Starting phenix.real_space_refine
on Sat Sep 12 08:31:43 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/5onv_3835/09_2026/5onv_3835.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5onv_3835/09_2026/5onv_3835.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/5onv_3835/09_2026/5onv_3835.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/5onv_3835/09_2026/5onv_3835.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5onv_3835/09_2026/5onv_3835.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5onv_3835/09_2026/5onv_3835.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/5onv_3835/09_2026/5onv_3835.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5onv_3835/09_2026/5onv_3835.map"
  }
  resolution = 4.1
  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=   0.013
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: 6
    Type Number    sf(0)   Gaussians
     P      10      5.49       5
     Mg      5      5.21       5
     S     105      5.16       5
     C    9235      2.51       5
     N    2470      2.21       5
     O    2815      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 91 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 14640
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2900
          Classifications: {'peptide': 371}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 351}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HIC:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 2.77, per 1000 atoms: 0.19
  Number of scatterers: 14640
  At special positions: 0
  Unit cell: (98.04, 85.5, 192.66, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S     105     16.00
     P      10     15.00
     Mg      5     11.99
     O    2815      8.00
     N    2470      7.00
     C    9235      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.31
  Conformation dependent library (CDL) restraints added in 690.8 milliseconds
  

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3430

  Finding SS restraints...
    Secondary structure from input PDB file:
      105 helices and 25 sheets defined
      52.3% alpha, 14.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 55 through 61
    Processing helix  chain 'A' and resid 78 through 93
    Processing helix  chain 'A' and resid 97 through 101
    Processing helix  chain 'A' and resid 113 through 124
    Processing helix  chain 'A' and resid 137 through 146
    Processing helix  chain 'A' and resid 171 through 175
    Processing helix  chain 'A' and resid 181 through 197
    Processing helix  chain 'A' and resid 202 through 217
    Processing helix  chain 'A' and resid 222 through 231
    Processing helix  chain 'A' and resid 252 through 260
      Proline residue:  A 258  - end of helix
    Processing helix  chain 'A' and resid 261 through 262
      No H-bonds generated for 'chain 'A' and resid 261 through 262'
    Processing helix  chain 'A' and resid 263 through 268
    Processing helix  chain 'A' and resid 273 through 284
    Processing helix  chain 'A' and resid 286 through 295
      removed outlier: 4.685A  pdb=" N   LYS A 291 " --> pdb=" O   ILE A 287 " (cutoff:3.500A)
      removed outlier: 5.835A  pdb=" N   ASP A 292 " --> pdb=" O   ASP A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 305
    Processing helix  chain 'A' and resid 308 through 321
    Processing helix  chain 'A' and resid 334 through 336
      No H-bonds generated for 'chain 'A' and resid 334 through 336'
    Processing helix  chain 'A' and resid 337 through 349
    Processing helix  chain 'A' and resid 350 through 355
    Processing helix  chain 'A' and resid 359 through 366
    Processing helix  chain 'A' and resid 367 through 374
    Processing helix  chain 'B' and resid 55 through 61
    Processing helix  chain 'B' and resid 78 through 93
    Processing helix  chain 'B' and resid 97 through 101
    Processing helix  chain 'B' and resid 113 through 124
    Processing helix  chain 'B' and resid 137 through 146
    Processing helix  chain 'B' and resid 171 through 175
    Processing helix  chain 'B' and resid 181 through 197
    Processing helix  chain 'B' and resid 202 through 217
    Processing helix  chain 'B' and resid 222 through 231
    Processing helix  chain 'B' and resid 252 through 260
      Proline residue:  B 258  - end of helix
    Processing helix  chain 'B' and resid 261 through 262
      No H-bonds generated for 'chain 'B' and resid 261 through 262'
    Processing helix  chain 'B' and resid 263 through 268
    Processing helix  chain 'B' and resid 273 through 284
    Processing helix  chain 'B' and resid 286 through 295
      removed outlier: 4.686A  pdb=" N   LYS B 291 " --> pdb=" O   ILE B 287 " (cutoff:3.500A)
      removed outlier: 5.835A  pdb=" N   ASP B 292 " --> pdb=" O   ASP B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 305
    Processing helix  chain 'B' and resid 308 through 321
    Processing helix  chain 'B' and resid 334 through 336
      No H-bonds generated for 'chain 'B' and resid 334 through 336'
    Processing helix  chain 'B' and resid 337 through 349
    Processing helix  chain 'B' and resid 350 through 355
    Processing helix  chain 'B' and resid 359 through 366
    Processing helix  chain 'B' and resid 367 through 374
    Processing helix  chain 'C' and resid 55 through 61
    Processing helix  chain 'C' and resid 78 through 93
    Processing helix  chain 'C' and resid 97 through 101
    Processing helix  chain 'C' and resid 113 through 124
    Processing helix  chain 'C' and resid 137 through 146
    Processing helix  chain 'C' and resid 171 through 175
    Processing helix  chain 'C' and resid 181 through 197
    Processing helix  chain 'C' and resid 202 through 217
    Processing helix  chain 'C' and resid 222 through 231
    Processing helix  chain 'C' and resid 252 through 260
      Proline residue:  C 258  - end of helix
    Processing helix  chain 'C' and resid 261 through 262
      No H-bonds generated for 'chain 'C' and resid 261 through 262'
    Processing helix  chain 'C' and resid 263 through 268
    Processing helix  chain 'C' and resid 273 through 284
    Processing helix  chain 'C' and resid 286 through 295
      removed outlier: 4.686A  pdb=" N   LYS C 291 " --> pdb=" O   ILE C 287 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   ASP C 292 " --> pdb=" O   ASP C 288 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 301 through 305
    Processing helix  chain 'C' and resid 308 through 321
    Processing helix  chain 'C' and resid 334 through 336
      No H-bonds generated for 'chain 'C' and resid 334 through 336'
    Processing helix  chain 'C' and resid 337 through 349
    Processing helix  chain 'C' and resid 350 through 355
    Processing helix  chain 'C' and resid 359 through 366
    Processing helix  chain 'C' and resid 367 through 374
    Processing helix  chain 'D' and resid 55 through 61
    Processing helix  chain 'D' and resid 78 through 93
    Processing helix  chain 'D' and resid 97 through 101
    Processing helix  chain 'D' and resid 113 through 124
    Processing helix  chain 'D' and resid 137 through 146
    Processing helix  chain 'D' and resid 171 through 175
    Processing helix  chain 'D' and resid 181 through 197
    Processing helix  chain 'D' and resid 202 through 217
    Processing helix  chain 'D' and resid 222 through 231
    Processing helix  chain 'D' and resid 252 through 260
      Proline residue:  D 258  - end of helix
    Processing helix  chain 'D' and resid 261 through 262
      No H-bonds generated for 'chain 'D' and resid 261 through 262'
    Processing helix  chain 'D' and resid 263 through 268
    Processing helix  chain 'D' and resid 273 through 284
    Processing helix  chain 'D' and resid 286 through 295
      removed outlier: 4.684A  pdb=" N   LYS D 291 " --> pdb=" O   ILE D 287 " (cutoff:3.500A)
      removed outlier: 5.835A  pdb=" N   ASP D 292 " --> pdb=" O   ASP D 288 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 301 through 305
    Processing helix  chain 'D' and resid 308 through 321
    Processing helix  chain 'D' and resid 334 through 336
      No H-bonds generated for 'chain 'D' and resid 334 through 336'
    Processing helix  chain 'D' and resid 337 through 349
    Processing helix  chain 'D' and resid 350 through 355
    Processing helix  chain 'D' and resid 359 through 366
    Processing helix  chain 'D' and resid 367 through 374
    Processing helix  chain 'E' and resid 55 through 61
    Processing helix  chain 'E' and resid 78 through 93
    Processing helix  chain 'E' and resid 97 through 101
    Processing helix  chain 'E' and resid 113 through 124
    Processing helix  chain 'E' and resid 137 through 146
    Processing helix  chain 'E' and resid 171 through 175
    Processing helix  chain 'E' and resid 181 through 197
    Processing helix  chain 'E' and resid 202 through 217
    Processing helix  chain 'E' and resid 222 through 231
    Processing helix  chain 'E' and resid 252 through 260
      Proline residue:  E 258  - end of helix
    Processing helix  chain 'E' and resid 261 through 262
      No H-bonds generated for 'chain 'E' and resid 261 through 262'
    Processing helix  chain 'E' and resid 263 through 268
    Processing helix  chain 'E' and resid 273 through 284
    Processing helix  chain 'E' and resid 286 through 295
      removed outlier: 4.685A  pdb=" N   LYS E 291 " --> pdb=" O   ILE E 287 " (cutoff:3.500A)
      removed outlier: 5.835A  pdb=" N   ASP E 292 " --> pdb=" O   ASP E 288 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 301 through 305
    Processing helix  chain 'E' and resid 308 through 321
    Processing helix  chain 'E' and resid 334 through 336
      No H-bonds generated for 'chain 'E' and resid 334 through 336'
    Processing helix  chain 'E' and resid 337 through 349
    Processing helix  chain 'E' and resid 350 through 355
    Processing helix  chain 'E' and resid 359 through 366
    Processing helix  chain 'E' and resid 367 through 374
    Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32
      removed outlier: 6.926A  pdb=" N   LEU A   8 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 8.586A  pdb=" N   THR A 106 " --> pdb=" O   LEU A   8 " (cutoff:3.500A)
      removed outlier: 8.434A  pdb=" N   CYS A  10 " --> pdb=" O   THR A 106 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54
    Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72
    Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178
    Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241
    Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32
      removed outlier: 6.926A  pdb=" N   LEU B   8 " --> pdb=" O   LEU B 104 " (cutoff:3.500A)
      removed outlier: 8.586A  pdb=" N   THR B 106 " --> pdb=" O   LEU B   8 " (cutoff:3.500A)
      removed outlier: 8.434A  pdb=" N   CYS B  10 " --> pdb=" O   THR B 106 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54
    Processing sheet with id=AA8, first strand: chain 'B' and resid 71 through 72
    Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 178
    Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 241
    Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 32
      removed outlier: 6.926A  pdb=" N   LEU C   8 " --> pdb=" O   LEU C 104 " (cutoff:3.500A)
      removed outlier: 8.586A  pdb=" N   THR C 106 " --> pdb=" O   LEU C   8 " (cutoff:3.500A)
      removed outlier: 8.435A  pdb=" N   CYS C  10 " --> pdb=" O   THR C 106 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54
    Processing sheet with id=AB4, first strand: chain 'C' and resid 71 through 72
    Processing sheet with id=AB5, first strand: chain 'C' and resid 176 through 178
    Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241
    Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 32
      removed outlier: 6.925A  pdb=" N   LEU D   8 " --> pdb=" O   LEU D 104 " (cutoff:3.500A)
      removed outlier: 8.586A  pdb=" N   THR D 106 " --> pdb=" O   LEU D   8 " (cutoff:3.500A)
      removed outlier: 8.435A  pdb=" N   CYS D  10 " --> pdb=" O   THR D 106 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 54
    Processing sheet with id=AB9, first strand: chain 'D' and resid 71 through 72
    Processing sheet with id=AC1, first strand: chain 'D' and resid 176 through 178
    Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 241
    Processing sheet with id=AC3, first strand: chain 'E' and resid 29 through 32
      removed outlier: 6.925A  pdb=" N   LEU E   8 " --> pdb=" O   LEU E 104 " (cutoff:3.500A)
      removed outlier: 8.586A  pdb=" N   THR E 106 " --> pdb=" O   LEU E   8 " (cutoff:3.500A)
      removed outlier: 8.434A  pdb=" N   CYS E  10 " --> pdb=" O   THR E 106 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'E' and resid 53 through 54
    Processing sheet with id=AC5, first strand: chain 'E' and resid 71 through 72
    Processing sheet with id=AC6, first strand: chain 'E' and resid 176 through 178
    Processing sheet with id=AC7, first strand: chain 'E' and resid 238 through 241

