Starting phenix.real_space_refine
on Wed Mar  4 00:18:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xwo_10633/03_2026/6xwo_10633.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xwo_10633/03_2026/6xwo_10633.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.39
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xwo_10633/03_2026/6xwo_10633.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xwo_10633/03_2026/6xwo_10633.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xwo_10633/03_2026/6xwo_10633.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xwo_10633/03_2026/6xwo_10633.map"
  }
  resolution = 3.39
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.020
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    6301      2.51       5
     N    1545      2.21       5
     O    1661      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9555
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 427, 3184
          Classifications: {'peptide': 427}
          Link IDs: {'PTRANS': 18, 'TRANS': 408}
    Chain: "B"
      Number of atoms: 3184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 427, 3184
          Classifications: {'peptide': 427}
          Link IDs: {'PTRANS': 18, 'TRANS': 408}
    Chain: "C"
      Number of atoms: 3187
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 427, 3187
          Classifications: {'peptide': 427}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 408}
          Chain breaks: 1
  Time building chain proxies: 2.08, per 1000 atoms: 0.22
  Number of scatterers: 9555
  At special positions: 0
  Unit cell: (79.948, 109.296, 120.428, 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    1661      8.00
     N    1545      7.00
     C    6301      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.80
  Conformation dependent library (CDL) restraints added in 418.6 milliseconds
  

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2292

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 0 sheets defined
      77.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 10
    Processing helix  chain 'A' and resid 13 through 36
    Processing helix  chain 'A' and resid 37 through 45
      removed outlier: 3.698A  pdb=" N   TYR A  44 " --> pdb=" O   ALA A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 58
      removed outlier: 3.736A  pdb=" N   GLY A  49 " --> pdb=" O   ILE A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 75
    Processing helix  chain 'A' and resid 81 through 110
      removed outlier: 3.996A  pdb=" N   VAL A  85 " --> pdb=" O   GLY A  81 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LYS A  86 " --> pdb=" O   ARG A  82 " (cutoff:3.500A)
      removed outlier: 3.751A  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 176 through 222
      Proline residue:  A 208  - end of helix
      removed outlier: 3.816A  pdb=" N   VAL A 218 " --> pdb=" O   LEU A 214 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLN A 222 " --> pdb=" O   VAL A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 256
      removed outlier: 4.846A  pdb=" N   PHE A 250 " --> pdb=" O   VAL A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 278
      removed outlier: 5.604A  pdb=" N   ASP A 269 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
      removed outlier: 5.315A  pdb=" N   ALA A 270 " --> pdb=" O   LYS A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 294
    Processing helix  chain 'A' and resid 298 through 303
    Processing helix  chain 'A' and resid 305 through 310
    Processing helix  chain 'A' and resid 314 through 332
      removed outlier: 3.763A  pdb=" N   VAL A 325 " --> pdb=" O   GLN A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 350
    Processing helix  chain 'A' and resid 351 through 353
      No H-bonds generated for 'chain 'A' and resid 351 through 353'
    Processing helix  chain 'A' and resid 362 through 374
    Processing helix  chain 'A' and resid 381 through 420
      removed outlier: 3.729A  pdb=" N   LEU A 385 " --> pdb=" O   SER A 381 " (cutoff:3.500A)
      removed outlier: 4.868A  pdb=" N   ALA A 395 " --> pdb=" O   LEU A 391 " (cutoff:3.500A)
      removed outlier: 5.703A  pdb=" N   ILE A 396 " --> pdb=" O   GLY A 392 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LEU A 397 " --> pdb=" O   ILE A 393 " (cutoff:3.500A)
      removed outlier: 4.900A  pdb=" N   MET A 399 " --> pdb=" O   ALA A 395 " (cutoff:3.500A)
      removed outlier: 5.107A  pdb=" N   GLY A 400 " --> pdb=" O   ILE A 396 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ASP A 409 " --> pdb=" O   ASN A 405 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU A 410 " --> pdb=" O   VAL A 406 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   VAL A 414 " --> pdb=" O   LEU A 410 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ILE A 415 " --> pdb=" O   ALA A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 428
    Processing helix  chain 'B' and resid 6 through 12
    Processing helix  chain 'B' and resid 17 through 32
    Processing helix  chain 'B' and resid 37 through 45
    Processing helix  chain 'B' and resid 45 through 58
      removed outlier: 3.884A  pdb=" N   GLY B  49 " --> pdb=" O   ILE B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 76
    Processing helix  chain 'B' and resid 81 through 109
      removed outlier: 3.740A  pdb=" N   VAL B  85 " --> pdb=" O   GLY B  81 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   TYR B  90 " --> pdb=" O   LYS B  86 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   SER B  95 " --> pdb=" O   TYR B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 139
    Processing helix  chain 'B' and resid 143 through 150
    Processing helix  chain 'B' and resid 152 through 172
      removed outlier: 3.575A  pdb=" N   VAL B 156 " --> pdb=" O   GLU B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 223
      Proline residue:  B 208  - end of helix
    Processing helix  chain 'B' and resid 227 through 255
      removed outlier: 4.570A  pdb=" N   GLY B 235 " --> pdb=" O   ALA B 231 " (cutoff:3.500A)
      removed outlier: 6.084A  pdb=" N   TYR B 238 " --> pdb=" O   VAL B 234 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   PHE B 250 " --> pdb=" O   VAL B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 278
      removed outlier: 5.706A  pdb=" N   ASP B 269 " --> pdb=" O   ARG B 265 " (cutoff:3.500A)
