Starting phenix.real_space_refine
on Tue Mar  3 15:29:24 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wuj_21914/03_2026/6wuj_21914.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wuj_21914/03_2026/6wuj_21914.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wuj_21914/03_2026/6wuj_21914.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wuj_21914/03_2026/6wuj_21914.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wuj_21914/03_2026/6wuj_21914.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wuj_21914/03_2026/6wuj_21914.map"
  }
  resolution = 3.7
  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=   0.015 sd=   0.109
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      13      5.16       5
     C    4260      2.51       5
     N    1198      2.21       5
     O    1228      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 37 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6699
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2191
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2191
          Classifications: {'peptide': 282}
          Link IDs: {'PTRANS': 22, 'TRANS': 259}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2352
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 318, 2352
          Classifications: {'peptide': 318}
          Link IDs: {'PTRANS': 19, 'TRANS': 298}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 2156
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2156
          Classifications: {'peptide': 284}
          Link IDs: {'PTRANS': 19, 'TRANS': 264}
          Chain breaks: 4
  Time building chain proxies: 1.32, per 1000 atoms: 0.20
  Number of scatterers: 6699
  At special positions: 0
  Unit cell: (83.74, 81.62, 125.08, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      13     16.00
     O    1228      8.00
     N    1198      7.00
     C    4260      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 219.0 milliseconds
  

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1620

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 10 sheets defined
      38.3% alpha, 17.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 44
      removed outlier: 4.019A  pdb=" N   LEU A  44 " --> pdb=" O   ARG A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 63
      removed outlier: 4.152A  pdb=" N   ARG A  62 " --> pdb=" O   ASP A  58 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   LEU A  63 " --> pdb=" O   SER A  59 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 58 through 63'
    Processing helix  chain 'A' and resid 69 through 82
      removed outlier: 4.666A  pdb=" N   TRP A  75 " --> pdb=" O   GLY A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 121
      No H-bonds generated for 'chain 'A' and resid 119 through 121'
    Processing helix  chain 'A' and resid 122 through 127
    Processing helix  chain 'A' and resid 152 through 162
      removed outlier: 3.622A  pdb=" N   TYR A 156 " --> pdb=" O   ARG A 152 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   ALA A 158 " --> pdb=" O   GLN A 154 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   LEU A 159 " --> pdb=" O   ALA A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 173
      removed outlier: 3.734A  pdb=" N   ASN A 166 " --> pdb=" O   HIS A 162 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ALA A 167 " --> pdb=" O   SER A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 177
      No H-bonds generated for 'chain 'A' and resid 175 through 177'
    Processing helix  chain 'A' and resid 178 through 187
      removed outlier: 3.995A  pdb=" N   VAL A 187 " --> pdb=" O   ARG A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 215
      removed outlier: 3.667A  pdb=" N   ALA A 198 " --> pdb=" O   ARG A 194 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   ALA A 199 " --> pdb=" O   ALA A 195 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLN A 203 " --> pdb=" O   ALA A 199 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ALA A 207 " --> pdb=" O   GLN A 203 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   GLU A 210 " --> pdb=" O   ARG A 206 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   ALA A 215 " --> pdb=" O   GLN A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 255
      removed outlier: 3.519A  pdb=" N   ASP A 248 " --> pdb=" O   ARG A 244 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ARG A 255 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 280
      removed outlier: 3.956A  pdb=" N   TYR A 278 " --> pdb=" O   ALA A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 285
    Processing helix  chain 'A' and resid 302 through 306
      removed outlier: 3.519A  pdb=" N   LYS A 306 " --> pdb=" O   GLY A 302 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 302 through 306'
    Processing helix  chain 'A' and resid 311 through 321
    Processing helix  chain 'B' and resid 369 through 374
      removed outlier: 3.852A  pdb=" N   ASP B 373 " --> pdb=" O   GLY B 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 461
      removed outlier: 3.532A  pdb=" N   VAL B 454 " --> pdb=" O   VAL B 450 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 18 through 32
    Processing helix  chain 'C' and resid 43 through 47