    780 hydrogen bonds defined for protein.
    2025 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: 2.67

  Time building geometry restraints manager: 1.72 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 3568
        1.33 -     1.45: 3352
        1.45 -     1.57: 7844
        1.57 -     1.69: 11
        1.69 -     1.81: 185
  Bond restraints: 14960
  Sorted by residual:
  bond pdb=" CA  ILE B 151 "
       pdb=" C   ILE B 151 "
    ideal  model  delta    sigma   weight residual
    1.522  1.481  0.041 1.21e-02 6.83e+03 1.16e+01
  bond pdb=" CA  ILE A 151 "
       pdb=" C   ILE A 151 "
    ideal  model  delta    sigma   weight residual
    1.522  1.481  0.041 1.21e-02 6.83e+03 1.14e+01
  bond pdb=" CA  ILE E 151 "
       pdb=" C   ILE E 151 "
    ideal  model  delta    sigma   weight residual
    1.522  1.481  0.041 1.21e-02 6.83e+03 1.13e+01
  bond pdb=" CA  ILE D 151 "
       pdb=" C   ILE D 151 "
    ideal  model  delta    sigma   weight residual
    1.522  1.481  0.041 1.21e-02 6.83e+03 1.12e+01
  bond pdb=" CA  ILE C 151 "
       pdb=" C   ILE C 151 "
    ideal  model  delta    sigma   weight residual
    1.522  1.482  0.040 1.21e-02 6.83e+03 1.11e+01
  ... (remaining 14955 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.76: 18932
        2.76 -     5.52: 1197
        5.52 -     8.27: 114
        8.27 -    11.03: 47
       11.03 -    13.79: 15
  Bond angle restraints: 20305
  Sorted by residual:
  angle pdb=" C   VAL B 129 "
        pdb=" N   PRO B 130 "
        pdb=" CA  PRO B 130 "
      ideal   model   delta    sigma   weight residual
     119.24  127.99   -8.75 1.04e+00 9.25e-01 7.08e+01
  angle pdb=" C   VAL E 129 "
        pdb=" N   PRO E 130 "
        pdb=" CA  PRO E 130 "
      ideal   model   delta    sigma   weight residual
     119.24  127.98   -8.74 1.04e+00 9.25e-01 7.06e+01
  angle pdb=" C   VAL D 129 "
        pdb=" N   PRO D 130 "
        pdb=" CA  PRO D 130 "
      ideal   model   delta    sigma   weight residual
     119.24  127.95   -8.71 1.04e+00 9.25e-01 7.01e+01
  angle pdb=" C   VAL A 129 "
        pdb=" N   PRO A 130 "
        pdb=" CA  PRO A 130 "
      ideal   model   delta    sigma   weight residual
     119.24  127.95   -8.71 1.04e+00 9.25e-01 7.01e+01
  angle pdb=" C   VAL C 129 "
        pdb=" N   PRO C 130 "
        pdb=" CA  PRO C 130 "
      ideal   model   delta    sigma   weight residual
     119.24  127.94   -8.70 1.04e+00 9.25e-01 7.00e+01
  ... (remaining 20300 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.98: 8735
       24.98 -    49.97: 195
       49.97 -    74.95: 55
       74.95 -    99.94: 5
       99.94 -   124.92: 5
  Dihedral angle restraints: 8995
    sinusoidal: 3635
      harmonic: 5360
  Sorted by residual:
  dihedral pdb=" C5' ADP B 401 "
           pdb=" O5' ADP B 401 "
           pdb=" PA  ADP B 401 "
           pdb=" O2A ADP B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   64.92 -124.92     1      2.00e+01 2.50e-03 3.77e+01
  dihedral pdb=" C5' ADP A 401 "
           pdb=" O5' ADP A 401 "
           pdb=" PA  ADP A 401 "
           pdb=" O2A ADP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   64.92 -124.91     1      2.00e+01 2.50e-03 3.77e+01
  dihedral pdb=" C5' ADP C 401 "
           pdb=" O5' ADP C 401 "
           pdb=" PA  ADP C 401 "
           pdb=" O2A ADP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   64.91 -124.91     1      2.00e+01 2.50e-03 3.77e+01
  ... (remaining 8992 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1159
       0.047 -    0.093: 794
       0.093 -    0.139: 229
       0.139 -    0.186: 68
       0.186 -    0.232: 5
  Chirality restraints: 2255
  Sorted by residual:
  chirality pdb=" CA  PRO E  32 "
            pdb=" N   PRO E  32 "
            pdb=" C   PRO E  32 "
            pdb=" CB  PRO E  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CA  PRO A  32 "
            pdb=" N   PRO A  32 "
            pdb=" C   PRO A  32 "
            pdb=" CB  PRO A  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CA  PRO B  32 "
            pdb=" N   PRO B  32 "
            pdb=" C   PRO B  32 "
            pdb=" CB  PRO B  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.33e+00
  ... (remaining 2252 not shown)

  Planarity restraints: 2595
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 375 "   -0.031 2.00e-02 2.50e+03   6.30e-02 3.97e+01
        pdb=" C   PHE A 375 "    0.109 2.00e-02 2.50e+03
        pdb=" O   PHE A 375 "   -0.039 2.00e-02 2.50e+03
        pdb=" OXT PHE A 375 "   -0.039 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE C 375 "   -0.031 2.00e-02 2.50e+03   6.30e-02 3.96e+01
        pdb=" C   PHE C 375 "    0.109 2.00e-02 2.50e+03
        pdb=" O   PHE C 375 "   -0.039 2.00e-02 2.50e+03
        pdb=" OXT PHE C 375 "   -0.039 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE D 375 "   -0.031 2.00e-02 2.50e+03   6.30e-02 3.96e+01
        pdb=" C   PHE D 375 "    0.109 2.00e-02 2.50e+03
        pdb=" O   PHE D 375 "   -0.039 2.00e-02 2.50e+03
        pdb=" OXT PHE D 375 "   -0.039 2.00e-02 2.50e+03
  ... (remaining 2592 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 73
        2.58 -     3.16: 13822
        3.16 -     3.74: 23147
        3.74 -     4.32: 35259
        4.32 -     4.90: 53364
  Nonbonded interactions: 125665
  Sorted by model distance:
  nonbonded pdb=" O1B ADP E 401 "
            pdb="MG    MG E 402 "
     model   vdw
     1.996 2.170
  nonbonded pdb=" O1B ADP B 401 "
            pdb="MG    MG B 402 "
     model   vdw
     1.996 2.170
  nonbonded pdb=" O1B ADP A 401 "
            pdb="MG    MG A 402 "
     model   vdw
     1.996 2.170
  nonbonded pdb=" O1B ADP C 401 "
            pdb="MG    MG C 402 "
     model   vdw
     1.996 2.170
  nonbonded pdb=" O1B ADP D 401 "
            pdb="MG    MG D 402 "
     model   vdw
     1.996 2.170
  ... (remaining 125660 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: 0.05
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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.650
  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:          0.210
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     14.510
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
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      :  0.013   0.059  14960  Z= 0.822
  Angle     :  1.559  13.788  20305  Z= 1.007
  Chirality :  0.065   0.232   2255
  Planarity :  0.018   0.148   2595
  Dihedral  : 11.903 124.921   5565
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  3.55 %
    Allowed  :  6.28 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  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: -2.61 (0.18), residues: 1830
  helix: -1.67 (0.14), residues: 840
  sheet: -1.16 (0.29), residues: 325
  loop : -1.83 (0.24), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 177 
 TYR   0.048   0.006   TYR C 306 
 PHE   0.024   0.004   PHE D 375 
 TRP   0.036   0.008   TRP C 340 
 HIS   0.007   0.002   HIS B  88 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01324 /  0.82 (14960)
  covalent geometry    : angle       1.55902 /  1.01 (20305)
  hydrogen bonds       : bond        0.14660 / 10.09 (  780)
  hydrogen bonds       : angle       7.95550 /  5.55 ( 2025)

