   VAL D 306 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   ILE D 308 " --> pdb=" O   VAL E 309 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 313 through 322
      removed outlier: 9.155A  pdb=" N   VAL B 313 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
      removed outlier: 8.532A  pdb=" N   SER C 316 " --> pdb=" O   VAL B 313 " (cutoff:3.500A)
      removed outlier: 9.573A  pdb=" N   LEU B 315 " --> pdb=" O   SER C 316 " (cutoff:3.500A)
      removed outlier: 9.555A  pdb=" N   VAL C 318 " --> pdb=" O   LEU B 315 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   LYS B 317 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
      removed outlier: 8.358A  pdb=" N   PHE C 320 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   THR B 319 " --> pdb=" O   PHE C 320 " (cutoff:3.500A)
      removed outlier: 7.848A  pdb=" N   CYS C 322 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   LYS B 321 " --> pdb=" O   CYS C 322 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   LEU C 315 " --> pdb=" O   ASP A 314 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   SER A 316 " --> pdb=" O   LEU C 315 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   LYS C 317 " --> pdb=" O   SER A 316 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   VAL A 318 " --> pdb=" O   LYS C 317 " (cutoff:3.500A)
      removed outlier: 9.155A  pdb=" N   VAL A 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
      removed outlier: 8.532A  pdb=" N   SER D 316 " --> pdb=" O   VAL A 313 " (cutoff:3.500A)
      removed outlier: 9.573A  pdb=" N   LEU A 315 " --> pdb=" O   SER D 316 " (cutoff:3.500A)
      removed outlier: 9.556A  pdb=" N   VAL D 318 " --> pdb=" O   LEU A 315 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   LYS A 317 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
      removed outlier: 8.359A  pdb=" N   PHE D 320 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   THR A 319 " --> pdb=" O   PHE D 320 " (cutoff:3.500A)
      removed outlier: 7.848A  pdb=" N   CYS D 322 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   LYS A 321 " --> pdb=" O   CYS D 322 " (cutoff:3.500A)
      removed outlier: 9.156A  pdb=" N   VAL D 313 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
      removed outlier: 8.532A  pdb=" N   SER E 316 " --> pdb=" O   VAL D 313 " (cutoff:3.500A)
      removed outlier: 9.574A  pdb=" N   LEU D 315 " --> pdb=" O   SER E 316 " (cutoff:3.500A)
      removed outlier: 9.555A  pdb=" N   VAL E 318 " --> pdb=" O   LEU D 315 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   LYS D 317 " --> pdb=" O   VAL E 318 " (cutoff:3.500A)
      removed outlier: 8.358A  pdb=" N   PHE E 320 " --> pdb=" O   LYS D 317 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   THR D 319 " --> pdb=" O   PHE E 320 " (cutoff:3.500A)
      removed outlier: 7.848A  pdb=" N   CYS E 322 " --> pdb=" O   THR D 319 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   LYS D 321 " --> pdb=" O   CYS E 322 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 325 through 328
      removed outlier: 6.551A  pdb=" N   GLY A 326 " --> pdb=" O   ASN C 327 " (cutoff:3.500A)

    30 hydrogen bonds defined for protein.
    90 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: 0.14