      removed outlier: 3.753A  pdb=" N   VAL C  47 " --> pdb=" O   PRO C  44 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 66 through 73
    Processing helix  chain 'C' and resid 106 through 120
      removed outlier: 3.861A  pdb=" N   SER C 120 " --> pdb=" O   THR C 116 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 123 through 130
      removed outlier: 4.001A  pdb=" N   SER C 130 " --> pdb=" O   LEU C 126 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 141 through 148
    Processing helix  chain 'C' and resid 153 through 156
      removed outlier: 3.550A  pdb=" N   TRP C 156 " --> pdb=" O   PRO C 153 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 153 through 156'
    Processing helix  chain 'C' and resid 157 through 169
      removed outlier: 3.570A  pdb=" N   ALA C 161 " --> pdb=" O   THR C 157 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 239 through 255
      removed outlier: 4.389A  pdb=" N   VAL C 249 " --> pdb=" O   ALA C 245 " (cutoff:3.500A)
      removed outlier: 4.704A  pdb=" N   VAL C 252 " --> pdb=" O   GLU C 248 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   GLU C 255 " --> pdb=" O   ASP C 251 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 271 through 282
      removed outlier: 3.742A  pdb=" N   GLY C 277 " --> pdb=" O   CYS C 273 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ALA C 280 " --> pdb=" O   PHE C 276 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   LEU C 281 " --> pdb=" O   GLY C 277 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 292 through 300
      removed outlier: 3.756A  pdb=" N   MET C 296 " --> pdb=" O   LEU C 292 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 300 through 315
      removed outlier: 3.586A  pdb=" N   PHE C 306 " --> pdb=" O   ALA C 302 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ARG C 311 " --> pdb=" O   VAL C 307 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 316 through 320
      removed outlier: 3.825A  pdb=" N   LYS C 320 " --> pdb=" O   GLN C 317 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 329 through 333
      removed outlier: 3.950A  pdb=" N   ALA C 333 " --> pdb=" O   GLN C 330 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 340 through 352
      removed outlier: 3.711A  pdb=" N   LEU C 344 " --> pdb=" O   SER C 340 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ALA C 352 " --> pdb=" O   ARG C 348 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 356 through 376
      removed outlier: 4.551A  pdb=" N   TRP C 360 " --> pdb=" O   LEU C 356 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ARG C 371 " --> pdb=" O   ALA C 367 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   GLU C 372 " --> pdb=" O   ARG C 368 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   VAL C 373 " --> pdb=" O   LYS C 369 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LEU C 374 " --> pdb=" O   LYS C 370 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA C 375 " --> pdb=" O   ARG C 371 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32
    Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 54
      removed outlier: 6.246A  pdb=" N   LEU A  52 " --> pdb=" O   LEU A  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 158 through 159
      removed outlier: 3.540A  pdb=" N   VAL B 159 " --> pdb=" O   THR B 168 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   THR B 168 " --> pdb=" O   VAL B 159 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 171 through 172
      removed outlier: 3.524A  pdb=" N   VAL B 171 " --> pdb=" O   ASN B 184 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 199 through 202
      removed outlier: 3.870A  pdb=" N   THR B 235 " --> pdb=" O   THR B 275 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ALA B 239 " --> pdb=" O   THR B 271 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   SER B 400 " --> pdb=" O   GLY B 338 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLY B 342 " --> pdb=" O   PHE B 396 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ALA B 397 " --> pdb=" O   ARG B 426 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 202
      removed outlier: 3.870A  pdb=" N   THR B 235 " --> pdb=" O   THR B 275 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ALA B 239 " --> pdb=" O   THR B 271 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   VAL B 314 " --> pdb=" O   LEU B 341 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   LEU B 339 " --> pdb=" O   ALA B 316 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   SER B 400 " --> pdb=" O   GLY B 338 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLY B 342 " --> pdb=" O   PHE B 396 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ALA B 397 " --> pdb=" O   ARG B 426 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 206 through 210
    Processing sheet with id=AA8, first strand: chain 'B' and resid 417 through 421
    Processing sheet with id=AA9, first strand: chain 'B' and resid 417 through 421
      removed outlier: 3.607A  pdb=" N   GLY B 508 " --> pdb=" O   ARG B 482 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 6
      removed outlier: 3.643A  pdb=" N   THR C  54 " --> pdb=" O   HIS C   6 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   THR C  62 " --> pdb=" O   ASP C  57 " (cutoff:3.500A)

    271 hydrogen bonds defined for protein.
