Starting phenix.real_space_refine
on Tue Nov 18 00:06:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xwq_10635/11_2025/6xwq_10635.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xwq_10635/11_2025/6xwq_10635.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.41
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xwq_10635/11_2025/6xwq_10635.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xwq_10635/11_2025/6xwq_10635.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xwq_10635/11_2025/6xwq_10635.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xwq_10635/11_2025/6xwq_10635.map"
  }
  resolution = 3.41
  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=   0.003 sd=   0.020
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      48      5.16       5
     C    6309      2.51       5
     N    1549      2.21       5
     O    1666      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9572
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 426, 3178
          Classifications: {'peptide': 426}
          Link IDs: {'PTRANS': 18, 'TRANS': 407}
    Chain: "B"
      Number of atoms: 3189
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 426, 3178
          Classifications: {'peptide': 426}
          Link IDs: {'PTRANS': 18, 'TRANS': 407}
      Conformer: "B"
        Number of residues, atoms: 426, 3178
          Classifications: {'peptide': 426}
          Link IDs: {'PTRANS': 18, 'TRANS': 407}
          bond proxies already assigned to first conformer: 3225
    Chain: "C"
      Number of atoms: 3178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 426, 3178
          Classifications: {'peptide': 426}
          Link IDs: {'PTRANS': 18, 'TRANS': 407}
    Chain: "A"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
    Chain: "B"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
    Chain: "C"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AARG B 265 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG B 265 " occ=0.50
  Time building chain proxies: 3.13, per 1000 atoms: 0.33
  Number of scatterers: 9572
  At special positions: 0
  Unit cell: (105.248, 108.284, 81.972, 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      48     16.00
     O    1666      8.00
     N    1549      7.00
     C    6309      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: 1.01
  Conformation dependent library (CDL) restraints added in 504.2 milliseconds
  

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2294

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 0 sheets defined
      81.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 36
      removed outlier: 3.644A  pdb=" N   ALA A  26 " --> pdb=" O   LEU A  22 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   VAL A  27 " --> pdb=" O   VAL A  23 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 44
    Processing helix  chain 'A' and resid 45 through 59
      removed outlier: 3.722A  pdb=" N   GLY A  49 " --> pdb=" O   ILE A  45 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU A  59 " --> pdb=" O   LEU A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 74
      removed outlier: 3.532A  pdb=" N   VAL A  64 " --> pdb=" O   VAL A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 110
      removed outlier: 4.029A  pdb=" N   TYR A  90 " --> pdb=" O   LYS A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 138
    Processing helix  chain 'A' and resid 143 through 150
    Processing helix  chain 'A' and resid 153 through 171
    Processing helix  chain 'A' and resid 175 through 223
      removed outlier: 3.621A  pdb=" N   LYS A 180 " --> pdb=" O   GLU A 176 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   SER A 181 " --> pdb=" O   ARG A 177 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ALA A 182 " --> pdb=" O   VAL A 178 " (cutoff:3.500A)
      Proline residue:  A 208  - end of helix
      removed outlier: 3.869A  pdb=" N   ALA A 216 " --> pdb=" O   PHE A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 257
      removed outlier: 3.667A  pdb=" N   VAL A 233 " --> pdb=" O   PRO A 229 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   TYR A 238 " --> pdb=" O   VAL A 234 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   THR A 239 " --> pdb=" O   GLY A 235 " (cutoff:3.500A)
      removed outlier: 4.534A  pdb=" N   PHE A 250 " --> pdb=" O   VAL A 246 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   ILE A 251 " --> pdb=" O   ILE A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 278
      removed outlier: 5.499A  pdb=" N   ASP A 269 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
      removed outlier: 5.459A  pdb=" N   ALA A 270 " --> pdb=" O   LYS A 266 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   THR A 273 " --> pdb=" O   ASP A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 293
      removed outlier: 3.527A  pdb=" N   GLU A 293 " --> pdb=" O   ARG A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 303
    Processing helix  chain 'A' and resid 304 through 310
    Processing helix  chain 'A' and resid 314 through 332
      removed outlier: 3.566A  pdb=" N   LEU A 326 " --> pdb=" O   GLY A 322 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ILE A 332 " --> pdb=" O   VAL A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 354
      removed outlier: 3.953A  pdb=" N   LEU A 346 " --> pdb=" O   LEU A 342 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   VAL A 349 " --> pdb=" O   VAL A 345 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   LEU A 350 " --> pdb=" O   LEU A 346 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   GLY A 354 " --> pdb=" O   LEU A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 365
      removed outlier: 3.869A  pdb=" N   ILE A 364 " --> pdb=" O   GLY A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 371
    Processing helix  chain 'A' and resid 381 through 393
      removed outlier: 3.978A  pdb=" N   LEU A 385 " --> pdb=" O   SER A 381 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   ILE A 393 " --> pdb=" O   MET A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 419
      removed outlier: 4.255A  pdb=" N   GLY A 400 " --> pdb=" O   ILE A 396 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   MET A 403 " --> pdb=" O   MET A 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 12
    Processing helix  chain 'B' and resid 13 through 36
      removed outlier: 3.670A  pdb=" N   LEU B  22 " --> pdb=" O   ILE B  18 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ALA B  26 " --> pdb=" O   LEU B  22 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   VAL B  27 " --> pdb=" O   VAL B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 44
    Processing helix  chain 'B' and resid 45 through 59
      removed outlier: 3.776A  pdb=" N   GLY B  49 " --> pdb=" O   ILE B  45 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU B  59 " --> pdb=" O   LEU B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 72
    Processing helix  chain 'B' and resid 76 through 110
      removed outlier: 3.749A  pdb=" N   ARG B  82 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   TYR B  90 " --> pdb=" O   LYS B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 138