      removed outlier: 5.632A  pdb=" N   ALA B 270 " --> pdb=" O   LYS B 266 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 293
    Processing helix  chain 'B' and resid 298 through 313
      removed outlier: 3.551A  pdb=" N   PHE B 302 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   PHE B 304 " --> pdb=" O   GLY B 300 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   LEU B 306 " --> pdb=" O   PHE B 302 " (cutoff:3.500A)
      Proline residue:  B 307  - end of helix
      removed outlier: 4.478A  pdb=" N   THR B 311 " --> pdb=" O   PRO B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 332
      removed outlier: 3.911A  pdb=" N   LEU B 326 " --> pdb=" O   GLY B 322 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   VAL B 328 " --> pdb=" O   THR B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 352
    Processing helix  chain 'B' and resid 360 through 374
      removed outlier: 3.707A  pdb=" N   ILE B 364 " --> pdb=" O   GLY B 360 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   MET B 365 " --> pdb=" O   ALA B 361 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU B 366 " --> pdb=" O   GLY B 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 393
      removed outlier: 3.567A  pdb=" N   LEU B 385 " --> pdb=" O   SER B 381 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ILE B 393 " --> pdb=" O   MET B 389 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 397 through 411
      removed outlier: 4.513A  pdb=" N   MET B 403 " --> pdb=" O   MET B 399 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   VAL B 404 " --> pdb=" O   GLY B 400 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ASN B 405 " --> pdb=" O   ARG B 401 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   VAL B 406 " --> pdb=" O   THR B 402 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   ASP B 409 " --> pdb=" O   ASN B 405 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LEU B 410 " --> pdb=" O   VAL B 406 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 419
    Processing helix  chain 'C' and resid 14 through 34
      removed outlier: 4.264A  pdb=" N   TRP C  20 " --> pdb=" O   TRP C  16 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLY C  21 " --> pdb=" O   LYS C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 59
      removed outlier: 3.559A  pdb=" N   GLY C  49 " --> pdb=" O   ILE C  45 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LEU C  59 " --> pdb=" O   LEU C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 60 through 73
      removed outlier: 3.885A  pdb=" N   SER C  67 " --> pdb=" O   ILE C  63 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LEU C  68 " --> pdb=" O   VAL C  64 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLY C  71 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 109
      removed outlier: 3.872A  pdb=" N   ARG C  82 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   PHE C 100 " --> pdb=" O   ALA C  96 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 132 through 138
    Processing helix  chain 'C' and resid 143 through 149
    Processing helix  chain 'C' and resid 152 through 171
      removed outlier: 3.881A  pdb=" N   VAL C 156 " --> pdb=" O   GLU C 152 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ALA C 166 " --> pdb=" O   ILE C 162 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 175 through 222
      removed outlier: 3.910A  pdb=" N   GLN C 205 " --> pdb=" O   GLY C 201 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   TYR C 206 " --> pdb=" O   GLY C 202 " (cutoff:3.500A)
      Proline residue:  C 208  - end of helix
      removed outlier: 3.615A  pdb=" N   VAL C 218 " --> pdb=" O   LEU C 214 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 230 through 247
      removed outlier: 3.621A  pdb=" N   TYR C 238 " --> pdb=" O   VAL C 234 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   THR C 239 " --> pdb=" O   GLY C 235 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 247 through 256
    Processing helix  chain 'C' and resid 259 through 275
      removed outlier: 5.608A  pdb=" N   ASP C 269 " --> pdb=" O   ARG C 265 " (cutoff:3.500A)
      removed outlier: 5.348A  pdb=" N   ALA C 270 " --> pdb=" O   LYS C 266 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 283 through 292
      removed outlier: 3.514A  pdb=" N   VAL C 290 " --> pdb=" O   VAL C 286 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 298 through 313
      removed outlier: 4.304A  pdb=" N   PHE C 304 " --> pdb=" O   GLY C 300 " (cutoff:3.500A)
      Proline residue:  C 307  - end of helix
      removed outlier: 4.574A  pdb=" N   THR C 311 " --> pdb=" O   PRO C 307 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 316 through 331
      removed outlier: 3.747A  pdb=" N   VAL C 323 " --> pdb=" O   LEU C 319 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   VAL C 325 " --> pdb=" O   GLN C 321 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 340 through 348
      removed outlier: 3.733A  pdb=" N   VAL C 344 " --> pdb=" O   GLN C 340 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   VAL C 345 " --> pdb=" O   GLN C 341 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 350 through 355
      removed outlier: 4.131A  pdb=" N   GLY C 354 " --> pdb=" O   LEU C 350 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   THR C 355 " --> pdb=" O   ALA C 351 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 350 through 355'
    Processing helix  chain 'C' and resid 361 through 371
      removed outlier: 3.629A  pdb=" N   MET C 365 " --> pdb=" O   ALA C 361 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ALA C 367 " --> pdb=" O   ALA C 363 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   MET C 368 " --> pdb=" O   ILE C 364 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 387 through 392
      removed outlier: 3.599A  pdb=" N   GLY C 392 " --> pdb=" O   ALA C 388 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 393 through 401
      removed outlier: 3.624A  pdb=" N   LEU C 397 " --> pdb=" O   ILE C 393 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   MET C 399 " --> pdb=" O   ALA C 395 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   GLY C 400 " --> pdb=" O   ILE C 396 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 403 through 420
      removed outlier: 3.789A  pdb=" N   ASP C 409 " --> pdb=" O   ASN C 405 " (cutoff:3.500A)

    650 hydrogen bonds defined for protein.