    756 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.78

  Time building geometry restraints manager: 0.80 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 1084
        1.30 -     1.43: 1844
        1.43 -     1.56: 3910
        1.56 -     1.68: 0
        1.68 -     1.81: 21
  Bond restraints: 6859
  Sorted by residual:
  bond pdb=" CA  ASP C 286 "
       pdb=" C   ASP C 286 "
    ideal  model  delta    sigma   weight residual
    1.524  1.454  0.070 1.27e-02 6.20e+03 3.00e+01
  bond pdb=" C   VAL A 223 "
       pdb=" O   VAL A 223 "
    ideal  model  delta    sigma   weight residual
    1.245  1.177  0.068 1.41e-02 5.03e+03 2.34e+01
  bond pdb=" N   VAL C 287 "
       pdb=" CA  VAL C 287 "
    ideal  model  delta    sigma   weight residual
    1.461  1.406  0.055 1.23e-02 6.61e+03 2.04e+01
  bond pdb=" C   SER A 224 "
       pdb=" O   SER A 224 "
    ideal  model  delta    sigma   weight residual
    1.234  1.187  0.047 1.09e-02 8.42e+03 1.83e+01
  bond pdb=" N   VAL A 223 "
       pdb=" CA  VAL A 223 "
    ideal  model  delta    sigma   weight residual
    1.460  1.424  0.036 8.60e-03 1.35e+04 1.78e+01
  ... (remaining 6854 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 8849
        1.82 -     3.64: 410
        3.64 -     5.45: 66
        5.45 -     7.27: 14
        7.27 -     9.09: 7
  Bond angle restraints: 9346
  Sorted by residual:
  angle pdb=" N   PHE C  12 "
        pdb=" CA  PHE C  12 "
        pdb=" C   PHE C  12 "
      ideal   model   delta    sigma   weight residual
     112.97  119.52   -6.55 1.06e+00 8.90e-01 3.82e+01
  angle pdb=" N   VAL C 287 "
        pdb=" CA  VAL C 287 "
        pdb=" CB  VAL C 287 "
      ideal   model   delta    sigma   weight residual
     111.21  103.78    7.43 1.40e+00 5.10e-01 2.82e+01
  angle pdb=" N   ASP C 286 "
        pdb=" CA  ASP C 286 "
        pdb=" C   ASP C 286 "
      ideal   model   delta    sigma   weight residual
     107.99   98.90    9.09 1.77e+00 3.19e-01 2.64e+01
  angle pdb=" C   PRO C 288 "
        pdb=" N   ARG C 289 "
        pdb=" CA  ARG C 289 "
      ideal   model   delta    sigma   weight residual
     123.16  116.92    6.24 1.23e+00 6.61e-01 2.58e+01
  angle pdb=" N   VAL A 223 "
        pdb=" CA  VAL A 223 "
        pdb=" C   VAL A 223 "
      ideal   model   delta    sigma   weight residual
     113.71  117.69   -3.98 9.50e-01 1.11e+00 1.76e+01
  ... (remaining 9341 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.36: 3654
       17.36 -    34.72: 358
       34.72 -    52.09: 44
       52.09 -    69.45: 3
       69.45 -    86.81: 3
  Dihedral angle restraints: 4062
    sinusoidal: 1545
      harmonic: 2517
  Sorted by residual:
  dihedral pdb=" CA  HIS C  51 "
           pdb=" C   HIS C  51 "
           pdb=" N   LEU C  52 "
           pdb=" CA  LEU C  52 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.25  -29.75     0      5.00e+00 4.00e-02 3.54e+01
  dihedral pdb=" CA  LEU A 101 "
           pdb=" C   LEU A 101 "
           pdb=" N   PRO A 102 "
           pdb=" CA  PRO A 102 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.30  -23.70     0      5.00e+00 4.00e-02 2.25e+01
  dihedral pdb=" CA  ALA B 213 "
           pdb=" C   ALA B 213 "
           pdb=" N   SER B 214 "
           pdb=" CA  SER B 214 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.10  -22.90     0      5.00e+00 4.00e-02 2.10e+01
  ... (remaining 4059 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 958
       0.082 -    0.163: 86
       0.163 -    0.245: 5
       0.245 -    0.326: 2
       0.326 -    0.408: 1
  Chirality restraints: 1052
  Sorted by residual:
  chirality pdb=" CB  VAL A 223 "
            pdb=" CA  VAL A 223 "
            pdb=" CG1 VAL A 223 "
            pdb=" CG2 VAL A 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.22   -0.41 2.00e-01 2.50e+01 4.16e+00
  chirality pdb=" CA  VAL A 223 "
            pdb=" N   VAL A 223 "
            pdb=" C   VAL A 223 "
            pdb=" CB  VAL A 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.14    0.31 2.00e-01 2.50e+01 2.34e+00
  chirality pdb=" CA  PHE C  12 "
            pdb=" N   PHE C  12 "
            pdb=" C   PHE C  12 "
            pdb=" CB  PHE C  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.54e+00
  ... (remaining 1049 not shown)

  Planarity restraints: 1211
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 287 "    0.057 5.00e-02 4.00e+02   8.68e-02 1.21e+01
        pdb=" N   PRO C 288 "   -0.150 5.00e-02 4.00e+02
        pdb=" CA  PRO C 288 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO C 288 "    0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO C 285 "   -0.015 2.00e-02 2.50e+03   2.93e-02 8.57e+00
        pdb=" C   PRO C 285 "    0.051 2.00e-02 2.50e+03
        pdb=" O   PRO C 285 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ASP C 286 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 222 "   -0.015 2.00e-02 2.50e+03   2.86e-02 8.20e+00
        pdb=" C   ILE A 222 "    0.050 2.00e-02 2.50e+03
        pdb=" O   ILE A 222 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   VAL A 223 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1208 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 102
        2.63 -     3.20: 6170
        3.20 -     3.76: 9408
        3.76 -     4.33: 13024
        4.33 -     4.90: 21934
  Nonbonded interactions: 50638
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 308 "
            pdb=" O   LEU B 347 "
     model   vdw
     2.059 3.040
  nonbonded pdb=" OG1 THR B 257 "
            pdb=" OD2 ASP B 386 "
     model   vdw
     2.078 3.040
  nonbonded pdb=" O   GLY C  13 "
            pdb=" NH1 ARG C 311 "
     model   vdw
     2.128 3.120
  nonbonded pdb=" OG1 THR B 230 "
            pdb=" OD1 ASP B 234 "