    Processing helix  chain 'B' and resid 143 through 150
    Processing helix  chain 'B' and resid 153 through 171
    Processing helix  chain 'B' and resid 175 through 223
      removed outlier: 3.591A  pdb=" N   LYS B 180 " --> pdb=" O   GLU B 176 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   SER B 181 " --> pdb=" O   ARG B 177 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   GLN B 205 " --> pdb=" O   GLY B 201 " (cutoff:3.500A)
      Proline residue:  B 208  - end of helix
      removed outlier: 3.563A  pdb=" N   ILE B 215 " --> pdb=" O   VAL B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 229 through 257
      removed outlier: 3.735A  pdb=" N   VAL B 233 " --> pdb=" O   PRO B 229 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   TYR B 238 " --> pdb=" O   VAL B 234 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   THR B 239 " --> pdb=" O   GLY B 235 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   PHE B 250 " --> pdb=" O   VAL B 246 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   ILE B 251 " --> pdb=" O   ILE B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 278
      removed outlier: 5.040A  pdb=" N   ASP B 269 " --> pdb=" O  AARG B 265 " (cutoff:3.500A)
      removed outlier: 5.592A  pdb=" N   ALA B 270 " --> pdb=" O   LYS B 266 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   THR B 273 " --> pdb=" O   ASP B 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 293
    Processing helix  chain 'B' and resid 304 through 313
      removed outlier: 4.210A  pdb=" N   THR B 311 " --> pdb=" O   PRO B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 332
      removed outlier: 3.747A  pdb=" N   LEU B 326 " --> pdb=" O   GLY B 322 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ILE B 332 " --> pdb=" O   VAL B 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 354
      removed outlier: 4.035A  pdb=" N   LEU B 346 " --> pdb=" O   LEU B 342 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   VAL B 349 " --> pdb=" O   VAL B 345 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   LEU B 350 " --> pdb=" O   LEU B 346 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   GLY B 354 " --> pdb=" O   LEU B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 361 through 366
    Processing helix  chain 'B' and resid 366 through 371
    Processing helix  chain 'B' and resid 382 through 393
      removed outlier: 3.872A  pdb=" N   ALA B 388 " --> pdb=" O   ALA B 384 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ILE B 393 " --> pdb=" O   MET B 389 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 419
      removed outlier: 3.640A  pdb=" N   LEU B 397 " --> pdb=" O   ILE B 393 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   GLY B 400 " --> pdb=" O   ILE B 396 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   MET B 403 " --> pdb=" O   MET B 399 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 7 through 12
      removed outlier: 3.693A  pdb=" N   ASP C  11 " --> pdb=" O   ARG C   7 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 13 through 36
      removed outlier: 3.591A  pdb=" N   LEU C  22 " --> pdb=" O   ILE C  18 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ALA C  26 " --> pdb=" O   LEU C  22 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   VAL C  27 " --> pdb=" O   VAL C  23 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 37 through 45
    Processing helix  chain 'C' and resid 45 through 59
      removed outlier: 3.799A  pdb=" N   GLY C  49 " --> pdb=" O   ILE C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 60 through 74
    Processing helix  chain 'C' and resid 76 through 110
      removed outlier: 3.950A  pdb=" N   TYR C  90 " --> pdb=" O   LYS C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 131 through 138
    Processing helix  chain 'C' and resid 143 through 150
    Processing helix  chain 'C' and resid 153 through 171
    Processing helix  chain 'C' and resid 175 through 223
      removed outlier: 3.881A  pdb=" N   SER C 181 " --> pdb=" O   ARG C 177 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   THR C 184 " --> pdb=" O   LYS C 180 " (cutoff:3.500A)
      Proline residue:  C 208  - end of helix
      removed outlier: 3.529A  pdb=" N   ALA C 213 " --> pdb=" O   ILE C 209 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   ALA C 216 " --> pdb=" O   PHE C 212 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 229 through 257
      removed outlier: 3.652A  pdb=" N   VAL C 233 " --> pdb=" O   PRO C 229 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   TYR C 238 " --> pdb=" O   VAL C 234 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   THR C 239 " --> pdb=" O   GLY C 235 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   PHE C 250 " --> pdb=" O   VAL C 246 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ILE C 251 " --> pdb=" O   ILE C 247 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 259 through 278
      removed outlier: 5.360A  pdb=" N   ASP C 269 " --> pdb=" O   ARG C 265 " (cutoff:3.500A)
      removed outlier: 5.512A  pdb=" N   ALA C 270 " --> pdb=" O   LYS C 266 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   THR C 273 " --> pdb=" O   ASP C 269 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 283 through 293
      removed outlier: 3.597A  pdb=" N   GLU C 293 " --> pdb=" O   ARG C 289 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 298 through 303
      removed outlier: 3.567A  pdb=" N   PHE C 302 " --> pdb=" O   ASP C 298 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 304 through 313
      removed outlier: 4.315A  pdb=" N   THR C 311 " --> pdb=" O   PRO C 307 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 314 through 332
      removed outlier: 3.661A  pdb=" N   LEU C 326 " --> pdb=" O   GLY C 322 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 337 through 354
      removed outlier: 3.965A  pdb=" N   LEU C 346 " --> pdb=" O   LEU C 342 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   VAL C 349 " --> pdb=" O   VAL C 345 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   LEU C 350 " --> pdb=" O   LEU C 346 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   GLY C 354 " --> pdb=" O   LEU C 350 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 360 through 365
      removed outlier: 3.919A  pdb=" N   ILE C 364 " --> pdb=" O   GLY C 360 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 366 through 371
    Processing helix  chain 'C' and resid 381 through 420
      removed outlier: 4.054A  pdb=" N   LEU C 385 " --> pdb=" O   SER C 381 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ILE C 393 " --> pdb=" O   MET C 389 " (cutoff:3.500A)
      removed outlier: 4.860A  pdb=" N   ALA C 395 " --> pdb=" O   LEU C 391 " (cutoff:3.500A)
      removed outlier: 5.665A  pdb=" N   ILE C 396 " --> pdb=" O   GLY C 392 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   GLY C 400 " --> pdb=" O   ILE C 396 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   MET C 403 " --> pdb=" O   MET C 399 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 424 through 429
      removed outlier: 4.335A  pdb=" N   TRP C 428 " --> pdb=" O   ASP C 424 " (cutoff:3.500A)

    698 hydrogen bonds defined for protein.