    1944 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.50

  Time building geometry restraints manager: 1.07 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2967
        1.34 -     1.46: 1444
        1.46 -     1.57: 5224
        1.57 -     1.69: 0
        1.69 -     1.81: 96
  Bond restraints: 9731
  Sorted by residual:
  bond pdb=" C   THR C 378 "
       pdb=" N   PRO C 379 "
    ideal  model  delta    sigma   weight residual
    1.330  1.356 -0.026 1.23e-02 6.61e+03 4.30e+00
  bond pdb=" CB  THR B 168 "
       pdb=" CG2 THR B 168 "
    ideal  model  delta    sigma   weight residual
    1.521  1.468  0.053 3.30e-02 9.18e+02 2.59e+00
  bond pdb=" CB  VAL B 115 "
       pdb=" CG2 VAL B 115 "
    ideal  model  delta    sigma   weight residual
    1.521  1.482  0.039 3.30e-02 9.18e+02 1.40e+00
  bond pdb=" CB  VAL A 233 "
       pdb=" CG2 VAL A 233 "
    ideal  model  delta    sigma   weight residual
    1.521  1.482  0.039 3.30e-02 9.18e+02 1.40e+00
  bond pdb=" CB  VAL B 404 "
       pdb=" CG2 VAL B 404 "
    ideal  model  delta    sigma   weight residual
    1.521  1.482  0.039 3.30e-02 9.18e+02 1.39e+00
  ... (remaining 9726 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 12867
        1.75 -     3.51: 311
        3.51 -     5.26: 57
        5.26 -     7.01: 8
        7.01 -     8.77: 1
  Bond angle restraints: 13244
  Sorted by residual:
  angle pdb=" N   TYR C 387 "
        pdb=" CA  TYR C 387 "
        pdb=" C   TYR C 387 "
      ideal   model   delta    sigma   weight residual
     114.56  109.64    4.92 1.27e+00 6.20e-01 1.50e+01
  angle pdb=" N   LEU C 385 "
        pdb=" CA  LEU C 385 "
        pdb=" C   LEU C 385 "
      ideal   model   delta    sigma   weight residual
     112.68  108.44    4.24 1.33e+00 5.65e-01 1.01e+01
  angle pdb=" N   ALA A 207 "
        pdb=" CA  ALA A 207 "
        pdb=" C   ALA A 207 "
      ideal   model   delta    sigma   weight residual
     109.81  116.37   -6.56 2.21e+00 2.05e-01 8.80e+00
  angle pdb=" N   ALA C 386 "
        pdb=" CA  ALA C 386 "
        pdb=" C   ALA C 386 "
      ideal   model   delta    sigma   weight residual
     112.93  110.04    2.89 1.12e+00 7.97e-01 6.66e+00
  angle pdb=" N   ASP A 394 "
        pdb=" CA  ASP A 394 "
        pdb=" C   ASP A 394 "
      ideal   model   delta    sigma   weight residual
     110.80  116.23   -5.43 2.13e+00 2.20e-01 6.51e+00
  ... (remaining 13239 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.74: 5204
       17.74 -    35.49: 455
       35.49 -    53.23: 65
       53.23 -    70.97: 9
       70.97 -    88.72: 4
  Dihedral angle restraints: 5737
    sinusoidal: 2126
      harmonic: 3611
  Sorted by residual:
  dihedral pdb=" CA  TRP C  16 "
           pdb=" C   TRP C  16 "
           pdb=" N   LYS C  17 "
           pdb=" CA  LYS C  17 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.04   25.96     0      5.00e+00 4.00e-02 2.70e+01
  dihedral pdb=" CA  PRO C 129 "
           pdb=" C   PRO C 129 "
           pdb=" N   PRO C 130 "
           pdb=" CA  PRO C 130 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.74  -24.26     0      5.00e+00 4.00e-02 2.35e+01
  dihedral pdb=" CA  TRP B  16 "
           pdb=" C   TRP B  16 "
           pdb=" N   LYS B  17 "
           pdb=" CA  LYS B  17 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.94   20.06     0      5.00e+00 4.00e-02 1.61e+01
  ... (remaining 5734 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 900
       0.032 -    0.063: 522
       0.063 -    0.095: 153
       0.095 -    0.126: 68
       0.126 -    0.158: 7
  Chirality restraints: 1650
  Sorted by residual:
  chirality pdb=" CG  LEU C 241 "
            pdb=" CB  LEU C 241 "
            pdb=" CD1 LEU C 241 "
            pdb=" CD2 LEU C 241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.24e-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    2.59   -0.15 2.00e-01 2.50e+01 5.86e-01
  chirality pdb=" CA  TRP C  16 "
            pdb=" N   TRP C  16 "
            pdb=" C   TRP C  16 "
            pdb=" CB  TRP C  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.58e-01
  ... (remaining 1647 not shown)

  Planarity restraints: 1627
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 245 "   -0.011 2.00e-02 2.50e+03   2.24e-02 5.01e+00
        pdb=" C   ILE B 245 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ILE B 245 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   VAL B 246 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 235 "    0.010 2.00e-02 2.50e+03   2.04e-02 4.15e+00
        pdb=" C   GLY B 235 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   GLY B 235 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ALA B 236 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 207 "    0.033 5.00e-02 4.00e+02   4.96e-02 3.94e+00
        pdb=" N   PRO C 208 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO C 208 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C 208 "    0.028 5.00e-02 4.00e+02
  ... (remaining 1624 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 403
        2.71 -     3.26: 10374
        3.26 -     3.81: 15713
        3.81 -     4.35: 19709
        4.35 -     4.90: 33672
  Nonbonded interactions: 79871
  Sorted by model distance:
  nonbonded pdb=" O   THR B 378 "
            pdb=" OG  SER B 381 "
     model   vdw
     2.167 3.040
  nonbonded pdb=" O   ASP C 269 "
            pdb=" OG1 THR C 273 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OH  TYR B 238 "
            pdb=" O   ILE B 396 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" OG1 THR B 305 "
            pdb=" OG1 THR B 413 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   TYR B   9 "
            pdb=" NZ  LYS B  17 "
     model   vdw
     2.247 3.120
  ... (remaining 79866 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 430)
  selection = (chain 'B' and resid 5 through 430)
  selection = (chain 'C' and resid 5 through 430)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.360
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
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      :  0.006   0.053   9731  Z= 0.259
  Angle     :  0.692   8.766  13244  Z= 0.372