  Time building geometry restraints manager: 0.14 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 468
        1.34 -     1.46: 443
        1.46 -     1.58: 1004
        1.58 -     1.70: 0
        1.70 -     1.82: 10
  Bond restraints: 1925
  Sorted by residual:
  bond pdb=" C   LYS B 311 "
       pdb=" O   LYS B 311 "
    ideal  model  delta    sigma   weight residual
    1.235  1.218  0.017 4.70e-03 4.53e+04 1.28e+01
  bond pdb=" C   LYS E 311 "
       pdb=" O   LYS E 311 "
    ideal  model  delta    sigma   weight residual
    1.235  1.219  0.016 4.70e-03 4.53e+04 1.20e+01
  bond pdb=" C   LYS D 311 "
       pdb=" O   LYS D 311 "
    ideal  model  delta    sigma   weight residual
    1.235  1.219  0.016 4.70e-03 4.53e+04 1.17e+01
  bond pdb=" C   LYS A 311 "
       pdb=" O   LYS A 311 "
    ideal  model  delta    sigma   weight residual
    1.235  1.219  0.016 4.70e-03 4.53e+04 1.16e+01
  bond pdb=" C   LYS C 311 "
       pdb=" O   LYS C 311 "
    ideal  model  delta    sigma   weight residual
    1.235  1.220  0.015 4.70e-03 4.53e+04 1.06e+01
  ... (remaining 1920 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.18: 1507
        1.18 -     2.36: 677
        2.36 -     3.54: 268
        3.54 -     4.72: 89
        4.72 -     5.90: 29
  Bond angle restraints: 2570
  Sorted by residual:
  angle pdb=" CA  HIS E 299 "
        pdb=" CB  HIS E 299 "
        pdb=" CG  HIS E 299 "
      ideal   model   delta    sigma   weight residual
     113.80  117.59   -3.79 1.00e+00 1.00e+00 1.44e+01
  angle pdb=" CA  HIS A 299 "
        pdb=" CB  HIS A 299 "
        pdb=" CG  HIS A 299 "
      ideal   model   delta    sigma   weight residual
     113.80  117.59   -3.79 1.00e+00 1.00e+00 1.43e+01
  angle pdb=" CA  HIS D 299 "
        pdb=" CB  HIS D 299 "
        pdb=" CG  HIS D 299 "
      ideal   model   delta    sigma   weight residual
     113.80  117.58   -3.78 1.00e+00 1.00e+00 1.43e+01
  angle pdb=" CA  HIS C 299 "
        pdb=" CB  HIS C 299 "
        pdb=" CG  HIS C 299 "
      ideal   model   delta    sigma   weight residual
     113.80  117.57   -3.77 1.00e+00 1.00e+00 1.42e+01
  angle pdb=" CA  HIS B 299 "
        pdb=" CB  HIS B 299 "
        pdb=" CG  HIS B 299 "
      ideal   model   delta    sigma   weight residual
     113.80  117.55   -3.75 1.00e+00 1.00e+00 1.41e+01
  ... (remaining 2565 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.90: 991
       11.90 -    23.79: 169
       23.79 -    35.69: 5
       35.69 -    47.58: 0
       47.58 -    59.48: 10
  Dihedral angle restraints: 1175
    sinusoidal: 470
      harmonic: 705
  Sorted by residual:
  dihedral pdb=" CA  THR C 319 "
           pdb=" C   THR C 319 "
           pdb=" N   PHE C 320 "
           pdb=" CA  PHE C 320 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.44   15.56     0      5.00e+00 4.00e-02 9.68e+00
  dihedral pdb=" CA  THR E 319 "
           pdb=" C   THR E 319 "
           pdb=" N   PHE E 320 "
           pdb=" CA  PHE E 320 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.45   15.55     0      5.00e+00 4.00e-02 9.67e+00
  dihedral pdb=" CA  THR A 319 "
           pdb=" C   THR A 319 "
           pdb=" N   PHE A 320 "
           pdb=" CA  PHE A 320 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.46   15.54     0      5.00e+00 4.00e-02 9.66e+00
  ... (remaining 1172 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 74
       0.038 -    0.077: 81
       0.077 -    0.115: 80
       0.115 -    0.153: 54
       0.153 -    0.191: 11
  Chirality restraints: 300
  Sorted by residual:
  chirality pdb=" CB  VAL A 287 "
            pdb=" CA  VAL A 287 "
            pdb=" CG1 VAL A 287 "
            pdb=" CG2 VAL A 287 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 9.14e-01
  chirality pdb=" CB  VAL C 287 "
            pdb=" CA  VAL C 287 "
            pdb=" CG1 VAL C 287 "
            pdb=" CG2 VAL C 287 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 9.06e-01
  chirality pdb=" CB  VAL B 287 "
            pdb=" CA  VAL B 287 "
            pdb=" CG1 VAL B 287 "
            pdb=" CG2 VAL B 287 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 9.05e-01
  ... (remaining 297 not shown)