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  729 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 729
  time to evaluate  : 0.612 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.6781 (m-30) cc_final: 0.6244 (t0)
REVERT: A   34 ILE cc_start: 0.9600 (mt) cc_final: 0.9175 (tp)
REVERT: A   78 ASN cc_start: 0.8024 (t0) cc_final: 0.6174 (t0)
REVERT: A   81 ASP cc_start: 0.8615 (m-30) cc_final: 0.7836 (m-30)
REVERT: A   86 TRP cc_start: 0.9000 (m-10) cc_final: 0.8463 (m-10)
REVERT: A  101 HIS cc_start: 0.8657 (p-80) cc_final: 0.8381 (p-80)
REVERT: A  103 THR cc_start: 0.9150 (m) cc_final: 0.8925 (t)
REVERT: A  205 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7334 (mt-10)
REVERT: A  212 ILE cc_start: 0.9101 (mt) cc_final: 0.8797 (mt)
REVERT: A  217 CYS cc_start: 0.8850 (m) cc_final: 0.8642 (m)
REVERT: A  287 ILE cc_start: 0.8526 (pt) cc_final: 0.8218 (tt)
REVERT: A  291 LYS cc_start: 0.8939 (tmmt) cc_final: 0.8398 (mptt)
REVERT: B   39 ARG cc_start: 0.7648 (ttp-170) cc_final: 0.7328 (ttp-170)
REVERT: B  153 LEU cc_start: 0.9277 (tp) cc_final: 0.8852 (mt)
REVERT: B  192 ILE cc_start: 0.8894 (pt) cc_final: 0.8645 (mm)
REVERT: B  280 ASN cc_start: 0.8454 (m-40) cc_final: 0.8098 (m-40)
REVERT: B  305 MET cc_start: 0.9134 (mmm) cc_final: 0.8281 (mmt)
REVERT: B  352 PHE cc_start: 0.8985 (t80) cc_final: 0.8538 (t80)
REVERT: B  370 VAL cc_start: 0.9205 (t) cc_final: 0.8988 (t)
REVERT: C   21 PHE cc_start: 0.6982 (m-80) cc_final: 0.6700 (m-80)
REVERT: C   47 MET cc_start: 0.5790 (mtm) cc_final: 0.5477 (ptp)
REVERT: C   78 ASN cc_start: 0.7367 (t0) cc_final: 0.5628 (t0)
REVERT: C   81 ASP cc_start: 0.8544 (m-30) cc_final: 0.7802 (m-30)
REVERT: C   87 HIS cc_start: 0.8818 (t70) cc_final: 0.8517 (t-170)
REVERT: C  161 HIS cc_start: 0.9368 (p90) cc_final: 0.9015 (p90)
REVERT: C  165 ILE cc_start: 0.9235 (mt) cc_final: 0.8850 (tp)
REVERT: C  176 MET cc_start: 0.7815 (mtt) cc_final: 0.7489 (mtp)
REVERT: C  227 MET cc_start: 0.8793 (tmm) cc_final: 0.8509 (tmm)
REVERT: C  267 ILE cc_start: 0.9221 (pt) cc_final: 0.8944 (mp)
REVERT: C  280 ASN cc_start: 0.8636 (m-40) cc_final: 0.8430 (m-40)
REVERT: C  292 ASP cc_start: 0.8383 (m-30) cc_final: 0.7878 (t0)
REVERT: C  305 MET cc_start: 0.8730 (mmm) cc_final: 0.8471 (mmt)
REVERT: C  340 TRP cc_start: 0.9034 (t60) cc_final: 0.8514 (t60)
REVERT: D   43 VAL cc_start: 0.8558 (t) cc_final: 0.7245 (t)
REVERT: D   47 MET cc_start: 0.6272 (mtm) cc_final: 0.5205 (ptp)
REVERT: D  106 THR cc_start: 0.7793 (t) cc_final: 0.7507 (t)
REVERT: D  127 PHE cc_start: 0.8855 (m-80) cc_final: 0.8612 (m-10)
REVERT: D  137 GLN cc_start: 0.8093 (mt0) cc_final: 0.7371 (mm-40)
REVERT: D  142 LEU cc_start: 0.9277 (mt) cc_final: 0.8956 (mt)
REVERT: D  155 SER cc_start: 0.8418 (t) cc_final: 0.8206 (t)
REVERT: D  157 ASP cc_start: 0.6757 (t70) cc_final: 0.6546 (t70)
REVERT: D  162 ASN cc_start: 0.8722 (t0) cc_final: 0.8288 (p0)
REVERT: D  165 ILE cc_start: 0.9133 (mt) cc_final: 0.8684 (tp)
REVERT: D  214 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7863 (mt-10)
REVERT: D  244 ASP cc_start: 0.9017 (p0) cc_final: 0.8807 (p0)
REVERT: D  270 GLU cc_start: 0.7542 (tt0) cc_final: 0.7237 (pt0)
REVERT: D  280 ASN cc_start: 0.9029 (m-40) cc_final: 0.7998 (m-40)
REVERT: D  288 ASP cc_start: 0.7521 (t70) cc_final: 0.7135 (t0)
REVERT: D  299 MET cc_start: 0.8340 (mtp) cc_final: 0.8128 (mtt)
REVERT: D  305 MET cc_start: 0.8509 (mmm) cc_final: 0.8294 (tpp)
REVERT: D  311 ASP cc_start: 0.8585 (m-30) cc_final: 0.8128 (t70)
REVERT: D  358 THR cc_start: 0.8877 (p) cc_final: 0.8602 (t)
REVERT: E   11 ASP cc_start: 0.8631 (t0) cc_final: 0.8362 (t0)
REVERT: E   21 PHE cc_start: 0.7217 (m-80) cc_final: 0.6829 (m-80)
REVERT: E   30 VAL cc_start: 0.9277 (t) cc_final: 0.9027 (m)
REVERT: E   43 VAL cc_start: 0.8529 (t) cc_final: 0.7362 (t)
REVERT: E   47 MET cc_start: 0.6952 (mtm) cc_final: 0.5810 (ttt)
REVERT: E   78 ASN cc_start: 0.8135 (t0) cc_final: 0.7279 (t0)
REVERT: E   87 HIS cc_start: 0.8871 (t70) cc_final: 0.8636 (t-170)
REVERT: E  104 LEU cc_start: 0.9137 (tp) cc_final: 0.8876 (tp)
REVERT: E  137 GLN cc_start: 0.8192 (mt0) cc_final: 0.7965 (mm-40)
REVERT: E  205 GLU cc_start: 0.7870 (mt-10) cc_final: 0.6965 (mt-10)
REVERT: E  211 ASP cc_start: 0.7563 (t70) cc_final: 0.7012 (t70)
REVERT: E  280 ASN cc_start: 0.9023 (m-40) cc_final: 0.7972 (m110)
REVERT: E  292 ASP cc_start: 0.8502 (m-30) cc_final: 0.8090 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 729
  average time/residue: 0.1250
  time to fit residues: 133.4827
Evaluate side-chains
  370 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 370
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 149 optimal weight:    7.9990
   overall best weight:    1.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 137 GLN
A 263 GLN
A 280 ASN
B  87 HIS
** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 173 HIS
** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 137 GLN
D  12 ASN
** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 353 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.094446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.082659 restraints weight = 35566.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.085691 restraints weight = 18975.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.087699 restraints weight = 11575.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.089061 restraints weight = 7741.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.090031 restraints weight = 5548.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.3790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  14960  Z= 0.161
  Angle     :  0.715   7.075  20305  Z= 0.373
  Chirality :  0.046   0.165   2255
  Planarity :  0.007   0.055   2595
  Dihedral  :  7.286  91.185   2085
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  4.81 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  2.17 %
    Favored  : 97.76 %
  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: -0.82 (0.19), residues: 1830
  helix:  0.23 (0.17), residues: 820
  sheet: -0.71 (0.29), residues: 325
  loop : -1.29 (0.23), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  39 
 TYR   0.018   0.001   TYR C 166 
 PHE   0.013   0.001   PHE A 127 
 TRP   0.017   0.002   TRP B  86 
 HIS   0.012   0.002   HIS C 275 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.16 (14960)
  covalent geometry    : angle       0.71517 /  0.37 (20305)
  hydrogen bonds       : bond        0.04477 /  3.05 (  780)
  hydrogen bonds       : angle       5.68851 /  4.01 ( 2025)