    2095 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.65

  Time building geometry restraints manager: 1.31 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2976
        1.34 -     1.46: 1339
        1.46 -     1.57: 5336
        1.57 -     1.69: 0
        1.69 -     1.80: 96
  Bond restraints: 9747
  Sorted by residual:
  bond pdb=" CA  VAL C 373 "
       pdb=" CB  VAL C 373 "
    ideal  model  delta    sigma   weight residual
    1.527  1.543 -0.017 1.31e-02 5.83e+03 1.61e+00
  bond pdb=" CG1 ILE B  18 "
       pdb=" CD1 ILE B  18 "
    ideal  model  delta    sigma   weight residual
    1.513  1.478  0.035 3.90e-02 6.57e+02 8.08e-01
  bond pdb=" CB  VAL C 200 "
       pdb=" CG2 VAL C 200 "
    ideal  model  delta    sigma   weight residual
    1.521  1.493  0.028 3.30e-02 9.18e+02 7.41e-01
  bond pdb=" CB  VAL A 200 "
       pdb=" CG2 VAL A 200 "
    ideal  model  delta    sigma   weight residual
    1.521  1.493  0.028 3.30e-02 9.18e+02 7.11e-01
  bond pdb=" N   ARG C 278 "
       pdb=" CA  ARG C 278 "
    ideal  model  delta    sigma   weight residual
    1.460  1.471 -0.011 1.42e-02 4.96e+03 6.28e-01
  ... (remaining 9742 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 12839
        1.46 -     2.91: 350
        2.91 -     4.37: 59
        4.37 -     5.82: 13
        5.82 -     7.28: 4
  Bond angle restraints: 13265
  Sorted by residual:
  angle pdb=" N   VAL B 211 "
        pdb=" CA  VAL B 211 "
        pdb=" C   VAL B 211 "
      ideal   model   delta    sigma   weight residual
     113.07  108.39    4.68 1.36e+00 5.41e-01 1.19e+01
  angle pdb=" C   LEU B   6 "
        pdb=" N   ARG B   7 "
        pdb=" CA  ARG B   7 "
      ideal   model   delta    sigma   weight residual
     121.54  127.66   -6.12 1.91e+00 2.74e-01 1.03e+01
  angle pdb=" C   LEU A   6 "
        pdb=" N   ARG A   7 "
        pdb=" CA  ARG A   7 "
      ideal   model   delta    sigma   weight residual
     121.54  127.37   -5.83 1.91e+00 2.74e-01 9.31e+00
  angle pdb=" C   VAL C 246 "
        pdb=" N   ILE C 247 "
        pdb=" CA  ILE C 247 "
      ideal   model   delta    sigma   weight residual
     121.84  118.82    3.02 1.13e+00 7.83e-01 7.12e+00
  angle pdb=" N   GLY A 235 "
        pdb=" CA  GLY A 235 "
        pdb=" C   GLY A 235 "
      ideal   model   delta    sigma   weight residual
     115.66  111.75    3.91 1.56e+00 4.11e-01 6.29e+00
  ... (remaining 13260 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.65: 5224
       17.65 -    35.30: 437
       35.30 -    52.95: 70
       52.95 -    70.60: 7
       70.60 -    88.25: 10
  Dihedral angle restraints: 5748
    sinusoidal: 2135
      harmonic: 3613
  Sorted by residual:
  dihedral pdb=" CA  GLN A 128 "
           pdb=" C   GLN A 128 "
           pdb=" N   PRO A 129 "
           pdb=" CA  PRO A 129 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.33   17.67     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CA  GLN B 128 "
           pdb=" C   GLN B 128 "
           pdb=" N   PRO B 129 "
           pdb=" CA  PRO B 129 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.36   16.64     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CA  GLN C 128 "
           pdb=" C   GLN C 128 "
           pdb=" N   PRO C 129 "
           pdb=" CA  PRO C 129 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.66   16.34     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 5745 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 934
       0.028 -    0.056: 495
       0.056 -    0.085: 155
       0.085 -    0.113: 55
       0.113 -    0.141: 12
  Chirality restraints: 1651
  Sorted by residual:
  chirality pdb=" CB  ILE B 258 "
            pdb=" CA  ILE B 258 "
            pdb=" CG1 ILE B 258 "
            pdb=" CG2 ILE B 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 4.96e-01
  chirality pdb=" CA  LEU B 284 "
            pdb=" N   LEU B 284 "
            pdb=" C   LEU B 284 "
            pdb=" CB  LEU B 284 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.45e-01
  chirality pdb=" CA  ILE C  75 "
            pdb=" N   ILE C  75 "
            pdb=" C   ILE C  75 "
            pdb=" CB  ILE C  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.85e-01
  ... (remaining 1648 not shown)

  Planarity restraints: 1632
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 207 "    0.038 5.00e-02 4.00e+02   5.75e-02 5.29e+00
        pdb=" N   PRO A 208 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A 208 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 208 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 207 "    0.036 5.00e-02 4.00e+02   5.48e-02 4.81e+00
        pdb=" N   PRO C 208 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO C 208 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO C 208 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 207 "   -0.036 5.00e-02 4.00e+02   5.39e-02 4.65e+00
        pdb=" N   PRO B 208 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO B 208 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 208 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 1629 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 277
        2.72 -     3.26: 10782
        3.26 -     3.81: 15857
        3.81 -     4.35: 18939
        4.35 -     4.90: 32473
  Nonbonded interactions: 78328
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B   9 "
            pdb=" O   GLN B 205 "
     model   vdw
     2.171 3.040
  nonbonded pdb=" OG1 THR A 402 "
            pdb=" N   ASP A 501 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" OG1 THR C 402 "
            pdb=" N   ASP C 501 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" OG1 THR B 402 "
            pdb=" N   ASP B 501 "
     model   vdw
     2.285 3.120
  nonbonded pdb=" ND2 ASN A 313 "
            pdb=" OD1 ASP A 409 "
     model   vdw
     2.302 3.120
  ... (remaining 78323 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 5 through 264 or resid 266 through 501))
  selection = (chain 'B' and (resid 5 through 264 or resid 266 through 501))
  selection = (chain 'C' and (resid 5 through 264 or resid 266 through 501))
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             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:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.760
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
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      :  0.003   0.035   9747  Z= 0.147
  Angle     :  0.609   7.275  13265  Z= 0.346
  Chirality :  0.039   0.141   1651
  Planarity :  0.005   0.057   1632
  Dihedral  : 13.417  88.247   3454
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.54 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.80 (0.21), residues: 1275
  helix: -1.55 (0.14), residues: 1008
  sheet:  None (None), residues: 0
  loop : -2.27 (0.36), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 278 
 TYR   0.013   0.001   TYR B 387 
 PHE   0.013   0.001   PHE C 302 
 TRP   0.022   0.002   TRP B 428 
 HIS   0.001   0.000   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 9747)