  Planarity restraints: 320
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN C 288 "    0.012 2.00e-02 2.50e+03   2.47e-02 6.09e+00
        pdb=" C   GLN C 288 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   GLN C 288 "    0.016 2.00e-02 2.50e+03
        pdb=" N   SER C 289 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B 288 "   -0.012 2.00e-02 2.50e+03   2.45e-02 5.98e+00
        pdb=" C   GLN B 288 "    0.042 2.00e-02 2.50e+03
        pdb=" O   GLN B 288 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   SER B 289 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN E 288 "    0.012 2.00e-02 2.50e+03   2.44e-02 5.97e+00
        pdb=" C   GLN E 288 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   GLN E 288 "    0.016 2.00e-02 2.50e+03
        pdb=" N   SER E 289 "    0.014 2.00e-02 2.50e+03
  ... (remaining 317 not shown)

  Histogram of nonbonded interaction distances:
        2.44 -     2.93: 716
        2.93 -     3.42: 1571
        3.42 -     3.91: 3101
        3.91 -     4.41: 3388
        4.41 -     4.90: 5882
  Nonbonded interactions: 14658
  Sorted by model distance:
  nonbonded pdb=" C   ASN D 327 "
            pdb=" OD1 ASN D 327 "
     model   vdw
     2.436 3.270
  nonbonded pdb=" C   ASN B 327 "
            pdb=" OD1 ASN B 327 "
     model   vdw
     2.436 3.270
  nonbonded pdb=" C   ASN A 327 "
            pdb=" OD1 ASN A 327 "
     model   vdw
     2.436 3.270
  nonbonded pdb=" C   ASN C 327 "
            pdb=" OD1 ASN C 327 "
     model   vdw
     2.437 3.270
  nonbonded pdb=" C   ASN E 327 "
            pdb=" OD1 ASN E 327 "
     model   vdw
     2.437 3.270
  ... (remaining 14653 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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:             3.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.020
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     2.490
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:4.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
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      :  0.010   0.051   1925  Z= 0.661
  Angle     :  1.665   5.898   2570  Z= 1.047
  Chirality :  0.089   0.191    300
  Planarity :  0.007   0.025    320
  Dihedral  : 11.352  59.475    725
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  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: -3.09 (0.33), residues: 245
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.35 (0.25), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.024   0.012   TYR D 310 
 PHE   0.013   0.006   PHE B 320 
 HIS   0.011   0.005   HIS E 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.01037 ( 1925)
  covalent geometry    : angle       1.66511 ( 2570)
  hydrogen bonds       : bond        0.18151 (   30)
  hydrogen bonds       : angle       6.83031 (   90)

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

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

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.082 
Fit side-chains
REVERT: A  294 LYS cc_start: 0.8859 (mttp) cc_final: 0.8630 (mttt)
REVERT: A  296 ASN cc_start: 0.8853 (m110) cc_final: 0.8535 (m-40)
REVERT: B  281 LYS cc_start: 0.8436 (tttt) cc_final: 0.8127 (mtpp)
REVERT: B  294 LYS cc_start: 0.9005 (mttp) cc_final: 0.8788 (mppt)
REVERT: B  321 LYS cc_start: 0.8698 (tttm) cc_final: 0.8438 (tptp)
REVERT: C  294 LYS cc_start: 0.8926 (mttp) cc_final: 0.8597 (mttm)
REVERT: D  281 LYS cc_start: 0.8112 (tttt) cc_final: 0.7893 (ttpt)
REVERT: D  294 LYS cc_start: 0.8904 (mttp) cc_final: 0.8625 (mtpt)
REVERT: D  321 LYS cc_start: 0.8734 (tttm) cc_final: 0.8354 (tptp)
REVERT: E  294 LYS cc_start: 0.8779 (mttp) cc_final: 0.8416 (mtpm)
REVERT: E  321 LYS cc_start: 0.8858 (tttm) cc_final: 0.8510 (tptp)
  outliers start: 0
  outliers final: 1
  residues processed: 53
  average time/residue: 0.3155
  time to fit residues: 17.1231
Evaluate side-chains
  45 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 44
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  325 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0980
   chunk 13 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0020
   chunk 16 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.4388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.101373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.084102 restraints weight = 2038.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 1.44
r_work: 0.3241 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 2.83 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8675
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   1925  Z= 0.103
  Angle     :  0.615   7.400   2570  Z= 0.310
  Chirality :  0.051   0.139    300
  Planarity :  0.001   0.006    320
  Dihedral  :  5.492  18.327    257
  Min Nonbonded Distance : 2.691

