Starting phenix.real_space_refine
on Fri Mar 14 00:54:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xwq_10635/03_2025/6xwq_10635.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xwq_10635/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xwq_10635/03_2025/6xwq_10635.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xwq_10635/03_2025/6xwq_10635.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xwq_10635/03_2025/6xwq_10635.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xwq_10635/03_2025/6xwq_10635.cif"
  }
  resolution = 3.41
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 7.40, per 1000 atoms: 0.77
  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: 2.81
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  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: 0.99
  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: 2.95

  Time building geometry restraints manager: 3.29 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 430 or resid 501))
  selection = (chain 'B' and (resid 5 through 264 or resid 266 through 430 or resid 501))
  selection = (chain 'C' and (resid 5 through 264 or resid 266 through 430 or resid 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:             0.520
  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:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     27.870
  Find NCS groups from input model:        0.460
  Set up NCS constraints:                  0.050
  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:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.300
-------------------------------------------------------------------------------
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= 0.206
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.022   0.002   TRP B 428 
 HIS   0.001   0.000   HIS B  34 
 PHE   0.013   0.001   PHE C 302 
 TYR   0.013   0.001   TYR B 387 
 ARG   0.003   0.000   ARG C 278 

*********************** 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  : 1.018 
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: 0.1865
  time to fit residues: 50.5233
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  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    9.9990
   chunk 95 optimal weight:   30.0000
   chunk 52 optimal weight:   10.0000
   chunk 32 optimal weight:    3.9990
   chunk 64 optimal weight:    6.9990
   chunk 51 optimal weight:    6.9990
   chunk 98 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 73 optimal weight:    7.9990
   chunk 114 optimal weight:    0.7980
   overall best weight:    3.7588

-------------------------------------------------------------------------------
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 321 GLN
** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 110 ASN
B 138 ASN
B 174 ASN
B 340 GLN
C 110 ASN
C 138 ASN
C 174 ASN
** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.069267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.053407 restraints weight = 51370.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.2972 rms_B_bonded: 4.94
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2974
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2974 r_free = 0.2974    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2974 r_free = 0.2974    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2974
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.1756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9747  Z= 0.314
  Angle     :  0.695  10.919  13265  Z= 0.345
  Chirality :  0.042   0.197   1651
  Planarity :  0.005   0.053   1632
  Dihedral  :  5.209  82.351   1368
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 15.21 %
    Favored  : 82.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.23), residues: 1275
  helix: -0.22 (0.16), residues: 1035
  sheet:  None (None), residues: 0
  loop : -1.63 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 428 
 HIS   0.002   0.001   HIS C 334 
 PHE   0.013   0.002   PHE A  28 
 TYR   0.017   0.002   TYR B 387 
 ARG   0.007   0.000   ARG B 289 