     model   vdw
     2.155 3.040
  nonbonded pdb=" O   LEU C  14 "
            pdb=" N   SER C  16 "
     model   vdw
     2.165 3.120
  ... (remaining 50633 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             0.550
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.400
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
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      :  0.007   0.107   6859  Z= 0.357
  Angle     :  0.926   9.088   9346  Z= 0.527
  Chirality :  0.051   0.408   1052
  Planarity :  0.006   0.087   1211
  Dihedral  : 13.198  86.810   2442
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 16.08 %
    Favored  : 83.80 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  5.98 %
    Favored  : 93.88 %
  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: -5.66 (0.22), residues: 858
  helix: -3.53 (0.20), residues: 310
  sheet: -3.16 (0.41), residues: 148
  loop : -4.19 (0.25), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 494 
 TYR   0.019   0.002   TYR B 421 
 PHE   0.015   0.002   PHE B 309 
 TRP   0.018   0.002   TRP C   8 
 HIS   0.005   0.001   HIS B 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00732 ( 6859)
  covalent geometry    : angle       0.92567 ( 9346)
  hydrogen bonds       : bond        0.25448 (  234)
  hydrogen bonds       : angle      10.35365 (  756)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  192 ASN cc_start: 0.8026 (t0) cc_final: 0.7624 (t0)
REVERT: B  248 THR cc_start: 0.8890 (p) cc_final: 0.8586 (t)
REVERT: C  250 LEU cc_start: 0.8856 (mm) cc_final: 0.8574 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 126
  average time/residue: 0.1100
  time to fit residues: 17.1056
Evaluate side-chains
  90 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 89
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 178 HIS
B 192 ASN
B 419 GLN
C  50 GLN
C  51 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.137596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.112069 restraints weight = 10123.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.114121 restraints weight = 7410.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.115549 restraints weight = 5964.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.116443 restraints weight = 5108.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.117191 restraints weight = 4633.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.1835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6859  Z= 0.141
  Angle     :  0.686   8.925   9346  Z= 0.344
  Chirality :  0.044   0.155   1052
  Planarity :  0.006   0.060   1211
  Dihedral  :  5.521  43.301    964
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.84 %
    Favored  : 89.16 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 11.08 %
    Favored  : 87.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.21 (0.26), residues: 858
  helix: -1.88 (0.26), residues: 314
  sheet: -2.40 (0.45), residues: 137
  loop : -3.74 (0.26), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 245 
 TYR   0.017   0.002   TYR B 289 
 PHE   0.024   0.002   PHE C 346 
 TRP   0.010   0.001   TRP C   8 
 HIS   0.003   0.001   HIS B 478 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 6859)
  covalent geometry    : angle       0.68632 ( 9346)
  hydrogen bonds       : bond        0.04171 (  234)
  hydrogen bonds       : angle       5.36039 (  756)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  192 ASN cc_start: 0.7844 (OUTLIER) cc_final: 0.7455 (t0)
REVERT: B  248 THR cc_start: 0.8687 (p) cc_final: 0.8408 (t)
REVERT: B  378 LYS cc_start: 0.8384 (ttpt) cc_final: 0.8080 (tttm)
REVERT: C  250 LEU cc_start: 0.8709 (mm) cc_final: 0.8374 (mm)
  outliers start: 11
  outliers final: 7
  residues processed: 114
  average time/residue: 0.0673
  time to fit residues: 10.8909
Evaluate side-chains
  96 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 SER
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain B residue  192 ASN
Chi-restraints excluded: chain B residue  388 VAL
Chi-restraints excluded: chain B residue  488 SER
Chi-restraints excluded: chain B residue  509 ILE
Chi-restraints excluded: chain C residue   16 SER
Chi-restraints excluded: chain C residue   21 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 75 optimal weight:    6.9990
   chunk 72 optimal weight:    7.9990
   chunk 4 optimal weight:    0.7980
   chunk 62 optimal weight:    8.9990
   chunk 31 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 23 optimal weight:    0.1980
   chunk 57 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
C  51 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.135044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.108319 restraints weight = 10124.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.110738 restraints weight = 7024.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.112369 restraints weight = 5484.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.113459 restraints weight = 4623.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.114068 restraints weight = 4105.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.1968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073   6859  Z= 0.200
  Angle     :  0.712   8.912   9346  Z= 0.352
  Chirality :  0.046   0.151   1052
  Planarity :  0.006   0.050   1211
  Dihedral  :  5.464  33.183    964
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.82 %
    Favored  : 87.18 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 13.70 %
    Favored  : 83.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.45 (0.28), residues: 858
  helix: -0.99 (0.29), residues: 303
  sheet: -2.17 (0.50), residues: 129
  loop : -3.40 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 319 