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  552 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 551
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 ASN cc_start: 0.8971 (t0) cc_final: 0.8434 (t0)
REVERT: A   24 ASP cc_start: 0.7160 (m-30) cc_final: 0.6488 (t70)
REVERT: A   34 ILE cc_start: 0.9568 (mt) cc_final: 0.9209 (tp)
REVERT: A   41 GLN cc_start: 0.7352 (tm-30) cc_final: 0.7002 (tm-30)
REVERT: A   43 VAL cc_start: 0.8078 (t) cc_final: 0.7709 (t)
REVERT: A   47 MET cc_start: 0.5229 (ptt) cc_final: 0.4938 (ptt)
REVERT: A   78 ASN cc_start: 0.7838 (t0) cc_final: 0.7636 (t0)
REVERT: A   82 MET cc_start: 0.8738 (tmm) cc_final: 0.8523 (tpt)
REVERT: A  118 LYS cc_start: 0.9104 (mmtt) cc_final: 0.8902 (mmtt)
REVERT: A  154 ASP cc_start: 0.8002 (t70) cc_final: 0.7148 (t0)
REVERT: A  161 HIS cc_start: 0.8348 (p90) cc_final: 0.7846 (p90)
REVERT: A  217 CYS cc_start: 0.8628 (m) cc_final: 0.8280 (m)
REVERT: A  252 ASN cc_start: 0.8912 (p0) cc_final: 0.8670 (p0)
REVERT: A  291 LYS cc_start: 0.8622 (tmmt) cc_final: 0.8385 (mptt)
REVERT: A  292 ASP cc_start: 0.7716 (m-30) cc_final: 0.7023 (t0)
REVERT: A  293 LEU cc_start: 0.9390 (mt) cc_final: 0.9187 (mp)
REVERT: B   31 PHE cc_start: 0.8890 (p90) cc_final: 0.8628 (p90)
REVERT: B   41 GLN cc_start: 0.7532 (tm-30) cc_final: 0.7214 (tm-30)
REVERT: B   47 MET cc_start: 0.5475 (mtm) cc_final: 0.4654 (tpp)
REVERT: B  105 LEU cc_start: 0.9385 (mp) cc_final: 0.9082 (mp)
REVERT: B  106 THR cc_start: 0.8438 (t) cc_final: 0.8040 (p)
REVERT: B  113 LYS cc_start: 0.8726 (ptmt) cc_final: 0.8499 (ptmt)
REVERT: B  117 GLU cc_start: 0.8386 (pt0) cc_final: 0.8178 (pp20)
REVERT: B  123 MET cc_start: 0.8716 (mmp) cc_final: 0.8465 (mmp)
REVERT: B  153 LEU cc_start: 0.9131 (tp) cc_final: 0.8540 (mt)
REVERT: B  192 ILE cc_start: 0.8620 (pt) cc_final: 0.8377 (pt)
REVERT: B  253 GLU cc_start: 0.7825 (mp0) cc_final: 0.7363 (mp0)
REVERT: B  362 TYR cc_start: 0.8329 (t80) cc_final: 0.8050 (t80)
REVERT: C   31 PHE cc_start: 0.8974 (p90) cc_final: 0.8717 (p90)
REVERT: C   80 ASP cc_start: 0.7704 (p0) cc_final: 0.7208 (p0)
REVERT: C   82 MET cc_start: 0.8181 (tmm) cc_final: 0.7895 (tmm)
REVERT: C  113 LYS cc_start: 0.8825 (ptmt) cc_final: 0.8351 (ttpt)
REVERT: C  161 HIS cc_start: 0.9027 (p90) cc_final: 0.8725 (p-80)
REVERT: C  227 MET cc_start: 0.8533 (tmm) cc_final: 0.8315 (tmm)
REVERT: C  246 GLN cc_start: 0.8373 (tp40) cc_final: 0.8093 (tp-100)
REVERT: C  252 ASN cc_start: 0.8720 (p0) cc_final: 0.8493 (p0)
REVERT: C  292 ASP cc_start: 0.8099 (m-30) cc_final: 0.7613 (t0)
REVERT: C  340 TRP cc_start: 0.8957 (t60) cc_final: 0.8339 (t60)
REVERT: D   47 MET cc_start: 0.5546 (mtm) cc_final: 0.4710 (ttt)
REVERT: D  121 GLN cc_start: 0.8736 (tp40) cc_final: 0.8384 (tp40)
REVERT: D  154 ASP cc_start: 0.8297 (t0) cc_final: 0.8025 (t0)
REVERT: D  162 ASN cc_start: 0.8187 (t0) cc_final: 0.7917 (p0)
REVERT: D  184 ASP cc_start: 0.8156 (t70) cc_final: 0.7917 (t70)
REVERT: D  217 CYS cc_start: 0.8084 (m) cc_final: 0.7733 (m)
REVERT: D  226 GLU cc_start: 0.7720 (tt0) cc_final: 0.7461 (tt0)
REVERT: D  305 MET cc_start: 0.8415 (mmm) cc_final: 0.7893 (tpp)
REVERT: D  314 GLN cc_start: 0.8494 (tt0) cc_final: 0.8193 (tm-30)
REVERT: D  316 GLU cc_start: 0.8197 (tp30) cc_final: 0.7704 (tp30)
REVERT: D  318 THR cc_start: 0.8940 (m) cc_final: 0.8584 (p)
REVERT: D  330 ILE cc_start: 0.9307 (mm) cc_final: 0.9084 (mm)
REVERT: D  355 MET cc_start: 0.8801 (mmm) cc_final: 0.8565 (mmm)
REVERT: D  356 TRP cc_start: 0.8471 (m100) cc_final: 0.8182 (m100)
REVERT: D  369 ILE cc_start: 0.9020 (tp) cc_final: 0.8810 (tp)
REVERT: E   47 MET cc_start: 0.6805 (mtm) cc_final: 0.6474 (ttt)
REVERT: E   51 ASP cc_start: 0.7629 (p0) cc_final: 0.7334 (p0)
REVERT: E   56 ASP cc_start: 0.8482 (p0) cc_final: 0.8247 (p0)
REVERT: E  121 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8184 (mm-40)
REVERT: E  154 ASP cc_start: 0.8483 (t0) cc_final: 0.8159 (t0)
REVERT: E  190 MET cc_start: 0.8352 (mtm) cc_final: 0.8044 (mtm)
REVERT: E  283 MET cc_start: 0.8583 (mmp) cc_final: 0.8314 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 552
  average time/residue: 0.1044
  time to fit residues: 88.1569
Evaluate side-chains
  345 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 345
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 79 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   chunk 16 optimal weight:    0.2980
   chunk 3 optimal weight:    7.9990
   chunk 80 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 8 optimal weight:    4.9990
   chunk 175 optimal weight:    7.9990
   chunk 14 optimal weight:    3.9990
   chunk 54 optimal weight:    7.9990
   chunk 32 optimal weight:    7.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 173 HIS
A 280 ASN
** B  12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 173 HIS
B 360 GLN
B 371 HIS
** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  12 ASN
E  87 HIS
E 137 GLN
** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.092437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.080804 restraints weight = 35936.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.083848 restraints weight = 18687.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.085808 restraints weight = 11207.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.087179 restraints weight = 7385.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.088161 restraints weight = 5233.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.4747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14960  Z= 0.139
  Angle     :  0.662   5.895  20305  Z= 0.335
  Chirality :  0.045   0.177   2255
  Planarity :  0.005   0.048   2595
  Dihedral  :  6.563  73.036   2085
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  4.10 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  2.24 %
    Favored  : 97.70 %
  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: -0.21 (0.19), residues: 1830
  helix:  0.70 (0.18), residues: 820
  sheet: -0.55 (0.29), residues: 315
  loop : -0.83 (0.24), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 335 
 TYR   0.030   0.001   TYR A 279 
 PHE   0.013   0.001   PHE E 255 
 TRP   0.010   0.002   TRP B  86 
 HIS   0.010   0.002   HIS C 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.14 (14960)
  covalent geometry    : angle       0.66183 /  0.34 (20305)
  hydrogen bonds       : bond        0.03897 /  2.68 (  780)
  hydrogen bonds       : angle       5.32276 /  3.77 ( 2025)

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  445 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 444
  time to evaluate  : 0.565 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.7162 (m-30) cc_final: 0.6521 (t0)
REVERT: A   34 ILE cc_start: 0.9637 (mt) cc_final: 0.9205 (tp)
REVERT: A   78 ASN cc_start: 0.7645 (t0) cc_final: 0.7429 (t0)
REVERT: A   86 TRP cc_start: 0.8925 (m-10) cc_final: 0.8640 (m-10)
REVERT: A  121 GLN cc_start: 0.8999 (pp30) cc_final: 0.8737 (pp30)
REVERT: A  154 ASP cc_start: 0.7887 (t70) cc_final: 0.6849 (t70)
REVERT: A  161 HIS cc_start: 0.8291 (p90) cc_final: 0.7633 (p90)
REVERT: A  217 CYS cc_start: 0.8640 (m) cc_final: 0.8263 (m)
REVERT: B   41 GLN cc_start: 0.7461 (tm-30) cc_final: 0.7260 (tm-30)
REVERT: B   43 VAL cc_start: 0.8598 (t) cc_final: 0.8124 (t)
REVERT: B   83 GLU cc_start: 0.9016 (pp20) cc_final: 0.8452 (pt0)
REVERT: B  117 GLU cc_start: 0.8550 (pt0) cc_final: 0.8235 (pp20)
REVERT: B  153 LEU cc_start: 0.9147 (tp) cc_final: 0.8462 (mt)
REVERT: B  253 GLU cc_start: 0.7843 (mp0) cc_final: 0.7602 (mp0)
REVERT: B  305 MET cc_start: 0.9011 (mmm) cc_final: 0.8125 (mmt)
REVERT: C    9 VAL cc_start: 0.9471 (p) cc_final: 0.9264 (m)
REVERT: C   81 ASP cc_start: 0.8515 (m-30) cc_final: 0.8282 (m-30)
REVERT: C   82 MET cc_start: 0.8528 (tmm) cc_final: 0.8017 (tmm)
REVERT: C  113 LYS cc_start: 0.8957 (ptmt) cc_final: 0.8604 (ttpt)
REVERT: C  119 MET cc_start: 0.9416 (ttp) cc_final: 0.9157 (ttp)
REVERT: C  227 MET cc_start: 0.8626 (tmm) cc_final: 0.8388 (tmm)
REVERT: C  276 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7469 (tm-30)
REVERT: C  292 ASP cc_start: 0.8086 (m-30) cc_final: 0.7723 (t0)
REVERT: C  340 TRP cc_start: 0.8926 (t60) cc_final: 0.8114 (t60)
REVERT: D   47 MET cc_start: 0.5451 (mtm) cc_final: 0.4309 (ttt)
REVERT: D   72 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7734 (tm-30)
REVERT: D   75 ILE cc_start: 0.9152 (mt) cc_final: 0.8657 (pt)
REVERT: D  113 LYS cc_start: 0.8634 (ptmt) cc_final: 0.7839 (ttmt)
REVERT: D  117 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8423 (mt-10)
REVERT: D  154 ASP cc_start: 0.8433 (t0) cc_final: 0.8198 (t0)
REVERT: D  184 ASP cc_start: 0.8216 (t70) cc_final: 0.7888 (t70)
REVERT: D  226 GLU cc_start: 0.7788 (tt0) cc_final: 0.7436 (tt0)
REVERT: D  269 MET cc_start: 0.8016 (tpp) cc_final: 0.7811 (tpp)
REVERT: D  299 MET cc_start: 0.8042 (mtt) cc_final: 0.7398 (mtt)
REVERT: D  305 MET cc_start: 0.8418 (mmm) cc_final: 0.8048 (tpp)
REVERT: D  356 TRP cc_start: 0.8422 (m100) cc_final: 0.7936 (m100)
REVERT: D  369 ILE cc_start: 0.8955 (tp) cc_final: 0.8665 (tp)
REVERT: E   39 ARG cc_start: 0.8691 (ttp-170) cc_final: 0.8102 (ttt90)
REVERT: E   43 VAL cc_start: 0.8223 (t) cc_final: 0.7806 (t)
REVERT: E   47 MET cc_start: 0.6569 (mtm) cc_final: 0.5321 (ttt)
REVERT: E   72 GLU cc_start: 0.8538 (pp20) cc_final: 0.8081 (pp20)
REVERT: E   80 ASP cc_start: 0.8319 (t70) cc_final: 0.7700 (t0)
REVERT: E  137 GLN cc_start: 0.8307 (mt0) cc_final: 0.8077 (mt0)
REVERT: E  154 ASP cc_start: 0.8466 (t0) cc_final: 0.8190 (t0)
REVERT: E  283 MET cc_start: 0.8569 (mmp) cc_final: 0.8308 (tpp)
REVERT: E  371 HIS cc_start: 0.7564 (t-90) cc_final: 0.7346 (t-90)
  outliers start: 1
  outliers final: 0
  residues processed: 445
  average time/residue: 0.0977
  time to fit residues: 67.3593
Evaluate side-chains
  300 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 300
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 43 optimal weight:    5.9990
   chunk 115 optimal weight:    4.9990
   chunk 178 optimal weight:    2.9990
   chunk 98 optimal weight:    8.9990
   chunk 48 optimal weight:    3.9990
   chunk 70 optimal weight:    8.9990
   chunk 82 optimal weight:    3.9990
   chunk 35 optimal weight:   10.0000
   chunk 47 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 173 HIS
B  12 ASN
** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 173 HIS
B 280 ASN
C  87 HIS
** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  12 ASN
E  40 HIS
E 111 ASN
** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 297 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.083791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.072467 restraints weight = 37482.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.075173 restraints weight = 20285.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.076958 restraints weight = 12554.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.078205 restraints weight = 8531.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.079075 restraints weight = 6208.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.5820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  14960  Z= 0.275
  Angle     :  0.795  10.045  20305  Z= 0.406
  Chirality :  0.049   0.182   2255
  Planarity :  0.005   0.042   2595
  Dihedral  :  6.864  61.821   2085
  Min Nonbonded Distance : 1.679