  covalent geometry    : angle       0.60888 (13265)
  hydrogen bonds       : bond        0.11759 (  698)
  hydrogen bonds       : angle       5.73183 ( 2095)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   92 LEU cc_start: 0.8706 (mt) cc_final: 0.8488 (mp)
REVERT: C  271 MET cc_start: 0.7915 (mtp) cc_final: 0.7667 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.0864
  time to fit residues: 23.8205
Evaluate side-chains
  126 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    0.4980
   chunk 113 optimal weight:   10.0000
   chunk 53 optimal weight:    0.0670
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 123 optimal weight:    5.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   overall best weight:    1.6922

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

Flipped N/Q/H residues before XYZ refinement:
A 110 ASN
A 138 ASN
A 174 ASN
A 340 GLN
B 110 ASN
B 138 ASN
B 174 ASN
B 340 GLN
C 110 ASN
C 138 ASN
C 174 ASN
C 340 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.071361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.055733 restraints weight = 44970.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.3016 rms_B_bonded: 4.66
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3015
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3015 r_free = 0.3015    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3015 r_free = 0.3015    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3015
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.1706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9747  Z= 0.137
  Angle     :  0.652  11.627  13265  Z= 0.318
  Chirality :  0.040   0.206   1651
  Planarity :  0.005   0.052   1632
  Dihedral  :  5.097  81.586   1368
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 14.81 %
    Favored  : 83.80 %
  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: -0.85 (0.23), residues: 1275
  helix: -0.19 (0.16), residues: 1032
  sheet:  None (None), residues: 0
  loop : -1.63 (0.39), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 289 
 TYR   0.015   0.001   TYR B 387 
 PHE   0.012   0.001   PHE C 302 
 TRP   0.007   0.001   TRP C 428 
 HIS   0.001   0.000   HIS C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 9747)
  covalent geometry    : angle       0.65229 (13265)
  hydrogen bonds       : bond        0.03701 (  698)
  hydrogen bonds       : angle       4.49751 ( 2095)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 143
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
REVERT: A  107 ARG cc_start: 0.7985 (mtm110) cc_final: 0.7578 (ttm-80)
REVERT: A  271 MET cc_start: 0.9021 (mtm) cc_final: 0.8680 (mtm)
REVERT: A  321 GLN cc_start: 0.9123 (mt0) cc_final: 0.8644 (mm-40)
REVERT: A  365 MET cc_start: 0.9343 (tpp) cc_final: 0.8886 (tpp)
REVERT: A  389 MET cc_start: 0.9528 (ptm) cc_final: 0.9283 (ptt)
REVERT: A  399 MET cc_start: 0.8559 (mmm) cc_final: 0.8077 (mmt)
REVERT: B  219 MET cc_start: 0.9147 (mmp) cc_final: 0.8731 (tpp)
REVERT: B  321 GLN cc_start: 0.9177 (mt0) cc_final: 0.8790 (mm110)
REVERT: C   61 MET cc_start: 0.8460 (tpp) cc_final: 0.8129 (mmt)
REVERT: C   90 TYR cc_start: 0.8841 (t80) cc_final: 0.8638 (t80)
REVERT: C  109 PHE cc_start: 0.7109 (OUTLIER) cc_final: 0.5810 (m-10)
REVERT: C  219 MET cc_start: 0.9222 (mmp) cc_final: 0.8745 (tpp)
REVERT: C  321 GLN cc_start: 0.9146 (mt0) cc_final: 0.8808 (mm-40)
REVERT: C  324 THR cc_start: 0.9280 (m) cc_final: 0.9038 (p)
REVERT: C  399 MET cc_start: 0.8711 (mmm) cc_final: 0.8214 (mmt)
  outliers start: 14
  outliers final: 8
  residues processed: 150
  average time/residue: 0.0729
  time to fit residues: 17.2530
Evaluate side-chains
  136 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 127
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue  109 PHE
Chi-restraints excluded: chain C residue  165 ILE
Chi-restraints excluded: chain C residue  311 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 84 optimal weight:   10.0000
   chunk 90 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 108 optimal weight:    5.9990
   chunk 92 optimal weight:    0.9980
   chunk 111 optimal weight:   10.0000
   chunk 25 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 5 optimal weight:    0.3980
   chunk 35 optimal weight:    2.9990
   chunk 110 optimal weight:    0.9990
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.074585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.057315 restraints weight = 82992.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 6.67
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3038
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3038
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.2162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9747  Z= 0.112
  Angle     :  0.612  10.652  13265  Z= 0.294
  Chirality :  0.039   0.193   1651
  Planarity :  0.005   0.050   1632
  Dihedral  :  4.886  84.102   1368
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 16.40 %
    Favored  : 81.71 %
  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:  0.20 (0.24), residues: 1275
  helix:  0.47 (0.17), residues: 1038
  sheet:  None (None), residues: 0
  loop : -0.92 (0.43), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 289 
 TYR   0.013   0.001   TYR B 387 
 PHE   0.013   0.001   PHE C 302 
 TRP   0.007   0.001   TRP C 428 
 HIS   0.001   0.000   HIS A 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 9747)
  covalent geometry    : angle       0.61209 (13265)
  hydrogen bonds       : bond        0.03380 (  698)
  hydrogen bonds       : angle       4.21705 ( 2095)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 150
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
REVERT: A  107 ARG cc_start: 0.8034 (mtm110) cc_final: 0.7640 (ttm-80)
REVERT: A  271 MET cc_start: 0.8971 (mtm) cc_final: 0.8671 (mtm)
REVERT: A  321 GLN cc_start: 0.9106 (mt0) cc_final: 0.8597 (mm-40)
REVERT: A  365 MET cc_start: 0.9387 (tpp) cc_final: 0.9054 (tpp)
REVERT: A  399 MET cc_start: 0.8350 (mmm) cc_final: 0.7978 (mmt)
REVERT: B   50 ASP cc_start: 0.9263 (t70) cc_final: 0.8931 (m-30)
REVERT: B   59 LEU cc_start: 0.9284 (mt) cc_final: 0.9049 (mp)
REVERT: B  109 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.6771 (m-10)
REVERT: B  321 GLN cc_start: 0.9119 (mt0) cc_final: 0.8726 (mm110)
REVERT: B  365 MET cc_start: 0.9354 (tpp) cc_final: 0.8995 (tpp)
REVERT: B  399 MET cc_start: 0.8485 (mtp) cc_final: 0.8229 (mmt)
REVERT: C   90 TYR cc_start: 0.8884 (t80) cc_final: 0.8681 (t80)
REVERT: C  109 PHE cc_start: 0.7128 (OUTLIER) cc_final: 0.6050 (m-10)
REVERT: C  324 THR cc_start: 0.9275 (m) cc_final: 0.9064 (p)
REVERT: C  365 MET cc_start: 0.9449 (tpp) cc_final: 0.9171 (tpp)
REVERT: C  399 MET cc_start: 0.8661 (mmm) cc_final: 0.8289 (mmt)
  outliers start: 19
  outliers final: 11
  residues processed: 161
  average time/residue: 0.0747
  time to fit residues: 18.7927
Evaluate side-chains
  145 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 132