 TYR   0.016   0.002   TYR B 421 
 PHE   0.017   0.002   PHE A  27 
 TRP   0.012   0.001   TRP C   8 
 HIS   0.004   0.001   HIS B 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 ( 6859)
  covalent geometry    : angle       0.71220 ( 9346)
  hydrogen bonds       : bond        0.03942 (  234)
  hydrogen bonds       : angle       4.95112 (  756)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  192 ASN cc_start: 0.7771 (t0) cc_final: 0.7418 (t0)
REVERT: B  248 THR cc_start: 0.8757 (p) cc_final: 0.8444 (t)
REVERT: C   40 ILE cc_start: 0.8795 (mm) cc_final: 0.8540 (mt)
REVERT: C  250 LEU cc_start: 0.8741 (mm) cc_final: 0.8388 (mm)
  outliers start: 18
  outliers final: 11
  residues processed: 107
  average time/residue: 0.0662
  time to fit residues: 9.9484
Evaluate side-chains
  98 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  209 GLN
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  388 VAL
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  488 SER
Chi-restraints excluded: chain C residue   16 SER
Chi-restraints excluded: chain C residue   21 CYS
Chi-restraints excluded: chain C residue  255 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 44 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 67 optimal weight:    0.7980
   chunk 73 optimal weight:   10.0000
   chunk 85 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0870
   chunk 66 optimal weight:    2.9990
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
B 215 HIS
C  51 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.138686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.112690 restraints weight = 10117.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.115131 restraints weight = 6944.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.116809 restraints weight = 5356.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.117816 restraints weight = 4481.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.118656 restraints weight = 3972.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.2432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   6859  Z= 0.122
  Angle     :  0.644   9.943   9346  Z= 0.317
  Chirality :  0.043   0.142   1052
  Planarity :  0.005   0.048   1211
  Dihedral  :  5.011  25.234    963
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.79 %
    Favored  : 90.21 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 14.43 %
    Favored  : 83.53 %
  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: -2.92 (0.29), residues: 858
  helix: -0.50 (0.30), residues: 313
  sheet: -1.76 (0.51), residues: 125
  loop : -3.24 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  62 
 TYR   0.016   0.001   TYR B 421 
 PHE   0.011   0.001   PHE A  27 
 TRP   0.009   0.001   TRP C  63 
 HIS   0.003   0.001   HIS B 478 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 6859)
  covalent geometry    : angle       0.64443 ( 9346)
  hydrogen bonds       : bond        0.03116 (  234)
  hydrogen bonds       : angle       4.49214 (  756)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  209 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7797 (tt0)
REVERT: B  248 THR cc_start: 0.8630 (p) cc_final: 0.8321 (t)
REVERT: C   40 ILE cc_start: 0.8779 (mm) cc_final: 0.8542 (mt)
REVERT: C  250 LEU cc_start: 0.8717 (mm) cc_final: 0.8362 (mm)
  outliers start: 14
  outliers final: 8
  residues processed: 109
  average time/residue: 0.0594
  time to fit residues: 9.1857
Evaluate side-chains
  103 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  209 GLN
Chi-restraints excluded: chain B residue  388 VAL
Chi-restraints excluded: chain B residue  488 SER
Chi-restraints excluded: chain C residue   16 SER
Chi-restraints excluded: chain C residue   21 CYS
Chi-restraints excluded: chain C residue  255 GLU
Chi-restraints excluded: chain C residue  314 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 78 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 79 optimal weight:    0.1980
   chunk 15 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 11 optimal weight:    0.2980
   chunk 52 optimal weight:    4.9990
   chunk 8 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 211 GLN
C  51 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.139956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.115384 restraints weight = 10106.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.117713 restraints weight = 7804.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.118375 restraints weight = 5979.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.118866 restraints weight = 5360.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.119025 restraints weight = 4937.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.2778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6859  Z= 0.109
  Angle     :  0.615   8.861   9346  Z= 0.302
  Chirality :  0.042   0.143   1052
  Planarity :  0.005   0.048   1211
  Dihedral  :  4.699  22.983    963
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.79 %
    Favored  : 90.21 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 16.18 %
    Favored  : 81.34 %
  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: -2.52 (0.29), residues: 858
  helix: -0.17 (0.30), residues: 317
  sheet: -1.50 (0.51), residues: 127
  loop : -3.04 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  62 
 TYR   0.015   0.001   TYR B 421 
 PHE   0.022   0.001   PHE C 276 
 TRP   0.010   0.001   TRP C  63 
 HIS   0.002   0.001   HIS C  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 6859)
  covalent geometry    : angle       0.61458 ( 9346)
  hydrogen bonds       : bond        0.02794 (  234)