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  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: -2.51 (0.40), residues: 245
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.90 (0.30), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR D 310 
 PHE   0.008   0.002   PHE A 320 
 HIS   0.005   0.002   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00188 ( 1925)
  covalent geometry    : angle       0.61488 ( 2570)
  hydrogen bonds       : bond        0.02936 (   30)
  hydrogen bonds       : angle       5.16689 (   90)

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

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

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.112 
Fit side-chains
REVERT: A  296 ASN cc_start: 0.8734 (m110) cc_final: 0.8454 (m-40)
REVERT: B  281 LYS cc_start: 0.8391 (tttt) cc_final: 0.8177 (mtpp)
REVERT: C  294 LYS cc_start: 0.8931 (mttp) cc_final: 0.8684 (mttm)
REVERT: D  294 LYS cc_start: 0.8957 (mttp) cc_final: 0.8753 (mtpt)
REVERT: E  294 LYS cc_start: 0.8957 (mttp) cc_final: 0.8707 (mttm)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.4448
  time to fit residues: 22.2896
Evaluate side-chains
  45 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 7 optimal weight:    9.9990
   chunk 15 optimal weight:    6.9990
   chunk 12 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 279 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.100796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.082861 restraints weight = 2091.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 1.48
r_work: 0.3234 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 2.78 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8685
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.013   1925  Z= 0.105
  Angle     :  0.595   5.667   2570  Z= 0.300
  Chirality :  0.051   0.133    300
  Planarity :  0.002   0.012    320
  Dihedral  :  5.236  14.526    255
  Min Nonbonded Distance : 2.684

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  8.44 %
    Favored  : 91.11 %
  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: -2.49 (0.41), residues: 245
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.89 (0.31), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR C 310 
 PHE   0.007   0.002   PHE B 320 
 HIS   0.005   0.002   HIS E 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 1925)
  covalent geometry    : angle       0.59493 ( 2570)
  hydrogen bonds       : bond        0.03364 (   30)
  hydrogen bonds       : angle       5.02615 (   90)

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

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

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 48
  time to evaluate  : 0.086 
Fit side-chains
REVERT: A  281 LYS cc_start: 0.7926 (ttmm) cc_final: 0.7279 (ttmt)
REVERT: A  296 ASN cc_start: 0.8738 (m110) cc_final: 0.8432 (m-40)
REVERT: A  325 LEU cc_start: 0.8873 (tt) cc_final: 0.8642 (OUTLIER)
REVERT: B  281 LYS cc_start: 0.8437 (tttt) cc_final: 0.8167 (mtpp)
REVERT: D  294 LYS cc_start: 0.8976 (mttp) cc_final: 0.8774 (mtpt)
REVERT: E  294 LYS cc_start: 0.9021 (mttp) cc_final: 0.8766 (mttm)
  outliers start: 1
  outliers final: 2
  residues processed: 48
  average time/residue: 0.4642
  time to fit residues: 22.7709
Evaluate side-chains
  44 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 43
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  285 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 8 optimal weight:    0.8980
   chunk 5 optimal weight:    8.9990
   chunk 22 optimal weight:    7.9990
   chunk 0 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   chunk 3 optimal weight:    0.0370
   chunk 21 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   overall best weight:    0.6658

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.102487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.084805 restraints weight = 2044.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 1.45
r_work: 0.3273 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3176 rms_B_bonded: 2.72 restraints_weight: 0.2500
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8662
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.009   1925  Z= 0.073
  Angle     :  0.549   7.975   2570  Z= 0.268
  Chirality :  0.050   0.125    300
  Planarity :  0.002   0.015    320
  Dihedral  :  4.953  14.233    255
  Min Nonbonded Distance : 2.686

Molprobity Statistics.
  All-atom Clashscore : 2.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  :  7.56 %
    Favored  : 90.67 %
  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: -2.38 (0.42), residues: 245
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.81 (0.32), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.000   TYR C 310 
 PHE   0.006   0.002   PHE C 320 
 HIS   0.004   0.001   HIS E 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00147 ( 1925)
  covalent geometry    : angle       0.54865 ( 2570)
  hydrogen bonds       : bond        0.02503 (   30)
  hydrogen bonds       : angle       4.51731 (   90)