*********************** 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
  156 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 1.085 
Fit side-chains
   revert: symmetry clash
REVERT: A  107 ARG cc_start: 0.8129 (mtm110) cc_final: 0.7618 (ttm-80)
REVERT: A  271 MET cc_start: 0.9013 (mtm) cc_final: 0.8688 (mtm)
REVERT: A  321 GLN cc_start: 0.9144 (mt0) cc_final: 0.8739 (mm-40)
REVERT: A  365 MET cc_start: 0.9343 (tpp) cc_final: 0.8865 (tpp)
REVERT: A  399 MET cc_start: 0.8743 (mmm) cc_final: 0.8249 (mmt)
REVERT: B  109 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.6555 (m-10)
REVERT: B  219 MET cc_start: 0.9164 (mmp) cc_final: 0.8729 (tpp)
REVERT: C   61 MET cc_start: 0.8613 (tpp) cc_final: 0.8275 (mmt)
REVERT: C   90 TYR cc_start: 0.8874 (t80) cc_final: 0.8654 (t80)
REVERT: C  109 PHE cc_start: 0.7156 (OUTLIER) cc_final: 0.5900 (m-10)
REVERT: C  321 GLN cc_start: 0.9165 (mt0) cc_final: 0.8914 (mm-40)
REVERT: C  324 THR cc_start: 0.9268 (m) cc_final: 0.9027 (p)
REVERT: C  399 MET cc_start: 0.8771 (mmm) cc_final: 0.8230 (mmt)
  outliers start: 21
  outliers final: 14
  residues processed: 145
  average time/residue: 0.1602
  time to fit residues: 35.8476
Evaluate side-chains
  141 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 125
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   63 ILE
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 A residue  358 VAL
Chi-restraints excluded: chain B residue  109 PHE
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  358 VAL
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  311 THR
Chi-restraints excluded: chain C residue  358 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 118 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9990
   chunk 67 optimal weight:    6.9990
   chunk 43 optimal weight:    5.9990
   chunk 92 optimal weight:    0.9980
   chunk 76 optimal weight:    3.9990
   chunk 86 optimal weight:    9.9990
   chunk 71 optimal weight:    7.9990
   chunk 63 optimal weight:    9.9990
   chunk 47 optimal weight:    2.9990
   chunk 109 optimal weight:    3.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 340 GLN
C 330 ASN
C 340 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.076929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.060728 restraints weight = 58462.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 5.39
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3049
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3049 r_free = 0.3049    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3050 r_free = 0.3050    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3050
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9747  Z= 0.240
  Angle     :  0.632  10.031  13265  Z= 0.310
  Chirality :  0.040   0.191   1651
  Planarity :  0.005   0.051   1632
  Dihedral  :  5.108  87.447   1368
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 17.00 %
    Favored  : 80.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.24), residues: 1275
  helix:  0.31 (0.17), residues: 1044
  sheet:  None (None), residues: 0
  loop : -1.03 (0.44), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  20 
 HIS   0.001   0.000   HIS C 334 
 PHE   0.012   0.001   PHE C 302 
 TYR   0.014   0.001   TYR B 387 
 ARG   0.006   0.000   ARG B 289 

*********************** 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
  163 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 138
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 LEU cc_start: 0.9405 (mt) cc_final: 0.8872 (mt)
REVERT: A  107 ARG cc_start: 0.8109 (mtm110) cc_final: 0.7661 (ttm-80)
REVERT: A  271 MET cc_start: 0.9006 (mtm) cc_final: 0.8693 (mtm)
REVERT: A  321 GLN cc_start: 0.9117 (mt0) cc_final: 0.8612 (mm-40)
REVERT: A  365 MET cc_start: 0.9365 (tpp) cc_final: 0.8944 (tpp)
REVERT: A  399 MET cc_start: 0.8537 (mmm) cc_final: 0.8137 (mmt)
REVERT: B  109 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.6620 (m-10)
REVERT: B  219 MET cc_start: 0.9240 (mmp) cc_final: 0.8764 (tpp)
REVERT: C   61 MET cc_start: 0.8618 (tpp) cc_final: 0.8325 (mmt)
REVERT: C   90 TYR cc_start: 0.8876 (t80) cc_final: 0.8654 (t80)
REVERT: C   97 MET cc_start: 0.8912 (mmm) cc_final: 0.8513 (mpp)
REVERT: C  109 PHE cc_start: 0.7130 (OUTLIER) cc_final: 0.5949 (m-10)
REVERT: C  321 GLN cc_start: 0.9152 (mt0) cc_final: 0.8855 (mm-40)
REVERT: C  324 THR cc_start: 0.9275 (m) cc_final: 0.9066 (p)
REVERT: C  399 MET cc_start: 0.8674 (mmm) cc_final: 0.8238 (mmt)
  outliers start: 25
  outliers final: 14
  residues processed: 154
  average time/residue: 0.1577
  time to fit residues: 37.2668
Evaluate side-chains
  148 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
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  261 ILE
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 B residue  281 SER
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  358 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 102 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 98 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 116 optimal weight:    0.6980
   chunk 28 optimal weight:    5.9990
   chunk 85 optimal weight:    7.9990
   chunk 65 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 21 optimal weight:    6.9990
   chunk 119 optimal weight:    3.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.3471 r_free = 0.3471 target = 0.073765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.057959 restraints weight = 48359.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3064 rms_B_bonded: 4.84
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3080
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3080
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.2383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9747  Z= 0.178
  Angle     :  0.627   9.812  13265  Z= 0.300
  Chirality :  0.040   0.169   1651
  Planarity :  0.005   0.050   1632
  Dihedral  :  5.002  89.582   1368
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 19.18 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.25), residues: 1275
  helix:  0.68 (0.17), residues: 1044
  sheet:  None (None), residues: 0
  loop : -0.64 (0.46), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 428 
 HIS   0.001   0.000   HIS A 334 
 PHE   0.013   0.001   PHE C 302 
 TYR   0.014   0.001   TYR B 387 
 ARG   0.005   0.000   ARG B 289 