  hydrogen bonds       : angle       4.21060 (  756)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
REVERT: B  209 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7753 (tt0)
REVERT: B  248 THR cc_start: 0.8570 (p) cc_final: 0.8236 (t)
REVERT: C  359 GLU cc_start: 0.8135 (mp0) cc_final: 0.7562 (mp0)
  outliers start: 17
  outliers final: 10
  residues processed: 108
  average time/residue: 0.0663
  time to fit residues: 10.1760
Evaluate side-chains
  98 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  216 SER
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  209 GLN
Chi-restraints excluded: chain B residue  388 VAL
Chi-restraints excluded: chain B residue  488 SER
Chi-restraints excluded: chain B residue  509 ILE
Chi-restraints excluded: chain C residue   16 SER
Chi-restraints excluded: chain C residue   18 ASP
Chi-restraints excluded: chain C residue   21 CYS
Chi-restraints excluded: chain C residue  314 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 55 optimal weight:    0.0270
   chunk 35 optimal weight:    2.9990
   chunk 29 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 48 optimal weight:    0.0770
   chunk 15 optimal weight:    3.9990
   chunk 64 optimal weight:    0.7980
   chunk 26 optimal weight:    6.9990
   chunk 56 optimal weight:    9.9990
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.9398

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

Flipped N/Q/H residues before XYZ refinement:
C  51 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.138756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.112619 restraints weight = 10210.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.115091 restraints weight = 7037.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.116831 restraints weight = 5446.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.117969 restraints weight = 4534.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.118763 restraints weight = 4003.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.2853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6859  Z= 0.125
  Angle     :  0.636   8.729   9346  Z= 0.311
  Chirality :  0.043   0.150   1052
  Planarity :  0.005   0.048   1211
  Dihedral  :  4.712  24.058    963
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.67 %
    Favored  : 90.33 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 17.06 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.31 (0.29), residues: 858
  helix:  0.02 (0.31), residues: 317
  sheet: -1.40 (0.51), residues: 128
  loop : -2.94 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 494 
 TYR   0.011   0.001   TYR B 421 
 PHE   0.014   0.001   PHE C 276 
 TRP   0.008   0.001   TRP C  63 
 HIS   0.006   0.001   HIS C  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6859)
  covalent geometry    : angle       0.63622 ( 9346)
  hydrogen bonds       : bond        0.02902 (  234)
  hydrogen bonds       : angle       4.15093 (  756)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A   30 ARG cc_start: 0.6341 (mtt90) cc_final: 0.5928 (mtt-85)
REVERT: B  209 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7787 (tt0)
REVERT: B  248 THR cc_start: 0.8639 (p) cc_final: 0.8298 (t)
REVERT: C  359 GLU cc_start: 0.8141 (mp0) cc_final: 0.7502 (mp0)
  outliers start: 18
  outliers final: 11
  residues processed: 103
  average time/residue: 0.0669
  time to fit residues: 9.8364
Evaluate side-chains
  97 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  216 SER
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  209 GLN
Chi-restraints excluded: chain B residue  388 VAL
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  488 SER
Chi-restraints excluded: chain B residue  509 ILE
Chi-restraints excluded: chain C residue   16 SER
Chi-restraints excluded: chain C residue   21 CYS
Chi-restraints excluded: chain C residue  255 GLU
Chi-restraints excluded: chain C residue  314 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 43 optimal weight:    6.9990
   chunk 79 optimal weight:   20.0000
   chunk 42 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 82 optimal weight:    5.9990
   chunk 41 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 310 ASN
C  51 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.140272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.116522 restraints weight = 9845.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.116809 restraints weight = 8064.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.117218 restraints weight = 6682.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.117527 restraints weight = 6371.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.117655 restraints weight = 6037.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.3032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6859  Z= 0.119
  Angle     :  0.633  12.094   9346  Z= 0.307
  Chirality :  0.042   0.143   1052
  Planarity :  0.005   0.048   1211
  Dihedral  :  4.619  23.315    963
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.32 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 18.08 %
    Favored  : 80.03 %
  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: -2.15 (0.30), residues: 858
  helix:  0.19 (0.31), residues: 317
  sheet: -1.49 (0.50), residues: 134
  loop : -2.82 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 299 
 TYR   0.011   0.001   TYR C 300 
 PHE   0.021   0.001   PHE C 276 
 TRP   0.008   0.001   TRP C  63 
 HIS   0.004   0.001   HIS C  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6859)
  covalent geometry    : angle       0.63327 ( 9346)
  hydrogen bonds       : bond        0.02737 (  234)
  hydrogen bonds       : angle       4.06438 (  756)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A   30 ARG cc_start: 0.6155 (mtt90) cc_final: 0.5732 (ttm-80)