  Chirality :  0.044   0.158   1650
  Planarity :  0.005   0.050   1627
  Dihedral  : 13.226  88.717   3445
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.76 %
    Favored  : 91.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.53 (0.20), residues: 1274
  helix: -2.02 (0.14), residues: 979
  sheet:  None (None), residues: 0
  loop : -2.77 (0.33), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 401 
 TYR   0.013   0.001   TYR C  37 
 PHE   0.017   0.002   PHE C 302 
 TRP   0.018   0.001   TRP C  16 
 HIS   0.006   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00643 ( 9731)
  covalent geometry    : angle       0.69186 (13244)
  hydrogen bonds       : bond        0.11247 (  650)
  hydrogen bonds       : angle       6.26438 ( 1944)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.382 
Fit side-chains
REVERT: B  394 ASP cc_start: 0.7528 (t70) cc_final: 0.7258 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.0924
  time to fit residues: 15.3643
Evaluate side-chains
  92 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    0.6980
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0370
   chunk 123 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.5980
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
A 371 GLN
B 321 GLN
B 330 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.072019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.058465 restraints weight = 27964.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.2875 rms_B_bonded: 3.36
r_work: 0.2748 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.1620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9731  Z= 0.122
  Angle     :  0.576   8.931  13244  Z= 0.291
  Chirality :  0.039   0.131   1650
  Planarity :  0.005   0.053   1627
  Dihedral  :  4.547  32.527   1365
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 13.53 %
    Favored  : 85.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.51 (0.23), residues: 1274
  helix: -0.53 (0.16), residues: 979
  sheet:  None (None), residues: 0
  loop : -2.17 (0.35), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 225 
 TYR   0.008   0.001   TYR C 238 
 PHE   0.018   0.001   PHE C 302 
 TRP   0.015   0.001   TRP C  16 
 HIS   0.002   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 9731)
  covalent geometry    : angle       0.57570 (13244)
  hydrogen bonds       : bond        0.03588 (  650)
  hydrogen bonds       : angle       4.58385 ( 1944)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.367 
Fit side-chains
REVERT: A   97 MET cc_start: 0.8670 (mmm) cc_final: 0.8446 (mmm)
REVERT: A  365 MET cc_start: 0.8577 (mtp) cc_final: 0.8342 (ttt)
REVERT: B  222 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7987 (tm-30)
REVERT: B  244 GLN cc_start: 0.8984 (tt0) cc_final: 0.8635 (tp40)
REVERT: B  288 MET cc_start: 0.8635 (mtp) cc_final: 0.8225 (mmt)
REVERT: B  312 ILE cc_start: 0.9335 (pt) cc_final: 0.9097 (mp)
REVERT: B  410 LEU cc_start: 0.9042 (pp) cc_final: 0.8800 (pp)
REVERT: C   90 TYR cc_start: 0.8415 (t80) cc_final: 0.8011 (t80)
REVERT: C  138 ASN cc_start: 0.9502 (m-40) cc_final: 0.9037 (m-40)
REVERT: C  219 MET cc_start: 0.9050 (mmt) cc_final: 0.8832 (mmp)
REVERT: C  225 ARG cc_start: 0.8075 (mtp85) cc_final: 0.7328 (mpt180)
REVERT: C  365 MET cc_start: 0.9127 (tpp) cc_final: 0.8746 (mmm)
REVERT: C  389 MET cc_start: 0.8570 (mtm) cc_final: 0.8346 (mtp)
REVERT: C  405 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.7981 (m-40)
  outliers start: 14
  outliers final: 4
  residues processed: 116
  average time/residue: 0.0746
  time to fit residues: 13.3220
Evaluate side-chains
  96 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain B residue  222 GLN
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain C residue  405 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 33 optimal weight:    9.9990
   chunk 125 optimal weight:    1.9990
   chunk 45 optimal weight:    8.9990
   chunk 113 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0030
   chunk 80 optimal weight:    0.6980
   chunk 83 optimal weight:    0.3980
   chunk 123 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 34 optimal weight:    4.9990
   overall best weight:    0.5190

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

Flipped N/Q/H residues before XYZ refinement:
A 340 GLN
** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 321 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.072711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.059051 restraints weight = 28026.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.2895 rms_B_bonded: 3.41
r_work: 0.2770 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.2094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052   9731  Z= 0.109
  Angle     :  0.530   7.815  13244  Z= 0.269
  Chirality :  0.039   0.179   1650
  Planarity :  0.005   0.055   1627
  Dihedral  :  4.192  21.296   1365
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 16.82 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.24), residues: 1274
  helix:  0.15 (0.17), residues: 974
  sheet:  None (None), residues: 0
  loop : -1.97 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG C 401 
 TYR   0.007   0.001   TYR C  37 
 PHE   0.014   0.001   PHE C 302 
 TRP   0.009   0.001   TRP C  16 
 HIS   0.002   0.000   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 9731)
  covalent geometry    : angle       0.53007 (13244)
  hydrogen bonds       : bond        0.03385 (  650)
  hydrogen bonds       : angle       4.25743 ( 1944)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.380 
Fit side-chains
REVERT: A   97 MET cc_start: 0.8812 (mmm) cc_final: 0.8201 (mmm)
REVERT: A  100 PHE cc_start: 0.8703 (t80) cc_final: 0.8284 (t80)
REVERT: A  204 MET cc_start: 0.8919 (mmm) cc_final: 0.8685 (mmm)
REVERT: B  204 MET cc_start: 0.9422 (mmm) cc_final: 0.9189 (mmm)
REVERT: B  244 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8615 (tp40)
REVERT: B  295 MET cc_start: 0.8824 (ttm) cc_final: 0.8562 (mtp)
REVERT: B  312 ILE cc_start: 0.9337 (pt) cc_final: 0.9095 (mp)
REVERT: B  410 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8772 (pp)