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

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

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.087 
Fit side-chains
REVERT: A  296 ASN cc_start: 0.8734 (m110) cc_final: 0.8414 (m-40)
REVERT: B  281 LYS cc_start: 0.8421 (tttt) cc_final: 0.8150 (mtpp)
REVERT: C  321 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8104 (tttm)
REVERT: D  294 LYS cc_start: 0.8948 (mttp) cc_final: 0.8746 (mtpt)
REVERT: E  294 LYS cc_start: 0.8960 (mttp) cc_final: 0.8760 (mtpt)
  outliers start: 4
  outliers final: 3
  residues processed: 49
  average time/residue: 0.4479
  time to fit residues: 22.4517
Evaluate side-chains
  47 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain C residue  321 LYS
Chi-restraints excluded: chain D residue  285 SER
Chi-restraints excluded: chain E residue  285 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 5 optimal weight:    8.9990
   chunk 14 optimal weight:    5.9990
   chunk 3 optimal weight:    0.7980
   chunk 24 optimal weight:    4.9990
   chunk 23 optimal weight:    0.3980
   chunk 12 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 1 optimal weight:    7.9990
   chunk 8 optimal weight:    0.4980
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.9382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.099523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.083295 restraints weight = 2176.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 1.37
r_work: 0.3251 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.3154 rms_B_bonded: 2.70 restraints_weight: 0.2500
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8664
moved from start:          0.2174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.010   1925  Z= 0.084
  Angle     :  0.580   8.198   2570  Z= 0.278
  Chirality :  0.050   0.127    300
  Planarity :  0.002   0.015    320
  Dihedral  :  4.897  14.196    255
  Min Nonbonded Distance : 2.680

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  :  9.78 %
    Favored  : 88.44 %
  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: -2.39 (0.42), residues: 245
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.81 (0.32), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR C 310 
 PHE   0.007   0.002   PHE B 320 
 HIS   0.003   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00183 ( 1925)
  covalent geometry    : angle       0.58005 ( 2570)
  hydrogen bonds       : bond        0.02826 (   30)
  hydrogen bonds       : angle       4.62142 (   90)

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

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

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 45
  time to evaluate  : 0.084 
Fit side-chains
REVERT: A  281 LYS cc_start: 0.7941 (ttmm) cc_final: 0.7408 (ttmt)
REVERT: A  296 ASN cc_start: 0.8702 (m110) cc_final: 0.8384 (m-40)
REVERT: B  281 LYS cc_start: 0.8399 (tttt) cc_final: 0.8121 (mtpp)
REVERT: C  321 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8099 (tttm)
  outliers start: 4
  outliers final: 3
  residues processed: 47
  average time/residue: 0.4450
  time to fit residues: 21.3989
Evaluate side-chains
  48 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain C residue  321 LYS
Chi-restraints excluded: chain D residue  285 SER
Chi-restraints excluded: chain E residue  285 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 10 optimal weight:   10.0000
   chunk 13 optimal weight:    6.9990
   chunk 15 optimal weight:    9.9990
   chunk 6 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 1 optimal weight:    5.9990
   chunk 24 optimal weight:    5.9990
   chunk 0 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   overall best weight:    2.4984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.097927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.081285 restraints weight = 2150.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 1.38
r_work: 0.3225 rms_B_bonded: 1.60 restraints_weight: 0.5000
r_work: 0.3130 rms_B_bonded: 2.61 restraints_weight: 0.2500
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8689
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   1925  Z= 0.172
  Angle     :  0.679   7.868   2570  Z= 0.339
  Chirality :  0.054   0.141    300
  Planarity :  0.002   0.013    320
  Dihedral  :  5.242  14.691    255
  Min Nonbonded Distance : 2.678

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 10.22 %
    Favored  : 88.00 %
  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: -2.58 (0.40), residues: 245
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.96 (0.31), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR C 310 
 PHE   0.011   0.003   PHE B 320 
 HIS   0.004   0.002   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 1925)
  covalent geometry    : angle       0.67945 ( 2570)
  hydrogen bonds       : bond        0.04389 (   30)
  hydrogen bonds       : angle       5.34275 (   90)