REVERT: B  209 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7780 (tt0)
REVERT: B  248 THR cc_start: 0.8616 (p) cc_final: 0.8284 (t)
REVERT: C  250 LEU cc_start: 0.8571 (mm) cc_final: 0.8222 (mm)
REVERT: C  359 GLU cc_start: 0.8142 (mp0) cc_final: 0.7475 (mp0)
  outliers start: 13
  outliers final: 9
  residues processed: 101
  average time/residue: 0.0703
  time to fit residues: 10.1112
Evaluate side-chains
  98 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  216 SER
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  209 GLN
Chi-restraints excluded: chain B residue  388 VAL
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  488 SER
Chi-restraints excluded: chain C residue   16 SER
Chi-restraints excluded: chain C residue   21 CYS
Chi-restraints excluded: chain C residue  314 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 26 optimal weight:    0.5980
   chunk 65 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 39 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 57 optimal weight:    4.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
A  69 ASN
A 211 GLN
C  51 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.135740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.110248 restraints weight = 10298.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.112686 restraints weight = 7830.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.113458 restraints weight = 5856.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.114030 restraints weight = 5312.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.114222 restraints weight = 4851.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.2928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   6859  Z= 0.178
  Angle     :  0.688  11.754   9346  Z= 0.334
  Chirality :  0.045   0.146   1052
  Planarity :  0.005   0.043   1211
  Dihedral  :  4.885  25.835    963
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.42 %
    Favored  : 88.58 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 18.08 %
    Favored  : 79.45 %
  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: -2.23 (0.30), residues: 858
  helix:  0.14 (0.31), residues: 316
  sheet: -1.62 (0.50), residues: 133
  loop : -2.83 (0.29), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 299 
 TYR   0.015   0.001   TYR C 278 
 PHE   0.015   0.002   PHE C 276 
 TRP   0.011   0.001   TRP A 168 
 HIS   0.004   0.001   HIS C  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 6859)
  covalent geometry    : angle       0.68815 ( 9346)
  hydrogen bonds       : bond        0.03184 (  234)
  hydrogen bonds       : angle       4.24460 (  756)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A   30 ARG cc_start: 0.6340 (mtt90) cc_final: 0.5920 (ttm-80)
REVERT: B  209 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7879 (tt0)
REVERT: B  248 THR cc_start: 0.8691 (p) cc_final: 0.8375 (t)
REVERT: C  243 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6919 (tm-30)
REVERT: C  250 LEU cc_start: 0.8802 (mm) cc_final: 0.8522 (mm)
REVERT: C  359 GLU cc_start: 0.8177 (mp0) cc_final: 0.7473 (mp0)
  outliers start: 17
  outliers final: 12
  residues processed: 98
  average time/residue: 0.0538
  time to fit residues: 7.6240
Evaluate side-chains
  99 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  216 SER
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  209 GLN
Chi-restraints excluded: chain B residue  388 VAL
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  488 SER
Chi-restraints excluded: chain B residue  503 LEU
Chi-restraints excluded: chain C residue   16 SER
Chi-restraints excluded: chain C residue   17 ILE
Chi-restraints excluded: chain C residue   21 CYS
Chi-restraints excluded: chain C residue  255 GLU
Chi-restraints excluded: chain C residue  314 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0980
   chunk 69 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 79 optimal weight:    5.9990
   chunk 43 optimal weight:    7.9990
   chunk 47 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 211 GLN
C  51 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.139070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.113880 restraints weight = 10230.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.115879 restraints weight = 7630.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.116598 restraints weight = 6077.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.117317 restraints weight = 5294.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.117507 restraints weight = 4962.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.3214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6859  Z= 0.115
  Angle     :  0.627   8.163   9346  Z= 0.308
  Chirality :  0.042   0.145   1052
  Planarity :  0.005   0.043   1211
  Dihedral  :  4.641  24.657    963
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.04 %
    Favored  : 91.96 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 18.95 %
    Favored  : 79.30 %
  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: -2.03 (0.30), residues: 858
  helix:  0.31 (0.31), residues: 317
  sheet: -1.48 (0.50), residues: 132
  loop : -2.74 (0.29), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 299 
 TYR   0.016   0.001   TYR B 240 
 PHE   0.023   0.001   PHE C 276 
 TRP   0.009   0.001   TRP C  63 
 HIS   0.003   0.001   HIS B 478 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 6859)
  covalent geometry    : angle       0.62672 ( 9346)
  hydrogen bonds       : bond        0.02614 (  234)
  hydrogen bonds       : angle       3.99921 (  756)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A   30 ARG cc_start: 0.6224 (mtt90) cc_final: 0.5748 (ttm-80)