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  5.57 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  3.96 %
    Favored  : 95.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.47 (0.19), residues: 1830
  helix:  0.36 (0.17), residues: 825
  sheet: -0.82 (0.29), residues: 325
  loop : -0.69 (0.24), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  39 
 TYR   0.032   0.002   TYR A 279 
 PHE   0.024   0.002   PHE B 255 
 TRP   0.019   0.003   TRP C  79 
 HIS   0.011   0.002   HIS B 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00618 /  0.27 (14960)
  covalent geometry    : angle       0.79532 /  0.41 (20305)
  hydrogen bonds       : bond        0.04730 /  3.25 (  780)
  hydrogen bonds       : angle       5.42745 /  3.80 ( 2025)

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  345 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 344
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.7711 (m-30) cc_final: 0.7182 (t0)
REVERT: A   34 ILE cc_start: 0.9683 (mt) cc_final: 0.9384 (tp)
REVERT: A  121 GLN cc_start: 0.9136 (pp30) cc_final: 0.8887 (pp30)
REVERT: A  154 ASP cc_start: 0.8188 (t70) cc_final: 0.7573 (t70)
REVERT: A  217 CYS cc_start: 0.8382 (m) cc_final: 0.8086 (m)
REVERT: A  292 ASP cc_start: 0.7751 (m-30) cc_final: 0.7275 (t0)
REVERT: B   83 GLU cc_start: 0.8879 (pp20) cc_final: 0.8570 (pt0)
REVERT: B   91 TYR cc_start: 0.8996 (m-80) cc_final: 0.8613 (m-10)
REVERT: B  113 LYS cc_start: 0.8841 (ptmt) cc_final: 0.8572 (pttm)
REVERT: B  305 MET cc_start: 0.9065 (mmm) cc_final: 0.8263 (tpp)
REVERT: C    9 VAL cc_start: 0.9689 (p) cc_final: 0.9449 (m)
REVERT: C   80 ASP cc_start: 0.8009 (p0) cc_final: 0.7665 (p0)
REVERT: C   82 MET cc_start: 0.8515 (tmm) cc_final: 0.8029 (tmm)
REVERT: C  190 MET cc_start: 0.8401 (mtm) cc_final: 0.8080 (mtt)
REVERT: C  227 MET cc_start: 0.8628 (tmm) cc_final: 0.8326 (tmm)
REVERT: C  269 MET cc_start: 0.8004 (mmm) cc_final: 0.7701 (tpp)
REVERT: C  276 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7592 (tm-30)
REVERT: C  283 MET cc_start: 0.8526 (mmm) cc_final: 0.8298 (mmm)
REVERT: C  288 ASP cc_start: 0.6962 (t70) cc_final: 0.6675 (t70)
REVERT: C  292 ASP cc_start: 0.8097 (m-30) cc_final: 0.7702 (t0)
REVERT: D   75 ILE cc_start: 0.9400 (mt) cc_final: 0.9078 (pt)
REVERT: D  184 ASP cc_start: 0.8415 (t70) cc_final: 0.8123 (t70)
REVERT: D  305 MET cc_start: 0.8389 (mmm) cc_final: 0.8114 (tpp)
REVERT: D  316 GLU cc_start: 0.8372 (tp30) cc_final: 0.7931 (tp30)
REVERT: E   72 GLU cc_start: 0.9008 (pp20) cc_final: 0.8567 (pp20)
REVERT: E   80 ASP cc_start: 0.8424 (t70) cc_final: 0.8123 (t0)
REVERT: E  154 ASP cc_start: 0.8537 (t0) cc_final: 0.8217 (t0)
REVERT: E  283 MET cc_start: 0.8796 (mmp) cc_final: 0.8388 (tpp)
REVERT: E  305 MET cc_start: 0.7738 (mmt) cc_final: 0.7309 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 345
  average time/residue: 0.1004
  time to fit residues: 54.7585
Evaluate side-chains
  254 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 254
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 117 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 118 optimal weight:    0.9990
   chunk 10 optimal weight:    6.9990
   chunk 90 optimal weight:    0.6980
   chunk 100 optimal weight:    3.9990
   chunk 107 optimal weight:    6.9990
   chunk 113 optimal weight:    0.1980
   chunk 160 optimal weight:    0.0770
   chunk 101 optimal weight:    0.9990
   overall best weight:    0.5942

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  12 ASN
** B  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 173 HIS
E 111 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.089774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.078534 restraints weight = 35993.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.081440 restraints weight = 18888.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.083355 restraints weight = 11356.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.084571 restraints weight = 7493.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.085489 restraints weight = 5358.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.6026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071  14960  Z= 0.125
  Angle     :  0.653   7.764  20305  Z= 0.327
  Chirality :  0.045   0.180   2255
  Planarity :  0.004   0.039   2595
  Dihedral  :  6.395  64.936   2085
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 11.87
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.54 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  2.75 %
    Favored  : 97.19 %
  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: -0.05 (0.20), residues: 1830
  helix:  0.73 (0.18), residues: 820
  sheet: -0.79 (0.28), residues: 325
  loop : -0.41 (0.25), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 206 
 TYR   0.031   0.001   TYR A 279 
 PHE   0.018   0.001   PHE D 352 
 TRP   0.018   0.002   TRP E  86 
 HIS   0.008   0.001   HIS B 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.12 (14960)
  covalent geometry    : angle       0.65330 /  0.33 (20305)
  hydrogen bonds       : bond        0.03653 /  2.53 (  780)
  hydrogen bonds       : angle       5.10116 /  3.61 ( 2025)

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  376 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 375
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.7575 (m-30) cc_final: 0.7181 (t0)
REVERT: A   34 ILE cc_start: 0.9657 (mt) cc_final: 0.9338 (tp)
REVERT: A  121 GLN cc_start: 0.9227 (pp30) cc_final: 0.9006 (pp30)
REVERT: A  154 ASP cc_start: 0.7912 (t70) cc_final: 0.7236 (t70)
REVERT: A  217 CYS cc_start: 0.8420 (m) cc_final: 0.8120 (m)
REVERT: A  240 TYR cc_start: 0.8670 (t80) cc_final: 0.8355 (t80)
REVERT: A  292 ASP cc_start: 0.7882 (m-30) cc_final: 0.7367 (t0)
REVERT: A  305 MET cc_start: 0.8333 (mmm) cc_final: 0.7626 (tpp)
REVERT: B   82 MET cc_start: 0.8261 (mmm) cc_final: 0.7957 (tpt)
REVERT: B   91 TYR cc_start: 0.9019 (m-80) cc_final: 0.8712 (m-10)
REVERT: B  113 LYS cc_start: 0.8890 (ptmt) cc_final: 0.8550 (pttt)
REVERT: B  200 PHE cc_start: 0.8978 (m-80) cc_final: 0.8543 (m-80)
REVERT: B  305 MET cc_start: 0.9051 (mmm) cc_final: 0.8384 (tpp)
REVERT: C   82 MET cc_start: 0.8366 (tmm) cc_final: 0.8061 (tmm)
REVERT: C  222 ASP cc_start: 0.7132 (p0) cc_final: 0.6793 (p0)
REVERT: C  227 MET cc_start: 0.8514 (tmm) cc_final: 0.8271 (tmm)
REVERT: C  269 MET cc_start: 0.7664 (mmm) cc_final: 0.7359 (tpp)
REVERT: C  276 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7571 (tm-30)
REVERT: C  292 ASP cc_start: 0.7940 (m-30) cc_final: 0.7661 (t0)
REVERT: D  316 GLU cc_start: 0.8339 (tp30) cc_final: 0.7842 (tp30)
REVERT: E   72 GLU cc_start: 0.8908 (pp20) cc_final: 0.8466 (pp20)
REVERT: E   87 HIS cc_start: 0.8592 (t-90) cc_final: 0.8360 (t-90)
REVERT: E  154 ASP cc_start: 0.8476 (t0) cc_final: 0.8152 (t0)
REVERT: E  157 ASP cc_start: 0.7022 (t70) cc_final: 0.6510 (t70)
REVERT: E  283 MET cc_start: 0.8626 (mmp) cc_final: 0.8395 (tpp)
REVERT: E  305 MET cc_start: 0.7735 (mmt) cc_final: 0.7282 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 376
  average time/residue: 0.1005
  time to fit residues: 59.6383
Evaluate side-chains
  267 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 267
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 168 optimal weight:    7.9990
   chunk 35 optimal weight:    8.9990
   chunk 169 optimal weight:    4.9990
   chunk 184 optimal weight:    8.9990
   chunk 108 optimal weight:    9.9990
   chunk 37 optimal weight:   10.0000
   chunk 121 optimal weight:    6.9990
   chunk 154 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 103 optimal weight:    3.9990
   overall best weight:    5.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 137 GLN
** B  12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 280 ASN
C  41 GLN
C  87 HIS
D  87 HIS
** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  12 ASN
** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 173 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.077962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.067247 restraints weight = 38496.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.069777 restraints weight = 20317.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.071478 restraints weight = 12314.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.072543 restraints weight = 8235.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.073369 restraints weight = 5998.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.6517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.059  14960  Z= 0.349
  Angle     :  0.845  11.138  20305  Z= 0.431
  Chirality :  0.050   0.195   2255
  Planarity :  0.005   0.042   2595
  Dihedral  :  7.058  63.349   2085
  Min Nonbonded Distance : 1.820