*********************** 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
  171 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 148
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
REVERT: A  107 ARG cc_start: 0.7959 (mtm110) cc_final: 0.7558 (ttm-80)
REVERT: A  271 MET cc_start: 0.8976 (mtm) cc_final: 0.8671 (mtm)
REVERT: A  365 MET cc_start: 0.9383 (tpp) cc_final: 0.8996 (tpp)
REVERT: A  389 MET cc_start: 0.9426 (ptm) cc_final: 0.9182 (ptt)
REVERT: A  399 MET cc_start: 0.8379 (mmm) cc_final: 0.8013 (mmt)
REVERT: B   50 ASP cc_start: 0.9202 (t70) cc_final: 0.8963 (m-30)
REVERT: C   19 LEU cc_start: 0.9314 (tt) cc_final: 0.9077 (pp)
REVERT: C   61 MET cc_start: 0.8515 (tpp) cc_final: 0.8273 (mmt)
REVERT: C   97 MET cc_start: 0.8854 (mmm) cc_final: 0.8499 (mmm)
REVERT: C  109 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6010 (m-10)
REVERT: C  399 MET cc_start: 0.8574 (mmm) cc_final: 0.8241 (mmt)
  outliers start: 23
  outliers final: 13
  residues processed: 164
  average time/residue: 0.1630
  time to fit residues: 40.8192
Evaluate side-chains
  145 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 131
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
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  261 ILE
Chi-restraints excluded: chain A residue  281 SER
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 77 optimal weight:    0.0170
   chunk 42 optimal weight:   10.0000
   chunk 7 optimal weight:    9.9990
   chunk 23 optimal weight:    5.9990
   chunk 116 optimal weight:    7.9990
   chunk 78 optimal weight:    4.9990
   chunk 91 optimal weight:    7.9990
   chunk 17 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   chunk 22 optimal weight:   10.0000
   overall best weight:    2.6026

-------------------------------------------------------------------------------
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 = 0.3446 r_free = 0.3446 target = 0.072687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.056027 restraints weight = 68203.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3023 rms_B_bonded: 5.68
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3044
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3044 r_free = 0.3044    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3044 r_free = 0.3044    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3044
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.2607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9747  Z= 0.242
  Angle     :  0.661  11.832  13265  Z= 0.317
  Chirality :  0.041   0.190   1651
  Planarity :  0.005   0.050   1632
  Dihedral  :  5.004  89.796   1368
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 20.78 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.25), residues: 1275
  helix:  0.84 (0.17), residues: 1047
  sheet:  None (None), residues: 0
  loop : -0.34 (0.47), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 428 
 HIS   0.001   0.000   HIS C 334 
 PHE   0.014   0.001   PHE C 302 
 TYR   0.014   0.002   TYR C  90 
 ARG   0.004   0.000   ARG B 289 