REVERT: B  425 GLU cc_start: 0.8625 (mp0) cc_final: 0.8422 (mp0)
REVERT: C   90 TYR cc_start: 0.8501 (t80) cc_final: 0.8005 (t80)
REVERT: C  134 GLN cc_start: 0.8646 (mm-40) cc_final: 0.7916 (mm-40)
REVERT: C  138 ASN cc_start: 0.9474 (m-40) cc_final: 0.8895 (m-40)
REVERT: C  225 ARG cc_start: 0.8153 (mtp85) cc_final: 0.7871 (mtp85)
REVERT: C  321 GLN cc_start: 0.9212 (mt0) cc_final: 0.8912 (mt0)
REVERT: C  365 MET cc_start: 0.9166 (tpp) cc_final: 0.8741 (mmm)
REVERT: C  368 MET cc_start: 0.8922 (tmm) cc_final: 0.8685 (tmm)
  outliers start: 20
  outliers final: 11
  residues processed: 118
  average time/residue: 0.0701
  time to fit residues: 12.9708
Evaluate side-chains
  108 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  353 ILE
Chi-restraints excluded: chain B residue   50 ASP
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  244 GLN
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  406 VAL
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  358 VAL
Chi-restraints excluded: chain C residue  383 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 94 optimal weight:    0.1980
   chunk 71 optimal weight:    0.9980
   chunk 18 optimal weight:    4.9990
   chunk 87 optimal weight:    8.9990
   chunk 119 optimal weight:    0.9990
   chunk 7 optimal weight:    0.4980
   chunk 3 optimal weight:    9.9990
   chunk 96 optimal weight:    9.9990
   chunk 23 optimal weight:    3.9990
   chunk 125 optimal weight:    3.9990
   chunk 107 optimal weight:    2.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
B 321 GLN
** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.071647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.057985 restraints weight = 28730.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.2866 rms_B_bonded: 3.43
r_work: 0.2740 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.2256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9731  Z= 0.130
  Angle     :  0.544   8.215  13244  Z= 0.273
  Chirality :  0.039   0.175   1650
  Planarity :  0.004   0.053   1627
  Dihedral  :  4.082  23.235   1365
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 17.81 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.15 (0.24), residues: 1274
  helix:  0.47 (0.17), residues: 976
  sheet:  None (None), residues: 0
  loop : -1.79 (0.36), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 401 
 TYR   0.013   0.001   TYR A  90 
 PHE   0.014   0.001   PHE C 302 
 TRP   0.013   0.001   TRP C  16 
 HIS   0.002   0.000   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 9731)
  covalent geometry    : angle       0.54414 (13244)
  hydrogen bonds       : bond        0.03408 (  650)
  hydrogen bonds       : angle       4.17055 ( 1944)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 0.397 
Fit side-chains
REVERT: A   90 TYR cc_start: 0.8305 (t80) cc_final: 0.8080 (t80)
REVERT: A  100 PHE cc_start: 0.8714 (t80) cc_final: 0.8272 (t80)
REVERT: A  204 MET cc_start: 0.8962 (mmm) cc_final: 0.8689 (mmm)
REVERT: B  288 MET cc_start: 0.8674 (mtp) cc_final: 0.8272 (mmt)
REVERT: B  295 MET cc_start: 0.8826 (ttm) cc_final: 0.8506 (mtp)
REVERT: B  312 ILE cc_start: 0.9351 (pt) cc_final: 0.9096 (mp)
REVERT: B  410 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8811 (pp)
REVERT: C   90 TYR cc_start: 0.8564 (t80) cc_final: 0.8048 (t80)
REVERT: C  134 GLN cc_start: 0.8681 (mm-40) cc_final: 0.7893 (mm-40)
REVERT: C  138 ASN cc_start: 0.9484 (m-40) cc_final: 0.8871 (m-40)
REVERT: C  225 ARG cc_start: 0.8299 (mtp85) cc_final: 0.7939 (mtp85)
REVERT: C  365 MET cc_start: 0.9124 (tpp) cc_final: 0.8817 (mmm)
REVERT: C  368 MET cc_start: 0.8965 (tmm) cc_final: 0.8728 (tmm)
  outliers start: 23
  outliers final: 14
  residues processed: 118
  average time/residue: 0.0727
  time to fit residues: 13.2500
Evaluate side-chains
  107 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  353 ILE
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  406 VAL
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain C residue    6 LEU
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain C residue  358 VAL
Chi-restraints excluded: chain C residue  383 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 89 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 118 optimal weight:    0.6980
   chunk 90 optimal weight:    0.8980
   chunk 91 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 35 optimal weight:    7.9990
   chunk 44 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0470
   overall best weight:    0.6278

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

Flipped N/Q/H residues before XYZ refinement:
** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 321 GLN
** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 321 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.074564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.061470 restraints weight = 28303.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 3.16
r_work: 0.2859 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.2615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049   9731  Z= 0.108
  Angle     :  0.532   7.256  13244  Z= 0.265
  Chirality :  0.039   0.189   1650
  Planarity :  0.004   0.053   1627
  Dihedral  :  3.979  22.173   1365
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 18.31 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.24), residues: 1274
  helix:  0.72 (0.17), residues: 978
  sheet:  None (None), residues: 0
  loop : -1.53 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 401 
 TYR   0.009   0.001   TYR A  90 
 PHE   0.012   0.001   PHE C 302 
 TRP   0.012   0.001   TRP C  16 
 HIS   0.002   0.000   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 9731)
  covalent geometry    : angle       0.53204 (13244)
  hydrogen bonds       : bond        0.03223 (  650)
  hydrogen bonds       : angle       4.06267 ( 1944)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.291 
Fit side-chains
REVERT: A  100 PHE cc_start: 0.8898 (t80) cc_final: 0.8481 (t80)
REVERT: A  194 GLU cc_start: 0.8678 (tp30) cc_final: 0.8401 (tp30)
REVERT: A  204 MET cc_start: 0.9038 (mmm) cc_final: 0.8785 (mmm)