REVERT: B  209 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7816 (tt0)
REVERT: B  248 THR cc_start: 0.8605 (p) cc_final: 0.8309 (t)
REVERT: C  243 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6596 (tm-30)
REVERT: C  250 LEU cc_start: 0.8612 (mm) cc_final: 0.8245 (mm)
REVERT: C  258 TRP cc_start: 0.8388 (m100) cc_final: 0.8168 (m100)
REVERT: C  359 GLU cc_start: 0.8183 (mp0) cc_final: 0.7456 (mp0)
  outliers start: 12
  outliers final: 11
  residues processed: 103
  average time/residue: 0.0633
  time to fit residues: 9.3768
Evaluate side-chains
  106 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  216 SER
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  209 GLN
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  388 VAL
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  488 SER
Chi-restraints excluded: chain C residue   16 SER
Chi-restraints excluded: chain C residue   21 CYS
Chi-restraints excluded: chain C residue  314 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 60 optimal weight:    0.2980
   chunk 50 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0370
   chunk 85 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    0.6460

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

Flipped N/Q/H residues before XYZ refinement:
A 211 GLN
B 192 ASN
C  51 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.139523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.113783 restraints weight = 10174.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.116135 restraints weight = 7065.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.117940 restraints weight = 5476.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.119054 restraints weight = 4569.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.119935 restraints weight = 4021.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.3333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6859  Z= 0.114
  Angle     :  0.651  14.714   9346  Z= 0.312
  Chirality :  0.042   0.142   1052
  Planarity :  0.005   0.042   1211
  Dihedral  :  4.522  25.055    963
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 18.80 %
    Favored  : 79.01 %
  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: -1.82 (0.30), residues: 858
  helix:  0.60 (0.32), residues: 310
  sheet: -1.39 (0.49), residues: 134
  loop : -2.65 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 299 
 TYR   0.015   0.001   TYR B 240 
 PHE   0.020   0.001   PHE C 276 
 TRP   0.008   0.001   TRP C  63 
 HIS   0.004   0.001   HIS C  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 6859)
  covalent geometry    : angle       0.65054 ( 9346)
  hydrogen bonds       : bond        0.02611 (  234)
  hydrogen bonds       : angle       3.92279 (  756)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.159 
Fit side-chains
REVERT: B  248 THR cc_start: 0.8593 (p) cc_final: 0.8253 (t)
REVERT: B  283 MET cc_start: 0.7168 (mtp) cc_final: 0.6966 (mtp)
REVERT: C  243 GLU cc_start: 0.7063 (tm-30) cc_final: 0.6555 (tm-30)
REVERT: C  250 LEU cc_start: 0.8613 (mm) cc_final: 0.8259 (mm)
REVERT: C  359 GLU cc_start: 0.8134 (mp0) cc_final: 0.7490 (mp0)
  outliers start: 15
  outliers final: 11
  residues processed: 101
  average time/residue: 0.0502
  time to fit residues: 7.4048
Evaluate side-chains
  100 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  216 SER
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  388 VAL
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  488 SER
Chi-restraints excluded: chain C residue   16 SER
Chi-restraints excluded: chain C residue   21 CYS
Chi-restraints excluded: chain C residue  314 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 63 optimal weight:    0.0770
   chunk 3 optimal weight:    0.5980
   chunk 13 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 83 optimal weight:   10.0000
   chunk 9 optimal weight:    0.0870
   chunk 4 optimal weight:    0.0470
   chunk 64 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   overall best weight:    0.3414

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

Flipped N/Q/H residues before XYZ refinement:
A 211 GLN
C  51 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.142065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.114998 restraints weight = 10230.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.117690 restraints weight = 6871.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.119596 restraints weight = 5219.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.120729 restraints weight = 4320.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.121720 restraints weight = 3803.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.3566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   6859  Z= 0.107
  Angle     :  0.641  14.789   9346  Z= 0.308
  Chirality :  0.041   0.139   1052
  Planarity :  0.005   0.043   1211
  Dihedral  :  4.363  22.218    963
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 19.97 %
    Favored  : 78.57 %
  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: -1.62 (0.30), residues: 858
  helix:  0.79 (0.32), residues: 309
  sheet: -1.34 (0.49), residues: 136
  loop : -2.54 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 299 
 TYR   0.016   0.001   TYR B 240 
 PHE   0.019   0.001   PHE C 276 
 TRP   0.009   0.001   TRP C  63 
 HIS   0.002   0.000   HIS B 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 6859)
  covalent geometry    : angle       0.64054 ( 9346)
  hydrogen bonds       : bond        0.02397 (  234)
  hydrogen bonds       : angle       3.80352 (  756)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1055.78 seconds
wall clock time: 18 minutes 55.95 seconds (1135.95 seconds total)