*********************** 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
  171 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 142
  time to evaluate  : 1.002 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 ARG cc_start: 0.8005 (mtm110) cc_final: 0.7600 (ttm-80)
REVERT: A  109 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.6787 (m-10)
REVERT: A  271 MET cc_start: 0.8946 (mtp) cc_final: 0.8640 (mtm)
REVERT: A  321 GLN cc_start: 0.9173 (mt0) cc_final: 0.8826 (mm-40)
REVERT: A  365 MET cc_start: 0.9426 (tpp) cc_final: 0.9066 (tpp)
REVERT: A  399 MET cc_start: 0.8484 (mmm) cc_final: 0.8098 (mmt)
REVERT: B   55 LEU cc_start: 0.9265 (mt) cc_final: 0.9061 (mt)
REVERT: B  107 ARG cc_start: 0.7834 (mtm110) cc_final: 0.7456 (ttm-80)
REVERT: B  109 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.6808 (m-10)
REVERT: B  365 MET cc_start: 0.9311 (tpp) cc_final: 0.9057 (tpp)
REVERT: C   61 MET cc_start: 0.8601 (tpp) cc_final: 0.8335 (mmt)
REVERT: C   97 MET cc_start: 0.8864 (mmm) cc_final: 0.8514 (mmm)
REVERT: C  107 ARG cc_start: 0.7884 (mtm110) cc_final: 0.7456 (ttm-80)
REVERT: C  109 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6154 (m-10)
REVERT: C  399 MET cc_start: 0.8704 (mmm) cc_final: 0.8384 (mmt)
  outliers start: 29
  outliers final: 18
  residues processed: 161
  average time/residue: 0.1712
  time to fit residues: 41.8189
Evaluate side-chains
  155 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 134
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  109 PHE
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  261 ILE
Chi-restraints excluded: chain B residue   35 PHE
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 B residue  306 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  219 MET
Chi-restraints excluded: chain C residue  224 VAL
Chi-restraints excluded: chain C residue  243 LEU
Chi-restraints excluded: chain C residue  358 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 118 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9990
   chunk 81 optimal weight:    4.9990
   chunk 85 optimal weight:    6.9990
   chunk 67 optimal weight:    1.9990
   chunk 94 optimal weight:   10.0000
   chunk 105 optimal weight:    0.0870
   chunk 89 optimal weight:    0.9990
   chunk 93 optimal weight:    6.9990
   chunk 103 optimal weight:    0.9980
   overall best weight:    1.0164

-------------------------------------------------------------------------------
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 = 0.3479 r_free = 0.3479 target = 0.074340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.057272 restraints weight = 69428.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 5.95
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3066
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3066 r_free = 0.3066    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3066 r_free = 0.3066    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3066
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.2893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9747  Z= 0.170
  Angle     :  0.653  12.847  13265  Z= 0.305
  Chirality :  0.040   0.147   1651
  Planarity :  0.004   0.051   1632
  Dihedral  :  4.864  89.419   1368
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 22.07 %
    Favored  : 75.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.25), residues: 1275
  helix:  1.10 (0.17), residues: 1029
  sheet:  None (None), residues: 0
  loop : -0.79 (0.43), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  20 
 HIS   0.001   0.000   HIS A  34 
 PHE   0.014   0.001   PHE C 302 
 TYR   0.014   0.001   TYR C  90 
 ARG   0.004   0.000   ARG B 289 

*********************** 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: 20
    poor density    : 154
  time to evaluate  : 1.083 
Fit side-chains
REVERT: A  107 ARG cc_start: 0.8016 (mtm110) cc_final: 0.7540 (ttm-80)
REVERT: A  137 LEU cc_start: 0.9396 (mp) cc_final: 0.9194 (pp)
REVERT: A  271 MET cc_start: 0.8956 (mtp) cc_final: 0.8658 (mtm)
REVERT: A  321 GLN cc_start: 0.9136 (mt0) cc_final: 0.8772 (mm-40)
REVERT: A  346 LEU cc_start: 0.9599 (tp) cc_final: 0.9390 (pp)
REVERT: A  365 MET cc_start: 0.9355 (tpp) cc_final: 0.9049 (tpp)
REVERT: B   50 ASP cc_start: 0.9306 (t70) cc_final: 0.9006 (m-30)
REVERT: B   55 LEU cc_start: 0.9198 (mt) cc_final: 0.8983 (mt)
REVERT: B  109 PHE cc_start: 0.7542 (OUTLIER) cc_final: 0.6708 (m-10)
REVERT: B  365 MET cc_start: 0.9320 (tpp) cc_final: 0.9037 (tpp)
REVERT: B  399 MET cc_start: 0.8465 (mtp) cc_final: 0.8226 (mmt)
REVERT: C   19 LEU cc_start: 0.9273 (tt) cc_final: 0.9041 (pp)
REVERT: C   61 MET cc_start: 0.8384 (tpp) cc_final: 0.8182 (mmt)
REVERT: C   97 MET cc_start: 0.8745 (mmm) cc_final: 0.8529 (mmm)
REVERT: C  107 ARG cc_start: 0.7860 (mtm110) cc_final: 0.7412 (ttm-80)
REVERT: C  109 PHE cc_start: 0.7328 (OUTLIER) cc_final: 0.6115 (m-10)
REVERT: C  399 MET cc_start: 0.8550 (mmm) cc_final: 0.8254 (mmt)
  outliers start: 20
  outliers final: 13
  residues processed: 169
  average time/residue: 0.1632
  time to fit residues: 42.0752
Evaluate side-chains
  154 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 139
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
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 B residue   35 PHE
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   35 PHE
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue  109 PHE
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  165 ILE
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  224 VAL
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 2 optimal weight:    8.9990
   chunk 125 optimal weight:    2.9990
   chunk 82 optimal weight:    9.9990
   chunk 86 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 108 optimal weight:    4.9990
   chunk 117 optimal weight:    0.9980
   chunk 23 optimal weight:    9.9990
   chunk 66 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   overall best weight:    2.1386