Molprobity Statistics.
  All-atom Clashscore : 14.01
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  6.01 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  3.00 %
    Favored  : 96.93 %
  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: -0.54 (0.19), residues: 1830
  helix:  0.34 (0.17), residues: 825
  sheet: -0.87 (0.29), residues: 325
  loop : -0.78 (0.24), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 290 
 TYR   0.028   0.003   TYR B 198 
 PHE   0.027   0.002   PHE B 255 
 TRP   0.027   0.003   TRP B 356 
 HIS   0.009   0.002   HIS B 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00778 /  0.35 (14960)
  covalent geometry    : angle       0.84514 /  0.43 (20305)
  hydrogen bonds       : bond        0.05067 /  3.48 (  780)
  hydrogen bonds       : angle       5.58986 /  3.91 ( 2025)

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 319
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 GLN cc_start: 0.7837 (tm-30) cc_final: 0.7473 (tm-30)
REVERT: A   43 VAL cc_start: 0.8532 (t) cc_final: 0.7883 (t)
REVERT: A   47 MET cc_start: 0.4838 (ptt) cc_final: 0.4039 (ptt)
REVERT: A   78 ASN cc_start: 0.8003 (t0) cc_final: 0.7732 (t0)
REVERT: A   82 MET cc_start: 0.8779 (tmm) cc_final: 0.8519 (tmm)
REVERT: A  121 GLN cc_start: 0.9378 (pp30) cc_final: 0.9042 (pp30)
REVERT: A  154 ASP cc_start: 0.8213 (t70) cc_final: 0.7599 (t70)
REVERT: A  217 CYS cc_start: 0.8579 (m) cc_final: 0.8293 (m)
REVERT: A  237 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8367 (mt-10)
REVERT: A  246 GLN cc_start: 0.8739 (mp-120) cc_final: 0.8344 (mp10)
REVERT: A  283 MET cc_start: 0.9136 (mmm) cc_final: 0.8878 (mmp)
REVERT: A  287 ILE cc_start: 0.8722 (pt) cc_final: 0.8452 (tt)
REVERT: B   91 TYR cc_start: 0.9104 (m-80) cc_final: 0.8586 (m-10)
REVERT: B  113 LYS cc_start: 0.9052 (ptmt) cc_final: 0.8715 (pttt)
REVERT: B  283 MET cc_start: 0.8597 (mmt) cc_final: 0.8338 (mmm)
REVERT: B  305 MET cc_start: 0.9106 (mmm) cc_final: 0.8303 (mmt)
REVERT: B  336 LYS cc_start: 0.8980 (tttt) cc_final: 0.8735 (ttmt)
REVERT: C   80 ASP cc_start: 0.8199 (p0) cc_final: 0.7819 (p0)
REVERT: C   82 MET cc_start: 0.8727 (tmm) cc_final: 0.8222 (tmm)
REVERT: C  121 GLN cc_start: 0.8863 (tm-30) cc_final: 0.8523 (tm-30)
REVERT: C  227 MET cc_start: 0.8743 (tmm) cc_final: 0.8387 (tmm)
REVERT: C  246 GLN cc_start: 0.8560 (tp-100) cc_final: 0.8332 (tp-100)
REVERT: C  253 GLU cc_start: 0.7920 (mp0) cc_final: 0.7686 (mp0)
REVERT: C  269 MET cc_start: 0.7962 (mmm) cc_final: 0.7733 (ttm)
REVERT: C  276 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7684 (tm-30)
REVERT: C  283 MET cc_start: 0.8617 (mmm) cc_final: 0.8364 (mmm)
REVERT: C  288 ASP cc_start: 0.7070 (t70) cc_final: 0.6771 (t70)
REVERT: C  292 ASP cc_start: 0.8001 (m-30) cc_final: 0.7701 (t0)
REVERT: C  299 MET cc_start: 0.8747 (ttm) cc_final: 0.8206 (mtp)
REVERT: D   75 ILE cc_start: 0.9400 (mt) cc_final: 0.9046 (pt)
REVERT: D   82 MET cc_start: 0.9254 (tmm) cc_final: 0.8922 (tmm)
REVERT: D  113 LYS cc_start: 0.8388 (ptpt) cc_final: 0.8024 (ptpt)
REVERT: D  257 CYS cc_start: 0.9378 (t) cc_final: 0.9143 (t)
REVERT: D  292 ASP cc_start: 0.8265 (m-30) cc_final: 0.7947 (t0)
REVERT: D  316 GLU cc_start: 0.8602 (tp30) cc_final: 0.7993 (tp30)
REVERT: D  352 PHE cc_start: 0.9031 (t80) cc_final: 0.8743 (t80)
REVERT: E   44 MET cc_start: 0.8733 (tmm) cc_final: 0.8065 (tmm)
REVERT: E   72 GLU cc_start: 0.9161 (pp20) cc_final: 0.8600 (pp20)
REVERT: E  105 LEU cc_start: 0.8906 (tp) cc_final: 0.8263 (tp)
REVERT: E  154 ASP cc_start: 0.8604 (t0) cc_final: 0.8262 (t0)
REVERT: E  157 ASP cc_start: 0.7567 (t70) cc_final: 0.6874 (t70)
REVERT: E  283 MET cc_start: 0.8686 (mmp) cc_final: 0.8327 (tpp)
REVERT: E  305 MET cc_start: 0.8108 (mmt) cc_final: 0.7718 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 320
  average time/residue: 0.1012
  time to fit residues: 50.7725
Evaluate side-chains
  235 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 96 optimal weight:    0.9990
   chunk 173 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 156 optimal weight:    0.8980
   chunk 139 optimal weight:    3.9990
   chunk 116 optimal weight:    7.9990
   chunk 38 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 133 optimal weight:    0.9990
   chunk 78 optimal weight:   10.0000
   chunk 141 optimal weight:    0.9990
   overall best weight:    0.9586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  87 HIS
** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  12 ASN
** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  41 GLN
C 371 HIS
** E 111 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 = 0.3112 r_free = 0.3112 target = 0.084610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.073357 restraints weight = 36208.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.076078 restraints weight = 18871.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.077936 restraints weight = 11426.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.079148 restraints weight = 7547.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.080067 restraints weight = 5418.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.6638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  14960  Z= 0.130
  Angle     :  0.673   8.065  20305  Z= 0.337
  Chirality :  0.045   0.198   2255
  Planarity :  0.004   0.041   2595
  Dihedral  :  6.624  66.206   2085
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.54 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  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: -0.17 (0.20), residues: 1830
  helix:  0.60 (0.18), residues: 820
  sheet: -0.72 (0.30), residues: 315
  loop : -0.50 (0.24), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 147 
 TYR   0.014   0.001   TYR B 166 
 PHE   0.011   0.001   PHE E 255 
 TRP   0.017   0.002   TRP D  86 
 HIS   0.007   0.001   HIS B 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.13 (14960)
  covalent geometry    : angle       0.67303 /  0.34 (20305)
  hydrogen bonds       : bond        0.03754 /  2.58 (  780)
  hydrogen bonds       : angle       5.15667 /  3.62 ( 2025)