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain B residue  109 PHE
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue  109 PHE
Chi-restraints excluded: chain C residue  165 ILE
Chi-restraints excluded: chain C residue  243 LEU
Chi-restraints excluded: chain C residue  406 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9990
   chunk 62 optimal weight:    4.9990
   chunk 85 optimal weight:    0.9990
   chunk 81 optimal weight:    9.9990
   chunk 59 optimal weight:    0.6980
   chunk 14 optimal weight:    0.0370
   chunk 106 optimal weight:    9.9990
   chunk 51 optimal weight:    0.9990
   chunk 23 optimal weight:    8.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    0.7464

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.074563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.057661 restraints weight = 65777.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 5.84
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3103
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3103 r_free = 0.3103    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3103 r_free = 0.3103    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3103
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.2554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9747  Z= 0.110
  Angle     :  0.604  10.259  13265  Z= 0.291
  Chirality :  0.039   0.193   1651
  Planarity :  0.004   0.050   1632
  Dihedral  :  4.830  85.928   1368
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 18.49 %
    Favored  : 79.22 %
  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:  0.60 (0.25), residues: 1275
  helix:  0.71 (0.17), residues: 1041
  sheet:  None (None), residues: 0
  loop : -0.58 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 289 
 TYR   0.012   0.001   TYR B 387 
 PHE   0.014   0.001   PHE C 302 
 TRP   0.006   0.001   TRP C 428 
 HIS   0.001   0.000   HIS A 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 9747)
  covalent geometry    : angle       0.60413 (13265)
  hydrogen bonds       : bond        0.03191 (  698)
  hydrogen bonds       : angle       4.10649 ( 2095)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 153
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
REVERT: A  107 ARG cc_start: 0.7970 (mtm110) cc_final: 0.7561 (ttm-80)
REVERT: A  271 MET cc_start: 0.8956 (mtm) cc_final: 0.8659 (mtm)
REVERT: A  321 GLN cc_start: 0.9155 (mt0) cc_final: 0.8638 (mm-40)
REVERT: A  365 MET cc_start: 0.9354 (tpp) cc_final: 0.9089 (tpp)
REVERT: A  399 MET cc_start: 0.8312 (mmm) cc_final: 0.7966 (mmt)
REVERT: B   50 ASP cc_start: 0.9273 (t70) cc_final: 0.8993 (m-30)
REVERT: B  109 PHE cc_start: 0.7553 (OUTLIER) cc_final: 0.6800 (m-10)
REVERT: B  241 LEU cc_start: 0.9563 (mt) cc_final: 0.9244 (mp)
REVERT: B  321 GLN cc_start: 0.9129 (mt0) cc_final: 0.8723 (mm110)
REVERT: B  365 MET cc_start: 0.9362 (tpp) cc_final: 0.9046 (tpp)
REVERT: B  399 MET cc_start: 0.8340 (mtp) cc_final: 0.8139 (mmt)
REVERT: C  109 PHE cc_start: 0.7279 (OUTLIER) cc_final: 0.6168 (m-10)
REVERT: C  321 GLN cc_start: 0.9096 (mt0) cc_final: 0.8787 (mm-40)
REVERT: C  365 MET cc_start: 0.9471 (tpp) cc_final: 0.9224 (tpp)
REVERT: C  399 MET cc_start: 0.8569 (mmm) cc_final: 0.8293 (mmt)
  outliers start: 23
  outliers final: 12
  residues processed: 168
  average time/residue: 0.0729
  time to fit residues: 19.1692
Evaluate side-chains
  149 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 135
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain B residue  109 PHE
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain C residue   35 PHE
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue  109 PHE
Chi-restraints excluded: chain C residue  165 ILE
Chi-restraints excluded: chain C residue  243 LEU
Chi-restraints excluded: chain C residue  406 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 71 optimal weight:    8.9990
   chunk 100 optimal weight:    0.3980
   chunk 64 optimal weight:    0.5980
   chunk 107 optimal weight:    9.9990
   chunk 92 optimal weight:    4.9990
   chunk 33 optimal weight:    0.3980
   chunk 30 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 38 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   overall best weight:    1.0782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.074699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.056907 restraints weight = 86821.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 6.83
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3086
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3086 r_free = 0.3086    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3086 r_free = 0.3086    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3086
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.2843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9747  Z= 0.114
  Angle     :  0.620  10.023  13265  Z= 0.297
  Chirality :  0.040   0.170   1651
  Planarity :  0.004   0.050   1632
  Dihedral  :  4.788  85.600   1368
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 19.48 %
    Favored  : 78.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.25), residues: 1275
  helix:  0.85 (0.17), residues: 1044
  sheet:  None (None), residues: 0
  loop : -0.47 (0.45), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 289 
 TYR   0.012   0.001   TYR C  90 
 PHE   0.014   0.001   PHE C 302 
 TRP   0.004   0.001   TRP C 428 
 HIS   0.000   0.000   HIS C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 9747)
  covalent geometry    : angle       0.61954 (13265)
  hydrogen bonds       : bond        0.03223 (  698)
  hydrogen bonds       : angle       4.06520 ( 2095)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 149
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
REVERT: A  107 ARG cc_start: 0.8037 (mtm110) cc_final: 0.7588 (ttm-80)
REVERT: A  271 MET cc_start: 0.8987 (mtm) cc_final: 0.8708 (mtm)
REVERT: A  321 GLN cc_start: 0.9157 (mt0) cc_final: 0.8612 (mm-40)
REVERT: A  365 MET cc_start: 0.9368 (tpp) cc_final: 0.9138 (tpp)
REVERT: A  399 MET cc_start: 0.8318 (mmm) cc_final: 0.8063 (mmt)
REVERT: B   50 ASP cc_start: 0.9267 (t70) cc_final: 0.9025 (m-30)
REVERT: B  107 ARG cc_start: 0.7720 (mtm110) cc_final: 0.7400 (ttm-80)
REVERT: B  109 PHE cc_start: 0.7513 (OUTLIER) cc_final: 0.6774 (m-10)
REVERT: B  241 LEU cc_start: 0.9585 (mt) cc_final: 0.9279 (mp)
REVERT: B  321 GLN cc_start: 0.9111 (mt0) cc_final: 0.8909 (mm-40)
REVERT: B  365 MET cc_start: 0.9341 (tpp) cc_final: 0.9087 (tpp)
REVERT: C  109 PHE cc_start: 0.7325 (OUTLIER) cc_final: 0.6225 (m-10)
REVERT: C  365 MET cc_start: 0.9462 (tpp) cc_final: 0.9013 (tpp)
REVERT: C  399 MET cc_start: 0.8619 (mmm) cc_final: 0.8262 (mmt)
  outliers start: 23
  outliers final: 13
  residues processed: 163
  average time/residue: 0.0778
  time to fit residues: 19.5304
Evaluate side-chains
  152 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 137
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain B residue  109 PHE
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue  109 PHE