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.074160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.056826 restraints weight = 87983.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 6.69
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3036
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3036
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.3014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9747  Z= 0.218
  Angle     :  0.660  12.103  13265  Z= 0.315
  Chirality :  0.041   0.157   1651
  Planarity :  0.004   0.051   1632
  Dihedral  :  4.750  84.636   1368
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 23.06 %
    Favored  : 74.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.25), residues: 1275
  helix:  1.21 (0.17), residues: 1029
  sheet:  None (None), residues: 0
  loop : -0.97 (0.42), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 428 
 HIS   0.000   0.000   HIS B  34 
 PHE   0.014   0.001   PHE C 302 
 TYR   0.015   0.002   TYR C  90 
 ARG   0.004   0.000   ARG B 289 

*********************** 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
  165 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 141
  time to evaluate  : 1.139 
Fit side-chains
REVERT: A  107 ARG cc_start: 0.8073 (mtm110) cc_final: 0.7596 (ttm-80)
REVERT: A  109 PHE cc_start: 0.7322 (OUTLIER) cc_final: 0.6765 (m-10)
REVERT: A  137 LEU cc_start: 0.9414 (mp) cc_final: 0.9179 (pp)
REVERT: A  259 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8381 (t0)
REVERT: A  271 MET cc_start: 0.8978 (mtp) cc_final: 0.8693 (mtm)
REVERT: A  321 GLN cc_start: 0.9138 (mt0) cc_final: 0.8806 (mm-40)
REVERT: A  346 LEU cc_start: 0.9605 (tp) cc_final: 0.9384 (pp)
REVERT: A  365 MET cc_start: 0.9391 (tpp) cc_final: 0.9077 (tpp)
REVERT: B   50 ASP cc_start: 0.9270 (t70) cc_final: 0.9053 (m-30)
REVERT: B  107 ARG cc_start: 0.7793 (mtm110) cc_final: 0.7399 (ttm-80)
REVERT: B  109 PHE cc_start: 0.7576 (OUTLIER) cc_final: 0.6749 (m-10)
REVERT: B  272 ILE cc_start: 0.8941 (mm) cc_final: 0.8718 (mp)
REVERT: B  365 MET cc_start: 0.9320 (tpp) cc_final: 0.9062 (tpp)
REVERT: C   59 LEU cc_start: 0.9317 (tp) cc_final: 0.9056 (tp)
REVERT: C   61 MET cc_start: 0.8543 (tpp) cc_final: 0.8298 (mmt)
REVERT: C  107 ARG cc_start: 0.7911 (mtm110) cc_final: 0.7473 (ttm-80)
REVERT: C  109 PHE cc_start: 0.7374 (OUTLIER) cc_final: 0.6185 (m-10)
REVERT: C  399 MET cc_start: 0.8602 (mmm) cc_final: 0.8324 (mmt)
  outliers start: 24
  outliers final: 16
  residues processed: 157
  average time/residue: 0.1806
  time to fit residues: 42.6734
Evaluate side-chains
  158 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 138
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  109 PHE
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  259 ASP
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain B residue   35 PHE
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 B residue  301 ILE
Chi-restraints excluded: chain C residue   35 PHE
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  219 MET
Chi-restraints excluded: chain C residue  224 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 19 optimal weight:    1.9990
   chunk 22 optimal weight:   20.0000
   chunk 59 optimal weight:    1.9990
   chunk 93 optimal weight:    9.9990
   chunk 28 optimal weight:    0.2980
   chunk 12 optimal weight:    0.0070
   chunk 80 optimal weight:    9.9990
   chunk 41 optimal weight:    5.9990
   chunk 76 optimal weight:    0.2980
   chunk 73 optimal weight:   10.0000
   chunk 115 optimal weight:    2.9990
   overall best weight:    0.9202