REVERT: A  393 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8524 (tp)
REVERT: B  288 MET cc_start: 0.8576 (mtp) cc_final: 0.8341 (mmt)
REVERT: C   90 TYR cc_start: 0.8822 (t80) cc_final: 0.8374 (t80)
REVERT: C   97 MET cc_start: 0.8624 (tpp) cc_final: 0.8323 (tpp)
REVERT: C  134 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8007 (mm-40)
REVERT: C  138 ASN cc_start: 0.9590 (m-40) cc_final: 0.8983 (m-40)
REVERT: C  225 ARG cc_start: 0.8226 (mtp85) cc_final: 0.7944 (mtp85)
REVERT: C  321 GLN cc_start: 0.8920 (mt0) cc_final: 0.8625 (mt0)
  outliers start: 20
  outliers final: 15
  residues processed: 125
  average time/residue: 0.0676
  time to fit residues: 13.1262
Evaluate side-chains
  110 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  353 ILE
Chi-restraints excluded: chain A residue  393 ILE
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  396 ILE
Chi-restraints excluded: chain B residue  406 VAL
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain C residue  358 VAL
Chi-restraints excluded: chain C residue  383 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 59 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   chunk 96 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 115 optimal weight:    4.9990
   chunk 6 optimal weight:    0.6980
   chunk 112 optimal weight:    0.9990
   chunk 39 optimal weight:    6.9990
   chunk 3 optimal weight:    9.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 GLN
** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.074296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.061020 restraints weight = 28425.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.2967 rms_B_bonded: 3.18
r_work: 0.2850 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.2752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9731  Z= 0.116
  Angle     :  0.548   8.129  13244  Z= 0.270
  Chirality :  0.039   0.207   1650
  Planarity :  0.004   0.053   1627
  Dihedral  :  3.975  24.990   1365
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 18.41 %
    Favored  : 78.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.24), residues: 1274
  helix:  0.91 (0.17), residues: 978
  sheet:  None (None), residues: 0
  loop : -1.37 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 401 
 TYR   0.008   0.001   TYR A 197 
 PHE   0.012   0.001   PHE C 302 
 TRP   0.010   0.001   TRP C  16 
 HIS   0.002   0.000   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 9731)
  covalent geometry    : angle       0.54786 (13244)
  hydrogen bonds       : bond        0.03263 (  650)
  hydrogen bonds       : angle       4.04735 ( 1944)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 99
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A  100 PHE cc_start: 0.8849 (t80) cc_final: 0.8424 (t80)
REVERT: A  194 GLU cc_start: 0.8709 (tp30) cc_final: 0.8427 (tp30)
REVERT: A  196 MET cc_start: 0.9508 (mmp) cc_final: 0.9198 (mmt)
REVERT: A  204 MET cc_start: 0.9077 (mmm) cc_final: 0.8781 (mmm)
REVERT: A  244 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8799 (tp-100)
REVERT: B  321 GLN cc_start: 0.8588 (mt0) cc_final: 0.8108 (mt0)
REVERT: B  365 MET cc_start: 0.8262 (ttm) cc_final: 0.7883 (ttm)
REVERT: C   90 TYR cc_start: 0.8859 (t80) cc_final: 0.8465 (t80)
REVERT: C   97 MET cc_start: 0.8618 (tpp) cc_final: 0.8301 (tpp)
REVERT: C  134 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8072 (mm-40)
REVERT: C  138 ASN cc_start: 0.9589 (m-40) cc_final: 0.9099 (m110)
REVERT: C  368 MET cc_start: 0.8997 (tmm) cc_final: 0.8656 (tmm)
  outliers start: 28
  outliers final: 17
  residues processed: 122
  average time/residue: 0.0719
  time to fit residues: 13.3206
Evaluate side-chains
  111 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  244 GLN
Chi-restraints excluded: chain A residue  353 ILE
Chi-restraints excluded: chain B residue   14 VAL
Chi-restraints excluded: chain B residue   76 SER
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  396 ILE
Chi-restraints excluded: chain B residue  406 VAL
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain C residue  358 VAL
Chi-restraints excluded: chain C residue  383 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 121 optimal weight:   10.0000
   chunk 54 optimal weight:    5.9990
   chunk 77 optimal weight:    6.9990
   chunk 104 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 4 optimal weight:    0.5980
   chunk 98 optimal weight:    2.9990
   chunk 11 optimal weight:   10.0000
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 321 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.071566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.058507 restraints weight = 28668.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.2901 rms_B_bonded: 3.13
r_work: 0.2785 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.2566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   9731  Z= 0.207
  Angle     :  0.615   7.150  13244  Z= 0.304
  Chirality :  0.041   0.201   1650
  Planarity :  0.004   0.054   1627
  Dihedral  :  4.080  24.655   1365
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 17.51 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.24), residues: 1274
  helix:  0.93 (0.17), residues: 984
  sheet:  None (None), residues: 0
  loop : -1.37 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 107 
 TYR   0.009   0.001   TYR C 238 
 PHE   0.014   0.001   PHE C 302 
 TRP   0.007   0.001   TRP C  16 
 HIS   0.003   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 ( 9731)
  covalent geometry    : angle       0.61475 (13244)
  hydrogen bonds       : bond        0.03677 (  650)
  hydrogen bonds       : angle       4.23669 ( 1944)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 90
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 PHE cc_start: 0.8858 (t80) cc_final: 0.8421 (t80)
REVERT: A  194 GLU cc_start: 0.8850 (tp30) cc_final: 0.8543 (tp30)
REVERT: A  196 MET cc_start: 0.9559 (mmp) cc_final: 0.9245 (mmt)
REVERT: A  204 MET cc_start: 0.9066 (mmm) cc_final: 0.8749 (mmm)
REVERT: B  321 GLN cc_start: 0.8651 (mt0) cc_final: 0.8421 (mt0)
REVERT: C   90 TYR cc_start: 0.8875 (t80) cc_final: 0.8381 (t80)