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

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

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.085 
Fit side-chains
REVERT: B  281 LYS cc_start: 0.8389 (tttt) cc_final: 0.8129 (mtpp)
REVERT: C  321 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8120 (tttm)
  outliers start: 4
  outliers final: 3
  residues processed: 45
  average time/residue: 0.4549
  time to fit residues: 20.9140
Evaluate side-chains
  48 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain C residue  321 LYS
Chi-restraints excluded: chain D residue  285 SER
Chi-restraints excluded: chain E residue  285 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 17 optimal weight:    0.4980
   chunk 8 optimal weight:    0.4980
   chunk 5 optimal weight:    8.9990
   chunk 12 optimal weight:    6.9990
   chunk 9 optimal weight:    9.9990
   chunk 19 optimal weight:    0.6980
   chunk 21 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 11 optimal weight:    8.9990
   overall best weight:    1.7384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.098500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.081603 restraints weight = 2146.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 1.41
r_work: 0.3234 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 2.66 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8682
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   1925  Z= 0.124
  Angle     :  0.628   8.236   2570  Z= 0.310
  Chirality :  0.052   0.138    300
  Planarity :  0.002   0.014    320
  Dihedral  :  5.157  15.003    255
  Min Nonbonded Distance : 2.681

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 10.67 %
    Favored  : 87.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.51 (0.41), residues: 245
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.90 (0.31), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR C 310 
 PHE   0.009   0.002   PHE B 320 
 HIS   0.004   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 1925)
  covalent geometry    : angle       0.62795 ( 2570)
  hydrogen bonds       : bond        0.03775 (   30)
  hydrogen bonds       : angle       5.12692 (   90)

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

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

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.051 
Fit side-chains
REVERT: B  281 LYS cc_start: 0.8363 (tttt) cc_final: 0.8129 (mtpp)
REVERT: C  321 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8124 (tttm)
  outliers start: 4
  outliers final: 3
  residues processed: 48
  average time/residue: 0.4079
  time to fit residues: 20.0223
Evaluate side-chains
  48 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain C residue  321 LYS
Chi-restraints excluded: chain D residue  285 SER
Chi-restraints excluded: chain E residue  285 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 20 optimal weight:    6.9990
   chunk 17 optimal weight:    9.9990
   chunk 1 optimal weight:    7.9990
   chunk 21 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 8 optimal weight:    0.5980
   chunk 18 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    2.2786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.098125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.081712 restraints weight = 2217.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 1.39
r_work: 0.3225 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.3129 rms_B_bonded: 2.68 restraints_weight: 0.2500
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8690
moved from start:          0.2162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.019   1925  Z= 0.157
  Angle     :  0.681   8.203   2570  Z= 0.338
  Chirality :  0.054   0.143    300
  Planarity :  0.002   0.012    320
  Dihedral  :  5.298  15.134    255
  Min Nonbonded Distance : 2.678

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 11.11 %
    Favored  : 87.11 %
  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: -2.53 (0.40), residues: 245
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.92 (0.30), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR C 310 
 PHE   0.011   0.002   PHE B 320 
 HIS   0.004   0.002   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 1925)
  covalent geometry    : angle       0.68121 ( 2570)
  hydrogen bonds       : bond        0.04327 (   30)
  hydrogen bonds       : angle       5.42550 (   90)

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

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

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.080 
Fit side-chains
REVERT: B  281 LYS cc_start: 0.8369 (tttt) cc_final: 0.8132 (mtpp)
REVERT: C  321 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8142 (tttm)
  outliers start: 4
  outliers final: 3
  residues processed: 46
  average time/residue: 0.4419
  time to fit residues: 20.7579
Evaluate side-chains
  48 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain C residue  321 LYS
Chi-restraints excluded: chain D residue  285 SER
Chi-restraints excluded: chain E residue  285 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 10 optimal weight:    9.9990
   chunk 22 optimal weight:    4.9990
   chunk 21 optimal weight:    0.6980
   chunk 11 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 19 optimal weight:   10.0000
   chunk 14 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0030
   overall best weight:    1.0994

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.099418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.082949 restraints weight = 2175.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.38
r_work: 0.3244 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.3147 rms_B_bonded: 2.70 restraints_weight: 0.2500
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8673
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   1925  Z= 0.094
  Angle     :  0.608   8.514   2570  Z= 0.296
  Chirality :  0.051   0.132    300
  Planarity :  0.002   0.015    320
  Dihedral  :  5.072  15.004    255
  Min Nonbonded Distance : 2.680