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.079338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.062382 restraints weight = 65165.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 5.92
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 = 0.26   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 = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3086
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.3214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9747  Z= 0.167
  Angle     :  0.672  10.861  13265  Z= 0.312
  Chirality :  0.041   0.156   1651
  Planarity :  0.004   0.051   1632
  Dihedral  :  4.676  82.708   1368
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 23.56 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.25), residues: 1275
  helix:  1.21 (0.17), residues: 1032
  sheet:  None (None), residues: 0
  loop : -1.02 (0.42), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  20 
 HIS   0.000   0.000   HIS A 334 
 PHE   0.014   0.001   PHE C 302 
 TYR   0.015   0.001   TYR A  90 
 ARG   0.004   0.000   ARG B 289 

*********************** 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
  174 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 150
  time to evaluate  : 2.176 
Fit side-chains
REVERT: A  107 ARG cc_start: 0.8047 (mtm110) cc_final: 0.7656 (ttm-80)
REVERT: A  109 PHE cc_start: 0.7257 (OUTLIER) cc_final: 0.6726 (m-10)
REVERT: A  137 LEU cc_start: 0.9379 (mp) cc_final: 0.9154 (pp)
REVERT: A  259 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8412 (t0)
REVERT: A  271 MET cc_start: 0.8947 (mtp) cc_final: 0.8656 (mtm)
REVERT: A  321 GLN cc_start: 0.9068 (mt0) cc_final: 0.8674 (mm-40)
REVERT: A  346 LEU cc_start: 0.9583 (tp) cc_final: 0.9382 (pp)
REVERT: A  365 MET cc_start: 0.9311 (tpp) cc_final: 0.9039 (tpp)
REVERT: B   50 ASP cc_start: 0.9227 (t70) cc_final: 0.9021 (m-30)
REVERT: B  107 ARG cc_start: 0.7635 (mtm110) cc_final: 0.7246 (ttm-80)
REVERT: B  109 PHE cc_start: 0.7505 (OUTLIER) cc_final: 0.6717 (m-10)
REVERT: B  110 ASN cc_start: 0.8896 (t0) cc_final: 0.8654 (t0)
REVERT: B  272 ILE cc_start: 0.8893 (mm) cc_final: 0.8664 (mp)
REVERT: B  365 MET cc_start: 0.9336 (tpp) cc_final: 0.9087 (tpp)
REVERT: B  399 MET cc_start: 0.8386 (mtp) cc_final: 0.8018 (mmt)
REVERT: C   19 LEU cc_start: 0.9214 (tt) cc_final: 0.8968 (pp)
REVERT: C   63 ILE cc_start: 0.9034 (mt) cc_final: 0.8747 (mt)
REVERT: C  107 ARG cc_start: 0.7871 (mtm110) cc_final: 0.7422 (ttm-80)
REVERT: C  109 PHE cc_start: 0.7434 (OUTLIER) cc_final: 0.6237 (m-10)
REVERT: C  271 MET cc_start: 0.8696 (mtp) cc_final: 0.8425 (mtm)
REVERT: C  399 MET cc_start: 0.8437 (mmm) cc_final: 0.8200 (mmt)
  outliers start: 24
  outliers final: 16
  residues processed: 167
  average time/residue: 0.2407
  time to fit residues: 61.6933
Evaluate side-chains
  161 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 141
  time to evaluate  : 1.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 VAL
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  109 PHE
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  259 ASP
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 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  224 VAL
Chi-restraints excluded: chain C residue  243 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 74 optimal weight:    8.9990
   chunk 90 optimal weight:    3.9990
   chunk 113 optimal weight:    0.0570
   chunk 24 optimal weight:    8.9990
   chunk 125 optimal weight:    0.9980
   chunk 121 optimal weight:    0.0670
   chunk 96 optimal weight:    5.9990
   chunk 112 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0980
   chunk 12 optimal weight:    0.0070
   overall best weight:    0.2454