REVERT: C   97 MET cc_start: 0.8698 (tpp) cc_final: 0.8390 (tpp)
REVERT: C  134 GLN cc_start: 0.8823 (mm-40) cc_final: 0.7983 (mm-40)
REVERT: C  138 ASN cc_start: 0.9607 (m-40) cc_final: 0.9030 (m110)
REVERT: C  321 GLN cc_start: 0.8922 (mt0) cc_final: 0.8617 (mt0)
REVERT: C  365 MET cc_start: 0.8848 (tpp) cc_final: 0.8306 (tpp)
REVERT: C  368 MET cc_start: 0.9049 (tmm) cc_final: 0.8546 (tmm)
  outliers start: 36
  outliers final: 23
  residues processed: 119
  average time/residue: 0.0687
  time to fit residues: 12.7857
Evaluate side-chains
  111 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  353 ILE
Chi-restraints excluded: chain A residue  393 ILE
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain B residue   14 VAL
Chi-restraints excluded: chain B residue   76 SER
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  396 ILE
Chi-restraints excluded: chain B residue  406 VAL
Chi-restraints excluded: chain C residue    6 LEU
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  174 ASN
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain C residue  358 VAL
Chi-restraints excluded: chain C residue  383 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 30 optimal weight:    6.9990
   chunk 75 optimal weight:    0.6980
   chunk 113 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 84 optimal weight:    2.9990
   chunk 92 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   chunk 112 optimal weight:    0.7980
   chunk 125 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN
** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.073995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.060910 restraints weight = 28249.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 3.14
r_work: 0.2848 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.2875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9731  Z= 0.117
  Angle     :  0.568  11.522  13244  Z= 0.278
  Chirality :  0.039   0.192   1650
  Planarity :  0.004   0.055   1627
  Dihedral  :  4.008  24.626   1365
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 18.91 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.25), residues: 1274
  helix:  1.06 (0.17), residues: 993
  sheet:  None (None), residues: 0
  loop : -1.13 (0.38), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 289 
 TYR   0.008   0.001   TYR A 197 
 PHE   0.011   0.001   PHE C 302 
 TRP   0.016   0.001   TRP C  16 
 HIS   0.001   0.000   HIS C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 9731)
  covalent geometry    : angle       0.56793 (13244)
  hydrogen bonds       : bond        0.03326 (  650)
  hydrogen bonds       : angle       4.10693 ( 1944)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A  100 PHE cc_start: 0.8787 (t80) cc_final: 0.8354 (t80)
REVERT: A  194 GLU cc_start: 0.8738 (tp30) cc_final: 0.8439 (tp30)
REVERT: A  204 MET cc_start: 0.9102 (mmm) cc_final: 0.8772 (mmm)
REVERT: B  288 MET cc_start: 0.8639 (mmm) cc_final: 0.8212 (mtt)
REVERT: B  321 GLN cc_start: 0.8450 (mt0) cc_final: 0.7285 (mt0)
REVERT: B  365 MET cc_start: 0.8173 (ttm) cc_final: 0.7675 (ttm)
REVERT: C   90 TYR cc_start: 0.8826 (t80) cc_final: 0.8380 (t80)
REVERT: C  134 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8039 (mm-40)
REVERT: C  138 ASN cc_start: 0.9621 (m-40) cc_final: 0.9128 (m110)
REVERT: C  225 ARG cc_start: 0.8017 (mtp85) cc_final: 0.7357 (tpm170)
REVERT: C  365 MET cc_start: 0.8806 (tpp) cc_final: 0.8301 (tpp)
REVERT: C  368 MET cc_start: 0.9045 (tmm) cc_final: 0.8560 (tmm)
  outliers start: 22
  outliers final: 19
  residues processed: 121
  average time/residue: 0.0708
  time to fit residues: 13.3628
Evaluate side-chains
  111 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 GLN
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  353 ILE
Chi-restraints excluded: chain A residue  393 ILE
Chi-restraints excluded: chain B residue   14 VAL
Chi-restraints excluded: chain B residue   76 SER
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  353 ILE
Chi-restraints excluded: chain B residue  396 ILE
Chi-restraints excluded: chain B residue  406 VAL
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain C residue  383 VAL
Chi-restraints excluded: chain C residue  396 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0770
   chunk 109 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 97 optimal weight:    0.0970
   chunk 61 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   chunk 49 optimal weight:    0.6980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.7538

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN
B 128 GLN
C 321 GLN
** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.074288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.061125 restraints weight = 28468.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.2964 rms_B_bonded: 3.16
r_work: 0.2846 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.2986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9731  Z= 0.116
  Angle     :  0.567   9.429  13244  Z= 0.278
  Chirality :  0.039   0.190   1650
  Planarity :  0.004   0.054   1627
  Dihedral  :  3.960  24.973   1365
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 18.91 %
    Favored  : 78.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.24), residues: 1274
  helix:  1.14 (0.17), residues: 993
  sheet:  None (None), residues: 0
  loop : -1.07 (0.38), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 225 
 TYR   0.007   0.001   TYR A 320 
 PHE   0.011   0.001   PHE C 302 
 TRP   0.016   0.001   TRP C  16 
 HIS   0.001   0.000   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 9731)
  covalent geometry    : angle       0.56666 (13244)
  hydrogen bonds       : bond        0.03319 (  650)
  hydrogen bonds       : angle       4.06228 ( 1944)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 PHE cc_start: 0.8801 (t80) cc_final: 0.8377 (t80)
REVERT: A  194 GLU cc_start: 0.8785 (tp30) cc_final: 0.8463 (tp30)
REVERT: A  204 MET cc_start: 0.9130 (mmm) cc_final: 0.8806 (mmm)
REVERT: B  288 MET cc_start: 0.8682 (mmm) cc_final: 0.8219 (mtt)
REVERT: B  321 GLN cc_start: 0.8435 (mt0) cc_final: 0.7262 (mt0)