Chi-restraints excluded: chain C residue  165 ILE
Chi-restraints excluded: chain C residue  243 LEU
Chi-restraints excluded: chain C residue  406 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 114 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 57 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 65 optimal weight:    7.9990
   chunk 21 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 120 optimal weight:   10.0000
   chunk 78 optimal weight:    0.0770
   overall best weight:    0.8942

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.075519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.058723 restraints weight = 74844.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3110 rms_B_bonded: 6.31
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3133
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3133 r_free = 0.3133    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3133 r_free = 0.3133    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3133
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.3087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9747  Z= 0.113
  Angle     :  0.638  11.142  13265  Z= 0.302
  Chirality :  0.040   0.179   1651
  Planarity :  0.004   0.051   1632
  Dihedral  :  4.769  86.993   1368
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 20.58 %
    Favored  : 77.14 %
  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:  0.97 (0.25), residues: 1275
  helix:  1.05 (0.17), residues: 1026
  sheet:  None (None), residues: 0
  loop : -0.83 (0.42), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 289 
 TYR   0.012   0.001   TYR C  90 
 PHE   0.014   0.001   PHE C 302 
 TRP   0.005   0.001   TRP B  20 
 HIS   0.000   0.000   HIS C  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 9747)
  covalent geometry    : angle       0.63771 (13265)
  hydrogen bonds       : bond        0.03157 (  698)
  hydrogen bonds       : angle       4.04175 ( 2095)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 151
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
REVERT: A  107 ARG cc_start: 0.8031 (mtm110) cc_final: 0.7585 (ttm-80)
REVERT: A  271 MET cc_start: 0.8965 (mtm) cc_final: 0.8685 (mtm)
REVERT: A  321 GLN cc_start: 0.9144 (mt0) cc_final: 0.8604 (mm-40)
REVERT: A  365 MET cc_start: 0.9313 (tpp) cc_final: 0.9102 (tpp)
REVERT: A  389 MET cc_start: 0.9372 (ptm) cc_final: 0.9098 (ptt)
REVERT: B   50 ASP cc_start: 0.9163 (t70) cc_final: 0.8943 (m-30)
REVERT: B  107 ARG cc_start: 0.7689 (mtm110) cc_final: 0.7325 (ttm-80)
REVERT: B  109 PHE cc_start: 0.7513 (OUTLIER) cc_final: 0.6713 (m-10)
REVERT: B  241 LEU cc_start: 0.9573 (mt) cc_final: 0.9288 (mp)
REVERT: B  321 GLN cc_start: 0.9071 (mt0) cc_final: 0.8857 (mm-40)
REVERT: B  365 MET cc_start: 0.9287 (tpp) cc_final: 0.9017 (tpp)
REVERT: B  403 MET cc_start: 0.9077 (tmm) cc_final: 0.8808 (tmm)
REVERT: C  109 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.6292 (m-10)
REVERT: C  114 ASN cc_start: 0.9367 (m-40) cc_final: 0.9149 (t0)
REVERT: C  271 MET cc_start: 0.8601 (mtp) cc_final: 0.8368 (mtm)
REVERT: C  365 MET cc_start: 0.9425 (tpp) cc_final: 0.8993 (tpp)
REVERT: C  399 MET cc_start: 0.8574 (mmm) cc_final: 0.8236 (mmt)
  outliers start: 23
  outliers final: 13
  residues processed: 166
  average time/residue: 0.0677
  time to fit residues: 17.1868
Evaluate side-chains
  156 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 141
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  109 PHE
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue  109 PHE
Chi-restraints excluded: chain C residue  165 ILE
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  243 LEU
Chi-restraints excluded: chain C residue  403 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 94 optimal weight:    6.9990
   chunk 15 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 66 optimal weight:   10.0000
   chunk 67 optimal weight:    5.9990
   chunk 105 optimal weight:    2.9990
   chunk 30 optimal weight:    5.9990
   chunk 12 optimal weight:    0.8980
   chunk 42 optimal weight:   10.0000
   chunk 27 optimal weight:    3.9990
   overall best weight:    2.1586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.074312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.057209 restraints weight = 69191.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 5.93
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3084
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3084
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.3172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9747  Z= 0.146
  Angle     :  0.660  10.836  13265  Z= 0.318
  Chirality :  0.041   0.202   1651
  Planarity :  0.004   0.051   1632
  Dihedral  :  4.723  84.708   1368
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 20.58 %
    Favored  : 76.84 %
  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:  1.10 (0.25), residues: 1275
  helix:  1.08 (0.17), residues: 1047
  sheet:  None (None), residues: 0
  loop : -0.61 (0.44), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 289 
 TYR   0.015   0.001   TYR C  90 
 PHE   0.014   0.001   PHE C 302 
 TRP   0.005   0.001   TRP B 428 
 HIS   0.000   0.000   HIS C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 9747)
  covalent geometry    : angle       0.65976 (13265)
  hydrogen bonds       : bond        0.03293 (  698)
  hydrogen bonds       : angle       4.10639 ( 2095)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 145
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.9528 (tmm) cc_final: 0.9311 (tmm)
REVERT: A   59 LEU cc_start: 0.9203 (tp) cc_final: 0.8868 (tt)
REVERT: A  107 ARG cc_start: 0.8069 (mtm110) cc_final: 0.7623 (ttm-80)
REVERT: A  271 MET cc_start: 0.9018 (mtm) cc_final: 0.8747 (mtm)
REVERT: A  365 MET cc_start: 0.9363 (tpp) cc_final: 0.9090 (tpp)
REVERT: A  389 MET cc_start: 0.9349 (ptm) cc_final: 0.9073 (ptt)
REVERT: B   50 ASP cc_start: 0.9281 (t70) cc_final: 0.9014 (m-30)
REVERT: B  107 ARG cc_start: 0.7756 (mtm110) cc_final: 0.7254 (ttm-80)
REVERT: B  109 PHE cc_start: 0.7588 (OUTLIER) cc_final: 0.6771 (m-10)
REVERT: B  241 LEU cc_start: 0.9595 (mt) cc_final: 0.9305 (mp)
REVERT: B  321 GLN cc_start: 0.9120 (mt0) cc_final: 0.8899 (mm-40)
REVERT: B  399 MET cc_start: 0.8686 (mmt) cc_final: 0.8440 (mmm)
REVERT: C   59 LEU cc_start: 0.9290 (tp) cc_final: 0.8904 (tt)
REVERT: C  109 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.6175 (m-10)
REVERT: C  271 MET cc_start: 0.8625 (mtp) cc_final: 0.8365 (mtm)
REVERT: C  365 MET cc_start: 0.9434 (tpp) cc_final: 0.9222 (tpp)
REVERT: C  399 MET cc_start: 0.8608 (mmm) cc_final: 0.8285 (mmt)
  outliers start: 26
  outliers final: 16
  residues processed: 163
  average time/residue: 0.0754
  time to fit residues: 18.9587
Evaluate side-chains
  153 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 135
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain B residue   35 PHE
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  109 PHE