-------------------------------------------------------------------------------
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 = 0.3525 r_free = 0.3525 target = 0.075923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.058518 restraints weight = 74101.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 6.26
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3114
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3114 r_free = 0.3114    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 = 0.3114 r_free = 0.3114    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3114
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.3507

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= 0.154
  Angle     :  0.677  12.685  13265  Z= 0.311
  Chirality :  0.041   0.177   1651
  Planarity :  0.004   0.050   1632
  Dihedral  :  4.524  79.149   1368
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 23.46 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.24), residues: 1275
  helix:  1.21 (0.17), residues: 1026
  sheet:  None (None), residues: 0
  loop : -0.95 (0.41), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 428 
 HIS   0.002   0.000   HIS C  34 
 PHE   0.012   0.001   PHE C 302 
 TYR   0.015   0.001   TYR C  37 
 ARG   0.003   0.000   ARG B 289 

*********************** 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
  187 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 162
  time to evaluate  : 1.091 
Fit side-chains
REVERT: A   56 LEU cc_start: 0.9073 (mt) cc_final: 0.8347 (tt)
REVERT: A   59 LEU cc_start: 0.9210 (tp) cc_final: 0.8841 (tt)
REVERT: A  107 ARG cc_start: 0.8053 (mtm110) cc_final: 0.7653 (ttm-80)
REVERT: A  271 MET cc_start: 0.8928 (mtp) cc_final: 0.8723 (mtm)
REVERT: A  321 GLN cc_start: 0.9058 (mt0) cc_final: 0.8663 (mm-40)
REVERT: A  368 MET cc_start: 0.9206 (tpp) cc_final: 0.8738 (tpp)
REVERT: A  389 MET cc_start: 0.9402 (ptm) cc_final: 0.9153 (ptt)
REVERT: B   50 ASP cc_start: 0.9199 (t70) cc_final: 0.8998 (m-30)
REVERT: B  109 PHE cc_start: 0.7531 (OUTLIER) cc_final: 0.6722 (m-10)
REVERT: B  110 ASN cc_start: 0.8847 (t0) cc_final: 0.8568 (t0)
REVERT: B  272 ILE cc_start: 0.8899 (mm) cc_final: 0.8666 (mp)
REVERT: B  365 MET cc_start: 0.9334 (tpp) cc_final: 0.9081 (tpp)
REVERT: C   19 LEU cc_start: 0.9196 (tt) cc_final: 0.8965 (pp)
REVERT: C  107 ARG cc_start: 0.7820 (mtm110) cc_final: 0.7395 (ttm-80)
REVERT: C  109 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.6261 (m-10)
REVERT: C  399 MET cc_start: 0.8450 (mmm) cc_final: 0.8159 (mmt)
  outliers start: 25
  outliers final: 16
  residues processed: 179
  average time/residue: 0.1674
  time to fit residues: 45.3632
Evaluate side-chains
  165 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 147
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 VAL
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   63 ILE
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   35 PHE
Chi-restraints excluded: chain B residue   56 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 B residue  403 MET
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 92 optimal weight:    0.1980
   chunk 113 optimal weight:    0.0770
   chunk 28 optimal weight:    1.9990
   chunk 97 optimal weight:    0.8980
   chunk 119 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 84 optimal weight:   10.0000
   chunk 90 optimal weight:    4.9990
   chunk 104 optimal weight:    3.9990
   chunk 10 optimal weight:   10.0000
   overall best weight:    0.8140