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 10.67 %
    Favored  : 87.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.43 (0.41), residues: 245
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.84 (0.31), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR C 310 
 PHE   0.007   0.002   PHE B 320 
 HIS   0.003   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 1925)
  covalent geometry    : angle       0.60833 ( 2570)
  hydrogen bonds       : bond        0.03179 (   30)
  hydrogen bonds       : angle       4.91049 (   90)

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

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

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 45
  time to evaluate  : 0.048 
Fit side-chains
REVERT: B  281 LYS cc_start: 0.8369 (tttt) cc_final: 0.8105 (mtpp)
REVERT: C  321 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8107 (tttm)
  outliers start: 4
  outliers final: 3
  residues processed: 47
  average time/residue: 0.3670
  time to fit residues: 17.6400
Evaluate side-chains
  49 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 45
  time to evaluate  : 0.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain C residue  321 LYS
Chi-restraints excluded: chain D residue  285 SER
Chi-restraints excluded: chain E residue  285 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 2 optimal weight:   10.0000
   chunk 22 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   chunk 15 optimal weight:    8.9990
   chunk 0 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 1 optimal weight:    0.8980
   overall best weight:    1.5786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.098854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.082165 restraints weight = 2193.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 1.38
r_work: 0.3245 rms_B_bonded: 1.59 restraints_weight: 0.5000
r_work: 0.3153 rms_B_bonded: 2.60 restraints_weight: 0.2500
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8671
moved from start:          0.2198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.015   1925  Z= 0.118
  Angle     :  0.635   8.416   2570  Z= 0.312
  Chirality :  0.052   0.136    300
  Planarity :  0.002   0.015    320
  Dihedral  :  5.134  15.262    255
  Min Nonbonded Distance : 2.668

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 11.56 %
    Favored  : 86.67 %
  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: -2.46 (0.41), residues: 245
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.87 (0.31), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR C 310 
 PHE   0.009   0.002   PHE B 320 
 HIS   0.003   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 1925)
  covalent geometry    : angle       0.63539 ( 2570)
  hydrogen bonds       : bond        0.03640 (   30)
  hydrogen bonds       : angle       5.08995 (   90)

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

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

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 45
  time to evaluate  : 0.057 
Fit side-chains
REVERT: B  281 LYS cc_start: 0.8364 (tttt) cc_final: 0.8114 (mtpp)
REVERT: B  316 SER cc_start: 0.8956 (t) cc_final: 0.8739 (m)
REVERT: C  321 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8109 (tttm)
  outliers start: 4
  outliers final: 3
  residues processed: 47
  average time/residue: 0.4111
  time to fit residues: 19.7733
Evaluate side-chains
  48 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain C residue  321 LYS
Chi-restraints excluded: chain D residue  285 SER
Chi-restraints excluded: chain E residue  285 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 17 optimal weight:    8.9990
   chunk 19 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 1 optimal weight:    6.9990
   chunk 8 optimal weight:    4.9990
   chunk 15 optimal weight:   10.0000
   chunk 14 optimal weight:    5.9990
   chunk 5 optimal weight:    8.9990
   chunk 22 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 329 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.097416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.080742 restraints weight = 2195.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 1.38
r_work: 0.3222 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 2.63 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8698
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.030   1925  Z= 0.236
  Angle     :  0.769   7.954   2570  Z= 0.389
  Chirality :  0.058   0.151    300
  Planarity :  0.003   0.013    320
  Dihedral  :  5.510  15.272    255
  Min Nonbonded Distance : 2.654

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 11.56 %
    Favored  : 86.67 %
  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: -2.59 (0.39), residues: 245
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.97 (0.30), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.002   TYR C 310 
 PHE   0.013   0.003   PHE B 320 
 HIS   0.004   0.002   HIS E 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00589 ( 1925)
  covalent geometry    : angle       0.76872 ( 2570)
  hydrogen bonds       : bond        0.05199 (   30)
  hydrogen bonds       : angle       5.76493 (   90)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1077.02 seconds
wall clock time: 19 minutes 2.99 seconds (1142.99 seconds total)