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue  109 PHE
Chi-restraints excluded: chain C residue  165 ILE
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  243 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 32 optimal weight:    7.9990
   chunk 27 optimal weight:    6.9990
   chunk 87 optimal weight:   10.0000
   chunk 81 optimal weight:    0.9990
   chunk 49 optimal weight:   10.0000
   chunk 112 optimal weight:    0.9990
   chunk 22 optimal weight:   30.0000
   chunk 48 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.9386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.075438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.058214 restraints weight = 77227.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 6.39
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3110
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3110 r_free = 0.3110    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3110 r_free = 0.3110    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3110
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.3377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9747  Z= 0.117
  Angle     :  0.666  10.223  13265  Z= 0.313
  Chirality :  0.041   0.199   1651
  Planarity :  0.004   0.051   1632
  Dihedral  :  4.708  83.812   1368
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 21.47 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.25), residues: 1275
  helix:  1.20 (0.17), residues: 1026
  sheet:  None (None), residues: 0
  loop : -0.98 (0.42), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 289 
 TYR   0.014   0.001   TYR C  90 
 PHE   0.014   0.001   PHE C 302 
 TRP   0.007   0.001   TRP B  20 
 HIS   0.000   0.000   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 9747)
  covalent geometry    : angle       0.66619 (13265)
  hydrogen bonds       : bond        0.03238 (  698)
  hydrogen bonds       : angle       4.02854 ( 2095)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 148
  time to evaluate  : 0.371 
Fit side-chains
REVERT: A   58 MET cc_start: 0.9515 (tmm) cc_final: 0.9261 (ppp)
REVERT: A   59 LEU cc_start: 0.9172 (tp) cc_final: 0.8817 (tt)
REVERT: A   80 LEU cc_start: 0.9251 (tt) cc_final: 0.8730 (pp)
REVERT: A  107 ARG cc_start: 0.8030 (mtm110) cc_final: 0.7673 (ttm-80)
REVERT: A  271 MET cc_start: 0.8996 (mtm) cc_final: 0.8781 (mtm)
REVERT: A  321 GLN cc_start: 0.9148 (mt0) cc_final: 0.8816 (mm-40)
REVERT: A  330 ASN cc_start: 0.9024 (m-40) cc_final: 0.8569 (t0)
REVERT: A  346 LEU cc_start: 0.9596 (tp) cc_final: 0.9375 (pp)
REVERT: A  365 MET cc_start: 0.9348 (tpp) cc_final: 0.9109 (tpp)
REVERT: A  389 MET cc_start: 0.9365 (ptm) cc_final: 0.9107 (ptt)
REVERT: B   99 VAL cc_start: 0.9435 (t) cc_final: 0.9176 (p)
REVERT: B  107 ARG cc_start: 0.7710 (mtm110) cc_final: 0.7368 (ttm-80)
REVERT: B  109 PHE cc_start: 0.7527 (OUTLIER) cc_final: 0.6696 (m-10)
REVERT: B  110 ASN cc_start: 0.8853 (t0) cc_final: 0.8606 (t0)
REVERT: B  241 LEU cc_start: 0.9576 (mt) cc_final: 0.9300 (mp)
REVERT: B  321 GLN cc_start: 0.9115 (mt0) cc_final: 0.8896 (mm-40)
REVERT: B  365 MET cc_start: 0.9338 (tpp) cc_final: 0.9095 (tpp)
REVERT: C   58 MET cc_start: 0.9474 (tmm) cc_final: 0.9134 (tmm)
REVERT: C   59 LEU cc_start: 0.9245 (tp) cc_final: 0.8957 (tt)
REVERT: C  109 PHE cc_start: 0.7424 (OUTLIER) cc_final: 0.6208 (m-10)
REVERT: C  114 ASN cc_start: 0.9421 (m-40) cc_final: 0.9140 (t0)
REVERT: C  271 MET cc_start: 0.8555 (mtp) cc_final: 0.8308 (mtm)
REVERT: C  365 MET cc_start: 0.9425 (tpp) cc_final: 0.9209 (tpp)
  outliers start: 21
  outliers final: 17
  residues processed: 159
  average time/residue: 0.0754
  time to fit residues: 18.3355
Evaluate side-chains
  164 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 145
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   35 PHE
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain B residue   35 PHE
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  109 PHE
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue  109 PHE
Chi-restraints excluded: chain C residue  165 ILE
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  243 LEU
Chi-restraints excluded: chain C residue  311 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 55 optimal weight:    0.6980
   chunk 12 optimal weight:    3.9990
   chunk 71 optimal weight:    9.9990
   chunk 68 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 120 optimal weight:   10.0000
   chunk 103 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0010
   chunk 41 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 115 optimal weight:    0.9990
   overall best weight:    0.9392

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

Flipped N/Q/H residues before XYZ refinement:
A 321 GLN
C 321 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.075234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.057733 restraints weight = 81224.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3105 rms_B_bonded: 6.54
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3107
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3107
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.3528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9747  Z= 0.118
  Angle     :  0.674  10.369  13265  Z= 0.317
  Chirality :  0.041   0.204   1651
  Planarity :  0.004   0.051   1632
  Dihedral  :  4.624  83.153   1368
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 22.17 %
    Favored  : 75.65 %
  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:  1.17 (0.25), residues: 1275
  helix:  1.14 (0.17), residues: 1047
  sheet:  None (None), residues: 0
  loop : -0.64 (0.44), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 289 
 TYR   0.015   0.001   TYR C  90 
 PHE   0.014   0.001   PHE C 302 
 TRP   0.005   0.001   TRP B  20 
 HIS   0.000   0.000   HIS C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 9747)
  covalent geometry    : angle       0.67407 (13265)
  hydrogen bonds       : bond        0.03196 (  698)
  hydrogen bonds       : angle       4.01219 ( 2095)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 150
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A   58 MET cc_start: 0.9523 (tmm) cc_final: 0.9286 (ppp)
REVERT: A   59 LEU cc_start: 0.9170 (tp) cc_final: 0.8806 (tt)
REVERT: A   80 LEU cc_start: 0.9260 (tt) cc_final: 0.8726 (pp)
REVERT: A  107 ARG cc_start: 0.8076 (mtm110) cc_final: 0.7707 (ttm-80)
REVERT: A  271 MET cc_start: 0.9002 (mtm) cc_final: 0.8791 (mtm)
REVERT: A  272 ILE cc_start: 0.8905 (mm) cc_final: 0.8673 (mp)
REVERT: A  321 GLN cc_start: 0.9130 (mt0) cc_final: 0.8796 (mm-40)
REVERT: A  330 ASN cc_start: 0.9030 (m-40) cc_final: 0.8651 (t0)
REVERT: A  346 LEU cc_start: 0.9610 (tp) cc_final: 0.9369 (pp)
REVERT: A  365 MET cc_start: 0.9328 (tpp) cc_final: 0.9104 (tpp)
REVERT: A  389 MET cc_start: 0.9365 (ptm) cc_final: 0.9103 (ptt)
REVERT: B   99 VAL cc_start: 0.9437 (t) cc_final: 0.9182 (p)
REVERT: B  107 ARG cc_start: 0.7712 (mtm110) cc_final: 0.7347 (ttm-80)
REVERT: B  109 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.6703 (m-10)