-------------------------------------------------------------------------------
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 = 0.3525 r_free = 0.3525 target = 0.075847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.058212 restraints weight = 76906.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3097 rms_B_bonded: 6.45
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3097
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    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 = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3097
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.3639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9747  Z= 0.169
  Angle     :  0.711  13.035  13265  Z= 0.321
  Chirality :  0.041   0.167   1651
  Planarity :  0.004   0.050   1632
  Dihedral  :  4.493  77.452   1368
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 25.55 %
    Favored  : 72.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.25), residues: 1275
  helix:  1.25 (0.17), residues: 1029
  sheet:  None (None), residues: 0
  loop : -1.26 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 428 
 HIS   0.000   0.000   HIS C 334 
 PHE   0.013   0.001   PHE C 302 
 TYR   0.015   0.001   TYR A  90 
 ARG   0.004   0.000   ARG B 289 

********************** 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
  165 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 146
  time to evaluate  : 1.002 
Fit side-chains
REVERT: A   56 LEU cc_start: 0.9106 (mt) cc_final: 0.8875 (mt)
REVERT: A   59 LEU cc_start: 0.9259 (tp) cc_final: 0.8856 (tt)
REVERT: A   80 LEU cc_start: 0.9223 (tt) cc_final: 0.8698 (pp)
REVERT: A  107 ARG cc_start: 0.8045 (mtm110) cc_final: 0.7631 (ttm-80)
REVERT: A  271 MET cc_start: 0.8924 (mtp) cc_final: 0.8708 (mtm)
REVERT: A  272 ILE cc_start: 0.8942 (mm) cc_final: 0.8714 (mp)
REVERT: A  321 GLN cc_start: 0.8998 (mt0) cc_final: 0.8627 (mm-40)
REVERT: A  368 MET cc_start: 0.9131 (tpp) cc_final: 0.8738 (tpp)
REVERT: B   50 ASP cc_start: 0.9232 (t70) cc_final: 0.8986 (m-30)
REVERT: B   58 MET cc_start: 0.9523 (tmm) cc_final: 0.9286 (ppp)
REVERT: B  109 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.6637 (m-10)
REVERT: B  110 ASN cc_start: 0.8804 (t0) cc_final: 0.8550 (t0)
REVERT: B  272 ILE cc_start: 0.8911 (mm) cc_final: 0.8671 (mp)
REVERT: B  365 MET cc_start: 0.9346 (tpp) cc_final: 0.9102 (tpp)
REVERT: C   19 LEU cc_start: 0.9178 (tt) cc_final: 0.8959 (pp)
REVERT: C  107 ARG cc_start: 0.7822 (mtm110) cc_final: 0.7412 (ttm-80)
REVERT: C  109 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.6287 (m-10)
REVERT: C  399 MET cc_start: 0.8464 (mmm) cc_final: 0.8196 (mmt)
  outliers start: 19
  outliers final: 16
  residues processed: 157
  average time/residue: 0.1614
  time to fit residues: 38.9084
Evaluate side-chains
  165 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 147
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 VAL
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   63 ILE
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  224 VAL
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  403 MET
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 31 optimal weight:   10.0000
   chunk 70 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 114 optimal weight:    2.9990
   chunk 80 optimal weight:    8.9990
   chunk 110 optimal weight:    7.9990
   chunk 87 optimal weight:   10.0000
   chunk 65 optimal weight:    9.9990
   chunk 84 optimal weight:   10.0000
   chunk 112 optimal weight:    0.0970
   chunk 92 optimal weight:    0.7980
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
C 114 ASN
C 321 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.075121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.056966 restraints weight = 79864.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3070 rms_B_bonded: 6.54
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3067
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3067 r_free = 0.3067    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3067 r_free = 0.3067    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3067
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.3664

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= 0.185
  Angle     :  0.702  13.029  13265  Z= 0.319
  Chirality :  0.041   0.169   1651
  Planarity :  0.004   0.050   1632
  Dihedral  :  4.442  75.583   1368
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 25.55 %
    Favored  : 72.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.25), residues: 1275
  helix:  1.27 (0.17), residues: 1032
  sheet:  None (None), residues: 0
  loop : -1.21 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 428 
 HIS   0.000   0.000   HIS A 334 
 PHE   0.013   0.001   PHE C 302 
 TYR   0.017   0.001   TYR A  90 
 ARG   0.004   0.000   ARG A 401 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3896.00 seconds
wall clock time: 69 minutes 14.62 seconds (4154.62 seconds total)