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  358 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 358
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 GLN cc_start: 0.7560 (tm-30) cc_final: 0.7247 (tm-30)
REVERT: A   47 MET cc_start: 0.4540 (ptt) cc_final: 0.3951 (ptt)
REVERT: A   78 ASN cc_start: 0.7911 (t0) cc_final: 0.7639 (t0)
REVERT: A  154 ASP cc_start: 0.7839 (t70) cc_final: 0.7096 (t70)
REVERT: A  217 CYS cc_start: 0.8534 (m) cc_final: 0.8109 (m)
REVERT: A  287 ILE cc_start: 0.8667 (pt) cc_final: 0.8340 (tt)
REVERT: A  292 ASP cc_start: 0.7949 (m-30) cc_final: 0.7620 (t0)
REVERT: A  305 MET cc_start: 0.8387 (mmm) cc_final: 0.7944 (ttp)
REVERT: A  360 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8612 (tm-30)
REVERT: B   91 TYR cc_start: 0.9098 (m-80) cc_final: 0.8662 (m-10)
REVERT: B  113 LYS cc_start: 0.9002 (ptmt) cc_final: 0.8583 (pttt)
REVERT: B  115 ASN cc_start: 0.9034 (m-40) cc_final: 0.8425 (t0)
REVERT: B  297 ASN cc_start: 0.8556 (m-40) cc_final: 0.8229 (m-40)
REVERT: B  305 MET cc_start: 0.9009 (mmm) cc_final: 0.8531 (tpp)
REVERT: C   82 MET cc_start: 0.8408 (tmm) cc_final: 0.8149 (tmm)
REVERT: C  121 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8492 (tm-30)
REVERT: C  227 MET cc_start: 0.8624 (tmm) cc_final: 0.8348 (tmm)
REVERT: C  246 GLN cc_start: 0.8593 (tp-100) cc_final: 0.8331 (tp-100)
REVERT: C  253 GLU cc_start: 0.7880 (mp0) cc_final: 0.7674 (mp0)
REVERT: C  276 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7492 (tm-30)
REVERT: C  288 ASP cc_start: 0.7078 (t70) cc_final: 0.6816 (t70)
REVERT: C  292 ASP cc_start: 0.8029 (m-30) cc_final: 0.7722 (t0)
REVERT: C  299 MET cc_start: 0.8624 (ttm) cc_final: 0.8335 (mtp)
REVERT: D   82 MET cc_start: 0.9216 (tmm) cc_final: 0.8794 (tmm)
REVERT: D  184 ASP cc_start: 0.8317 (t70) cc_final: 0.7992 (t0)
REVERT: D  316 GLU cc_start: 0.8482 (tp30) cc_final: 0.7932 (tp30)
REVERT: D  356 TRP cc_start: 0.8536 (m100) cc_final: 0.8320 (m100)
REVERT: E   72 GLU cc_start: 0.9071 (pp20) cc_final: 0.8556 (pp20)
REVERT: E  154 ASP cc_start: 0.8524 (t0) cc_final: 0.8093 (t0)
REVERT: E  184 ASP cc_start: 0.7904 (t70) cc_final: 0.7647 (t0)
REVERT: E  305 MET cc_start: 0.7965 (mmt) cc_final: 0.7565 (tpp)
REVERT: E  368 SER cc_start: 0.8981 (p) cc_final: 0.8650 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 358
  average time/residue: 0.0983
  time to fit residues: 55.7646
Evaluate side-chains
  274 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 274
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 52 optimal weight:   10.0000
   chunk 78 optimal weight:   10.0000
   chunk 109 optimal weight:    0.9990
   chunk 120 optimal weight:    0.1980
   chunk 165 optimal weight:    5.9990
   chunk 122 optimal weight:    7.9990
   chunk 105 optimal weight:    4.9990
   chunk 150 optimal weight:    1.9990
   chunk 175 optimal weight:    0.9990
   chunk 172 optimal weight:    7.9990
   chunk 136 optimal weight:    0.5980
   overall best weight:    0.9586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 111 ASN
** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  12 ASN
** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  41 GLN
C 297 ASN
D 173 HIS
** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 173 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.085964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.074678 restraints weight = 36082.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.077463 restraints weight = 18798.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.079303 restraints weight = 11230.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.080568 restraints weight = 7377.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.081466 restraints weight = 5247.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.6800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  14960  Z= 0.127
  Angle     :  0.662   8.622  20305  Z= 0.330
  Chirality :  0.045   0.206   2255
  Planarity :  0.004   0.041   2595
  Dihedral  :  6.380  62.850   2085
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  5.14 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  0.89 %
    Favored  : 99.04 %
  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: -0.05 (0.20), residues: 1830
  helix:  0.72 (0.18), residues: 820
  sheet: -0.64 (0.30), residues: 315
  loop : -0.48 (0.24), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 147 
 TYR   0.024   0.001   TYR A 166 
 PHE   0.011   0.001   PHE B 124 
 TRP   0.012   0.002   TRP C  86 
 HIS   0.006   0.001   HIS B 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.13 (14960)
  covalent geometry    : angle       0.66203 /  0.33 (20305)
  hydrogen bonds       : bond        0.03661 /  2.53 (  780)
  hydrogen bonds       : angle       5.06222 /  3.56 ( 2025)

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  345 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 344
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.4657 (ptt) cc_final: 0.4132 (ptt)
REVERT: A   78 ASN cc_start: 0.7979 (t0) cc_final: 0.7589 (t0)
REVERT: A  121 GLN cc_start: 0.9341 (pp30) cc_final: 0.9064 (pp30)
REVERT: A  137 GLN cc_start: 0.7354 (mt0) cc_final: 0.7120 (mm-40)
REVERT: A  154 ASP cc_start: 0.7816 (t70) cc_final: 0.7271 (t70)
REVERT: A  176 MET cc_start: 0.7901 (mpp) cc_final: 0.7700 (mpp)
REVERT: A  217 CYS cc_start: 0.8565 (m) cc_final: 0.8187 (m)
REVERT: A  287 ILE cc_start: 0.8653 (pt) cc_final: 0.8381 (tt)
REVERT: A  305 MET cc_start: 0.8436 (mmm) cc_final: 0.7959 (tpp)
REVERT: A  360 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8552 (tm-30)
REVERT: B   91 TYR cc_start: 0.9116 (m-80) cc_final: 0.8599 (m-10)
REVERT: B  113 LYS cc_start: 0.8887 (ptmt) cc_final: 0.8498 (pttt)
REVERT: B  176 MET cc_start: 0.7876 (mtt) cc_final: 0.7567 (mtt)
REVERT: B  280 ASN cc_start: 0.8270 (m-40) cc_final: 0.7468 (m110)
REVERT: B  297 ASN cc_start: 0.8488 (m-40) cc_final: 0.8086 (m-40)
REVERT: B  305 MET cc_start: 0.9021 (mmm) cc_final: 0.8569 (tpp)
REVERT: C  121 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8478 (tm-30)
REVERT: C  227 MET cc_start: 0.8615 (tmm) cc_final: 0.8350 (tmm)
REVERT: C  246 GLN cc_start: 0.8617 (tp-100) cc_final: 0.8374 (tp-100)
REVERT: C  276 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7493 (tm-30)
REVERT: C  288 ASP cc_start: 0.7066 (t70) cc_final: 0.6802 (t70)
REVERT: C  292 ASP cc_start: 0.8096 (m-30) cc_final: 0.7661 (t0)
REVERT: D   82 MET cc_start: 0.9165 (tmm) cc_final: 0.8959 (tmm)
REVERT: D  180 LEU cc_start: 0.8884 (tp) cc_final: 0.8638 (tp)
REVERT: D  184 ASP cc_start: 0.8278 (t70) cc_final: 0.7913 (t70)
REVERT: D  316 GLU cc_start: 0.8514 (tp30) cc_final: 0.7948 (tp30)
REVERT: D  356 TRP cc_start: 0.8479 (m100) cc_final: 0.8269 (m100)
REVERT: E   47 MET cc_start: 0.3023 (mtt) cc_final: 0.2533 (mtt)
REVERT: E   72 GLU cc_start: 0.9103 (pp20) cc_final: 0.8626 (pp20)
REVERT: E  154 ASP cc_start: 0.8545 (t0) cc_final: 0.8059 (t0)
REVERT: E  184 ASP cc_start: 0.7952 (t70) cc_final: 0.7633 (t0)
REVERT: E  305 MET cc_start: 0.7933 (mmt) cc_final: 0.7544 (tpp)
REVERT: E  373 LYS cc_start: 0.8867 (mmtt) cc_final: 0.8352 (ptmt)
  outliers start: 1
  outliers final: 0
  residues processed: 345
  average time/residue: 0.1043
  time to fit residues: 56.7355
Evaluate side-chains
  267 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 267
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 48 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 136 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 179 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   chunk 2 optimal weight:    0.6980
   chunk 168 optimal weight:    0.9980
   overall best weight:    1.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 111 ASN
A 137 GLN
** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  41 GLN
C  87 HIS
C 371 HIS
D 173 HIS
** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.085775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.074626 restraints weight = 36450.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.077369 restraints weight = 19096.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.079153 restraints weight = 11500.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.080420 restraints weight = 7628.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.081242 restraints weight = 5447.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.6930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14960  Z= 0.138
  Angle     :  0.663   9.066  20305  Z= 0.330
  Chirality :  0.045   0.196   2255
  Planarity :  0.004   0.042   2595
  Dihedral  :  6.288  61.757   2085
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.97 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  0.64 %
    Favored  : 99.30 %
  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: -0.02 (0.20), residues: 1830
  helix:  0.72 (0.18), residues: 820
  sheet: -0.72 (0.30), residues: 320
  loop : -0.37 (0.24), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 147 
 TYR   0.013   0.001   TYR B 362 
 PHE   0.011   0.001   PHE D 200 
 TRP   0.020   0.002   TRP D  86 
 HIS   0.007   0.001   HIS E  87 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.14 (14960)
  covalent geometry    : angle       0.66322 /  0.33 (20305)
  hydrogen bonds       : bond        0.03680 /  2.54 (  780)
  hydrogen bonds       : angle       5.07099 /  3.55 ( 2025)