REVERT: B  110 ASN cc_start: 0.8853 (t0) cc_final: 0.8615 (t0)
REVERT: B  241 LEU cc_start: 0.9578 (mt) cc_final: 0.9297 (mp)
REVERT: B  321 GLN cc_start: 0.9105 (mt0) cc_final: 0.8880 (mm-40)
REVERT: B  365 MET cc_start: 0.9345 (tpp) cc_final: 0.9115 (tpp)
REVERT: C   58 MET cc_start: 0.9493 (tmm) cc_final: 0.9152 (tmm)
REVERT: C   59 LEU cc_start: 0.9291 (tp) cc_final: 0.9020 (tt)
REVERT: C   97 MET cc_start: 0.8570 (mmt) cc_final: 0.8359 (mmm)
REVERT: C  109 PHE cc_start: 0.7412 (OUTLIER) cc_final: 0.6179 (m-10)
REVERT: C  114 ASN cc_start: 0.9419 (m-40) cc_final: 0.9150 (t0)
REVERT: C  271 MET cc_start: 0.8525 (mtp) cc_final: 0.8277 (mtm)
  outliers start: 22
  outliers final: 17
  residues processed: 162
  average time/residue: 0.0739
  time to fit residues: 18.6198
Evaluate side-chains
  162 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 143
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   35 PHE
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain B residue   35 PHE
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  109 PHE
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue  109 PHE
Chi-restraints excluded: chain C residue  165 ILE
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  243 LEU
Chi-restraints excluded: chain C residue  311 THR
Chi-restraints excluded: chain C residue  403 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 12 optimal weight:    7.9990
   chunk 117 optimal weight:    9.9990
   chunk 123 optimal weight:    5.9990
   chunk 80 optimal weight:   10.0000
   chunk 72 optimal weight:    0.6980
   chunk 26 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   overall best weight:    1.6784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.075067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.058793 restraints weight = 51397.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 5.11
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3132
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3132 r_free = 0.3132    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3132 r_free = 0.3132    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3132
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.3545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9747  Z= 0.133
  Angle     :  0.702  10.216  13265  Z= 0.329
  Chirality :  0.042   0.193   1651
  Planarity :  0.004   0.051   1632
  Dihedral  :  4.538  78.905   1368
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 21.97 %
    Favored  : 75.84 %
  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:  1.19 (0.25), residues: 1275
  helix:  1.17 (0.17), residues: 1050
  sheet:  None (None), residues: 0
  loop : -0.75 (0.44), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 289 
 TYR   0.016   0.001   TYR A  90 
 PHE   0.014   0.001   PHE C 302 
 TRP   0.004   0.001   TRP C  16 
 HIS   0.000   0.000   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 9747)
  covalent geometry    : angle       0.70152 (13265)
  hydrogen bonds       : bond        0.03240 (  698)
  hydrogen bonds       : angle       4.05725 ( 2095)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.371 
Fit side-chains
REVERT: A   58 MET cc_start: 0.9559 (tmm) cc_final: 0.9296 (ppp)
REVERT: A   59 LEU cc_start: 0.9237 (tp) cc_final: 0.8873 (tt)
REVERT: A   80 LEU cc_start: 0.9247 (tt) cc_final: 0.8720 (pp)
REVERT: A  107 ARG cc_start: 0.8035 (mtm110) cc_final: 0.7669 (ttm-80)
REVERT: A  271 MET cc_start: 0.8994 (mtm) cc_final: 0.8771 (mtm)
REVERT: A  272 ILE cc_start: 0.8931 (mm) cc_final: 0.8694 (mp)
REVERT: A  321 GLN cc_start: 0.9097 (mt0) cc_final: 0.8736 (mm-40)
REVERT: A  365 MET cc_start: 0.9334 (tpp) cc_final: 0.9123 (tpp)
REVERT: A  389 MET cc_start: 0.9348 (ptm) cc_final: 0.9085 (ptt)
REVERT: B   59 LEU cc_start: 0.9210 (tp) cc_final: 0.8916 (tt)
REVERT: B  107 ARG cc_start: 0.7678 (mtm110) cc_final: 0.7328 (ttm-80)
REVERT: B  109 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.6704 (m-10)
REVERT: B  110 ASN cc_start: 0.8821 (t0) cc_final: 0.8560 (t0)
REVERT: B  321 GLN cc_start: 0.9141 (mt0) cc_final: 0.8915 (mm-40)
REVERT: B  365 MET cc_start: 0.9336 (tpp) cc_final: 0.9103 (tpp)
REVERT: C   58 MET cc_start: 0.9500 (tmm) cc_final: 0.9162 (tmm)
REVERT: C   59 LEU cc_start: 0.9303 (tp) cc_final: 0.9047 (tt)
REVERT: C   97 MET cc_start: 0.8542 (mmt) cc_final: 0.8288 (mmm)
REVERT: C  109 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.6157 (m-10)
REVERT: C  271 MET cc_start: 0.8527 (mtp) cc_final: 0.8272 (mtm)
  outliers start: 22
  outliers final: 19
  residues processed: 152
  average time/residue: 0.0727
  time to fit residues: 17.1992
Evaluate side-chains
  160 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 139
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   35 PHE
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain B residue   35 PHE
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  109 PHE
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue  109 PHE
Chi-restraints excluded: chain C residue  165 ILE
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  243 LEU
Chi-restraints excluded: chain C residue  311 THR
Chi-restraints excluded: chain C residue  403 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   chunk 80 optimal weight:    7.9990
   chunk 76 optimal weight:   10.0000
   chunk 99 optimal weight:    0.7980
   chunk 87 optimal weight:    8.9990
   chunk 66 optimal weight:    1.9990
   chunk 101 optimal weight:   10.0000
   chunk 95 optimal weight:    9.9990
   chunk 62 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
C 114 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.074666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.057668 restraints weight = 66216.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3109 rms_B_bonded: 5.86
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3104
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3104
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.3582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9747  Z= 0.135
  Angle     :  0.704  11.332  13265  Z= 0.329
  Chirality :  0.042   0.191   1651
  Planarity :  0.004   0.051   1632
  Dihedral  :  4.468  76.714   1368
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 22.37 %
    Favored  : 75.35 %
  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:  1.19 (0.25), residues: 1275
  helix:  1.18 (0.17), residues: 1050
  sheet:  None (None), residues: 0
  loop : -0.77 (0.44), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 289 
 TYR   0.016   0.001   TYR A  90 
 PHE   0.016   0.001   PHE B 242 
 TRP   0.004   0.001   TRP C  16 
 HIS   0.000   0.000   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 9747)
  covalent geometry    : angle       0.70413 (13265)
  hydrogen bonds       : bond        0.03253 (  698)
  hydrogen bonds       : angle       4.07836 ( 2095)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1787.95 seconds
wall clock time: 31 minutes 34.02 seconds (1894.02 seconds total)