REVERT: B  365 MET cc_start: 0.8171 (ttm) cc_final: 0.7636 (ttm)
REVERT: C   90 TYR cc_start: 0.8833 (t80) cc_final: 0.8402 (t80)
REVERT: C  134 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8042 (mm-40)
REVERT: C  138 ASN cc_start: 0.9623 (m-40) cc_final: 0.9134 (m110)
REVERT: C  365 MET cc_start: 0.8908 (tpp) cc_final: 0.8370 (tpp)
REVERT: C  368 MET cc_start: 0.9040 (tmm) cc_final: 0.8571 (tmm)
  outliers start: 23
  outliers final: 21
  residues processed: 115
  average time/residue: 0.0700
  time to fit residues: 12.7462
Evaluate side-chains
  113 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 GLN
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  353 ILE
Chi-restraints excluded: chain A residue  393 ILE
Chi-restraints excluded: chain B residue   14 VAL
Chi-restraints excluded: chain B residue   76 SER
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  353 ILE
Chi-restraints excluded: chain B residue  396 ILE
Chi-restraints excluded: chain B residue  406 VAL
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  337 THR
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain C residue  383 VAL
Chi-restraints excluded: chain C residue  396 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 80 optimal weight:    1.9990
   chunk 117 optimal weight:    0.5980
   chunk 28 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 83 optimal weight:    5.9990
   chunk 109 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 79 optimal weight:    4.9990
   chunk 58 optimal weight:    0.5980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN
B 128 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.073602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.060584 restraints weight = 28236.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 3.07
r_work: 0.2844 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.2989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9731  Z= 0.134
  Angle     :  0.574   8.511  13244  Z= 0.283
  Chirality :  0.040   0.196   1650
  Planarity :  0.004   0.054   1627
  Dihedral  :  3.962  24.910   1365
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 18.91 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.25), residues: 1274
  helix:  1.20 (0.17), residues: 993
  sheet:  None (None), residues: 0
  loop : -1.02 (0.38), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 225 
 TYR   0.012   0.001   TYR A 197 
 PHE   0.011   0.001   PHE C 302 
 TRP   0.014   0.001   TRP C  16 
 HIS   0.002   0.000   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 9731)
  covalent geometry    : angle       0.57415 (13244)
  hydrogen bonds       : bond        0.03385 (  650)
  hydrogen bonds       : angle       4.07824 ( 1944)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 PHE cc_start: 0.8842 (t80) cc_final: 0.8422 (t80)
REVERT: A  194 GLU cc_start: 0.8749 (tp30) cc_final: 0.8479 (tp30)
REVERT: A  204 MET cc_start: 0.9114 (mmm) cc_final: 0.8790 (mmm)
REVERT: B  288 MET cc_start: 0.8617 (mmm) cc_final: 0.8151 (mtt)
REVERT: B  321 GLN cc_start: 0.8424 (mt0) cc_final: 0.8188 (mt0)
REVERT: C   90 TYR cc_start: 0.8852 (t80) cc_final: 0.8432 (t80)
REVERT: C  100 PHE cc_start: 0.8893 (t80) cc_final: 0.8676 (t80)
REVERT: C  134 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8005 (mm-40)
REVERT: C  138 ASN cc_start: 0.9606 (m-40) cc_final: 0.9030 (m110)
REVERT: C  365 MET cc_start: 0.8866 (tpp) cc_final: 0.8422 (tpp)
REVERT: C  368 MET cc_start: 0.9044 (tmm) cc_final: 0.8584 (tmm)
  outliers start: 22
  outliers final: 21
  residues processed: 112
  average time/residue: 0.0739
  time to fit residues: 12.9634
Evaluate side-chains
  113 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 GLN
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  353 ILE
Chi-restraints excluded: chain A residue  393 ILE
Chi-restraints excluded: chain B residue   14 VAL
Chi-restraints excluded: chain B residue   76 SER
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  128 GLN
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  353 ILE
Chi-restraints excluded: chain B residue  396 ILE
Chi-restraints excluded: chain B residue  406 VAL
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  337 THR
Chi-restraints excluded: chain C residue  352 SER
Chi-restraints excluded: chain C residue  383 VAL
Chi-restraints excluded: chain C residue  396 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 42 optimal weight:    8.9990
   chunk 51 optimal weight:    2.9990
   chunk 63 optimal weight:    0.7980
   chunk 31 optimal weight:    5.9990
   chunk 56 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 119 optimal weight:    0.5980
   chunk 81 optimal weight:    1.9990
   chunk 108 optimal weight:    4.9990
   chunk 97 optimal weight:    5.9990
   chunk 59 optimal weight:    0.6980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
B 128 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.073983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.061073 restraints weight = 28008.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.2967 rms_B_bonded: 3.09
r_work: 0.2851 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.3022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9731  Z= 0.123
  Angle     :  0.575   7.997  13244  Z= 0.283
  Chirality :  0.040   0.195   1650
  Planarity :  0.004   0.054   1627
  Dihedral  :  3.962  24.998   1365
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 19.10 %
    Favored  : 78.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.25), residues: 1274
  helix:  1.25 (0.17), residues: 993
  sheet:  None (None), residues: 0
  loop : -0.99 (0.38), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 225 
 TYR   0.006   0.001   TYR A 320 
 PHE   0.011   0.001   PHE C 302 
 TRP   0.014   0.001   TRP C  16 
 HIS   0.001   0.000   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 9731)
  covalent geometry    : angle       0.57500 (13244)
  hydrogen bonds       : bond        0.03357 (  650)
  hydrogen bonds       : angle       4.07212 ( 1944)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1702.85 seconds
wall clock time: 30 minutes 1.20 seconds (1801.20 seconds total)