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  332 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 331
  time to evaluate  : 0.566 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.4660 (ptt) cc_final: 0.4209 (ptt)
REVERT: A   78 ASN cc_start: 0.7839 (t0) cc_final: 0.7480 (t0)
REVERT: A  118 LYS cc_start: 0.8965 (mmtt) cc_final: 0.8724 (tttm)
REVERT: A  137 GLN cc_start: 0.7438 (mt0) cc_final: 0.7060 (mm-40)
REVERT: A  154 ASP cc_start: 0.7851 (t70) cc_final: 0.7288 (t70)
REVERT: A  176 MET cc_start: 0.7983 (mpp) cc_final: 0.7721 (mpp)
REVERT: A  217 CYS cc_start: 0.8549 (m) cc_final: 0.8143 (m)
REVERT: A  287 ILE cc_start: 0.8688 (pt) cc_final: 0.8426 (tt)
REVERT: A  305 MET cc_start: 0.8474 (mmm) cc_final: 0.7896 (tpp)
REVERT: A  340 TRP cc_start: 0.9111 (t60) cc_final: 0.8337 (t60)
REVERT: A  360 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8549 (tm-30)
REVERT: B   91 TYR cc_start: 0.9062 (m-80) cc_final: 0.8596 (m-10)
REVERT: B  113 LYS cc_start: 0.9001 (ptmt) cc_final: 0.8592 (pttt)
REVERT: B  176 MET cc_start: 0.7840 (mtt) cc_final: 0.7553 (mtt)
REVERT: B  257 CYS cc_start: 0.9289 (t) cc_final: 0.9046 (t)
REVERT: B  280 ASN cc_start: 0.8180 (m-40) cc_final: 0.7297 (m110)
REVERT: B  297 ASN cc_start: 0.8411 (m-40) cc_final: 0.8074 (m-40)
REVERT: B  305 MET cc_start: 0.9027 (mmm) cc_final: 0.8567 (tpp)
REVERT: B  363 ASP cc_start: 0.7864 (p0) cc_final: 0.7551 (m-30)
REVERT: C   49 GLN cc_start: 0.5765 (pm20) cc_final: 0.5431 (pm20)
REVERT: C  121 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8056 (tm-30)
REVERT: C  227 MET cc_start: 0.8576 (tmm) cc_final: 0.8304 (tmm)
REVERT: C  246 GLN cc_start: 0.8655 (tp-100) cc_final: 0.8421 (tp-100)
REVERT: C  253 GLU cc_start: 0.7962 (mp0) cc_final: 0.7682 (mp0)
REVERT: C  276 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7462 (tm-30)
REVERT: C  288 ASP cc_start: 0.7030 (t70) cc_final: 0.6759 (t70)
REVERT: C  292 ASP cc_start: 0.8020 (m-30) cc_final: 0.7567 (t0)
REVERT: C  336 LYS cc_start: 0.8852 (mtpt) cc_final: 0.8522 (mmmt)
REVERT: D   82 MET cc_start: 0.9209 (tmm) cc_final: 0.8805 (tmm)
REVERT: D  180 LEU cc_start: 0.8818 (tp) cc_final: 0.8578 (tp)
REVERT: D  184 ASP cc_start: 0.8389 (t70) cc_final: 0.8105 (t70)
REVERT: D  283 MET cc_start: 0.8424 (mmt) cc_final: 0.8039 (mmp)
REVERT: D  316 GLU cc_start: 0.8470 (tp30) cc_final: 0.7921 (tp30)
REVERT: E   47 MET cc_start: 0.3045 (mtt) cc_final: 0.2470 (mtt)
REVERT: E   72 GLU cc_start: 0.9081 (pp20) cc_final: 0.8606 (pp20)
REVERT: E  154 ASP cc_start: 0.8532 (t0) cc_final: 0.8064 (t0)
REVERT: E  184 ASP cc_start: 0.7999 (t70) cc_final: 0.7735 (t0)
REVERT: E  305 MET cc_start: 0.7780 (mmt) cc_final: 0.7352 (tpp)
REVERT: E  373 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8298 (ptmt)
  outliers start: 1
  outliers final: 0
  residues processed: 332
  average time/residue: 0.0983
  time to fit residues: 51.5508
Evaluate side-chains
  261 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 134 optimal weight:    8.9990
   chunk 92 optimal weight:    2.9990
   chunk 29 optimal weight:    9.9990
   chunk 102 optimal weight:    0.7980
   chunk 183 optimal weight:    0.8980
   chunk 137 optimal weight:    0.7980
   chunk 135 optimal weight:    3.9990
   chunk 60 optimal weight:    0.0770
   chunk 42 optimal weight:    8.9990
   chunk 129 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.6538

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  12 ASN
A 111 ASN
** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  12 ASN
C  41 GLN
C  87 HIS
C 371 HIS
D 173 HIS
E 173 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.087977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.076734 restraints weight = 35534.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.079590 restraints weight = 18545.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.081440 restraints weight = 11096.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.082701 restraints weight = 7332.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.083598 restraints weight = 5198.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.7065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14960  Z= 0.122
  Angle     :  0.661   9.137  20305  Z= 0.330
  Chirality :  0.045   0.203   2255
  Planarity :  0.004   0.042   2595
  Dihedral  :  6.169  61.163   2085
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  5.08 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  0.64 %
    Favored  : 99.30 %
  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:  0.04 (0.20), residues: 1830
  helix:  0.75 (0.18), residues: 820
  sheet: -0.64 (0.30), residues: 320
  loop : -0.33 (0.24), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 147 
 TYR   0.013   0.001   TYR B 362 
 PHE   0.014   0.001   PHE D 200 
 TRP   0.032   0.002   TRP D 356 
 HIS   0.005   0.001   HIS B 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.12 (14960)
  covalent geometry    : angle       0.66115 /  0.33 (20305)
  hydrogen bonds       : bond        0.03624 /  2.54 (  780)
  hydrogen bonds       : angle       5.03247 /  3.53 ( 2025)

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

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

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3660 Ramachandran restraints generated.
    1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  352 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 351
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.4493 (ptt) cc_final: 0.4123 (ptt)
REVERT: A   78 ASN cc_start: 0.7969 (t0) cc_final: 0.7549 (t0)
REVERT: A   82 MET cc_start: 0.8655 (tmm) cc_final: 0.8410 (tmm)
REVERT: A   87 HIS cc_start: 0.8563 (t-90) cc_final: 0.8354 (t-170)
REVERT: A  154 ASP cc_start: 0.7836 (t70) cc_final: 0.7200 (t70)
REVERT: A  167 GLU cc_start: 0.8306 (mp0) cc_final: 0.8062 (mp0)
REVERT: A  176 MET cc_start: 0.7984 (mpp) cc_final: 0.7754 (mpp)
REVERT: A  217 CYS cc_start: 0.8499 (m) cc_final: 0.8096 (m)
REVERT: A  283 MET cc_start: 0.8836 (mmp) cc_final: 0.8447 (mmp)
REVERT: A  287 ILE cc_start: 0.8647 (pt) cc_final: 0.8415 (tt)
REVERT: A  305 MET cc_start: 0.8456 (mmm) cc_final: 0.7919 (tpp)
REVERT: A  340 TRP cc_start: 0.9091 (t60) cc_final: 0.8330 (t60)
REVERT: A  360 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8534 (tm-30)
REVERT: B   43 VAL cc_start: 0.8611 (t) cc_final: 0.8304 (t)
REVERT: B   91 TYR cc_start: 0.9063 (m-80) cc_final: 0.8603 (m-10)
REVERT: B  111 ASN cc_start: 0.8726 (m-40) cc_final: 0.8447 (m-40)
REVERT: B  113 LYS cc_start: 0.9013 (ptmt) cc_final: 0.8563 (pttt)
REVERT: B  176 MET cc_start: 0.7878 (mtt) cc_final: 0.7632 (mtt)
REVERT: B  276 GLU cc_start: 0.8359 (tp30) cc_final: 0.7889 (tm-30)
REVERT: B  280 ASN cc_start: 0.8491 (m-40) cc_final: 0.7299 (m110)
REVERT: B  283 MET cc_start: 0.8654 (mmm) cc_final: 0.8408 (mmm)
REVERT: B  297 ASN cc_start: 0.8322 (m-40) cc_final: 0.7920 (m-40)
REVERT: B  305 MET cc_start: 0.9023 (mmm) cc_final: 0.8584 (tpp)
REVERT: B  363 ASP cc_start: 0.7912 (p0) cc_final: 0.7614 (m-30)
REVERT: C   49 GLN cc_start: 0.5792 (pm20) cc_final: 0.5453 (pm20)
REVERT: C  121 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8584 (tm-30)
REVERT: C  227 MET cc_start: 0.8563 (tmm) cc_final: 0.8296 (tmm)
REVERT: C  276 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7441 (tm-30)
REVERT: C  288 ASP cc_start: 0.6979 (t70) cc_final: 0.6725 (t70)
REVERT: C  292 ASP cc_start: 0.8027 (m-30) cc_final: 0.7591 (t0)
REVERT: C  336 LYS cc_start: 0.8856 (mtpt) cc_final: 0.8521 (mmmt)
REVERT: D   82 MET cc_start: 0.9044 (tmm) cc_final: 0.8754 (tmm)
REVERT: D  180 LEU cc_start: 0.8712 (tp) cc_final: 0.8508 (tp)
REVERT: D  184 ASP cc_start: 0.8384 (t70) cc_final: 0.8093 (t70)
REVERT: D  283 MET cc_start: 0.8449 (mmt) cc_final: 0.8065 (mmp)
REVERT: D  316 GLU cc_start: 0.8472 (tp30) cc_final: 0.7874 (tp30)
REVERT: D  318 THR cc_start: 0.8844 (m) cc_final: 0.8503 (p)
REVERT: E   47 MET cc_start: 0.3013 (mtt) cc_final: 0.2445 (mtt)
REVERT: E   72 GLU cc_start: 0.9056 (pp20) cc_final: 0.8599 (pp20)
REVERT: E  154 ASP cc_start: 0.8535 (t0) cc_final: 0.8015 (t0)
REVERT: E  305 MET cc_start: 0.7761 (mmt) cc_final: 0.7318 (tpp)
REVERT: E  373 LYS cc_start: 0.8757 (mmtt) cc_final: 0.8285 (ptmt)
  outliers start: 1
  outliers final: 0
  residues processed: 351
  average time/residue: 0.1015
  time to fit residues: 56.5330
Evaluate side-chains
  266 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 266
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 3 optimal weight:    6.9990
   chunk 75 optimal weight:   10.0000
   chunk 54 optimal weight:    0.6980
   chunk 148 optimal weight:    9.9990
   chunk 168 optimal weight:    3.9990
   chunk 175 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   chunk 108 optimal weight:    0.3980
   chunk 126 optimal weight:    8.9990
   overall best weight:    1.3984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 111 ASN
** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  12 ASN
C 115 ASN
C 371 HIS
D 101 HIS
D 173 HIS
D 353 GLN
E 371 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.086645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.075578 restraints weight = 35898.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.078359 restraints weight = 18636.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.080233 restraints weight = 11131.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.081473 restraints weight = 7284.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.082292 restraints weight = 5139.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.7156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14960  Z= 0.142
  Angle     :  0.679  10.017  20305  Z= 0.337
  Chirality :  0.045   0.202   2255
  Planarity :  0.004   0.040   2595
  Dihedral  :  6.123  59.671   2085
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  5.08 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  0.64 %
    Favored  : 99.30 %
  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:  0.05 (0.20), residues: 1830
  helix:  0.71 (0.18), residues: 825
  sheet: -0.49 (0.30), residues: 310
  loop : -0.35 (0.24), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 147 
 TYR   0.015   0.001   TYR D 294 
 PHE   0.014   0.001   PHE D 200 
 TRP   0.015   0.002   TRP C  86 
 HIS   0.005   0.001   HIS B 101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.14 (14960)
  covalent geometry    : angle       0.67875 /  0.34 (20305)
  hydrogen bonds       : bond        0.03751 /  2.56 (  780)
  hydrogen bonds       : angle       5.13559 /  3.61 ( 2025)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2213.11 seconds
wall clock time: 39 minutes 13.79 seconds (2353.79 seconds total)