Starting phenix.real_space_refine
on Thu Feb 13 23:16:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xwr_10636/02_2025/6xwr_10636.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xwr_10636/02_2025/6xwr_10636.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.22
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xwr_10636/02_2025/6xwr_10636.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xwr_10636/02_2025/6xwr_10636.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xwr_10636/02_2025/6xwr_10636.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xwr_10636/02_2025/6xwr_10636.cif"
  }
  resolution = 3.22
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.021
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    6309      2.51       5
     N    1551      2.21       5
     O    1656      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9564
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3189
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 426, 3178
          Classifications: {'peptide': 426}
          Link IDs: {'PTRANS': 18, 'TRANS': 407}
      Conformer: "B"
        Number of residues, atoms: 426, 3178
          Classifications: {'peptide': 426}
          Link IDs: {'PTRANS': 18, 'TRANS': 407}
          bond proxies already assigned to first conformer: 3225
    Chain: "B"
      Number of atoms: 3187
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 426, 3178
          Classifications: {'peptide': 426}
          Link IDs: {'PTRANS': 18, 'TRANS': 407}
      Conformer: "B"
        Number of residues, atoms: 426, 3178
          Classifications: {'peptide': 426}
          Link IDs: {'PTRANS': 18, 'TRANS': 407}
          bond proxies already assigned to first conformer: 3227
    Chain: "C"
      Number of atoms: 3188
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 426, 3178
          Classifications: {'peptide': 426}
          Link IDs: {'PTRANS': 18, 'TRANS': 407}
      Conformer: "B"
        Number of residues, atoms: 426, 3178
          Classifications: {'peptide': 426}
          Link IDs: {'PTRANS': 18, 'TRANS': 407}
          bond proxies already assigned to first conformer: 3225
  Residues with excluded nonbonded symmetry interactions: 3
    residue:
      pdb=" N  AARG A   8 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A   8 " occ=0.50
    residue:
      pdb=" N  ALYS B  86 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS B  86 " occ=0.50
    residue:
      pdb=" N  AHIS C 334 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS C 334 " occ=0.50
  Time building chain proxies: 10.50, per 1000 atoms: 1.10
  Number of scatterers: 9564
  At special positions: 0
  Unit cell: (82.984, 102.212, 116.38, 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    1656      8.00
     N    1551      7.00
     C    6309      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.52
  Conformation dependent library (CDL) restraints added in 2.7 seconds
  

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 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:
      63 helices and 0 sheets defined
      81.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 11
      removed outlier: 3.541A  pdb=" N   TYR A   9 " --> pdb=" O   LEU A   5 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ASP A  11 " --> pdb=" O   ARG A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 13 through 36
    Processing helix  chain 'A' and resid 37 through 44
    Processing helix  chain 'A' and resid 45 through 58
      removed outlier: 3.907A  pdb=" N   GLY A  49 " --> pdb=" O   ILE A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 75
    Processing helix  chain 'A' and resid 81 through 110
      removed outlier: 3.813A  pdb=" N   VAL A  85 " --> pdb=" O   GLY A  81 " (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 152 through 172
      removed outlier: 3.787A  pdb=" N   VAL A 156 " --> pdb=" O   GLU A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 222
      Proline residue:  A 208  - end of helix
    Processing helix  chain 'A' and resid 226 through 255
      removed outlier: 3.529A  pdb=" N   ALA A 231 " --> pdb=" O   VAL A 227 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   PHE A 250 " --> pdb=" O   VAL A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 267
    Processing helix  chain 'A' and resid 267 through 278
    Processing helix  chain 'A' and resid 283 through 294
    Processing helix  chain 'A' and resid 298 through 303
      removed outlier: 3.615A  pdb=" N   SER A 303 " --> pdb=" O   LYS A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 313
      removed outlier: 4.109A  pdb=" N   THR A 311 " --> pdb=" O   PRO A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 332
      removed outlier: 3.627A  pdb=" N   GLY A 322 " --> pdb=" O   ALA A 318 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   LEU A 326 " --> pdb=" O   GLY A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 350
    Processing helix  chain 'A' and resid 351 through 355
    Processing helix  chain 'A' and resid 360 through 374
      removed outlier: 3.507A  pdb=" N   GLY A 374 " --> pdb=" O   LEU A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 420
      removed outlier: 3.813A  pdb=" N   LEU A 385 " --> pdb=" O   SER A 381 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   ALA A 395 " --> pdb=" O   LEU A 391 " (cutoff:3.500A)
      removed outlier: 5.595A  pdb=" N   ILE A 396 " --> pdb=" O   GLY A 392 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   LEU A 397 " --> pdb=" O   ILE A 393 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   MET A 399 " --> pdb=" O   ALA A 395 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   GLY A 400 " --> pdb=" O   ILE A 396 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   THR A 402 " --> pdb=" O   ASP A 398 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   MET A 403 " --> pdb=" O   MET A 399 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ASP A 409 " --> pdb=" O   ASN A 405 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LEU A 410 " --> pdb=" O   VAL A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 428
    Processing helix  chain 'B' and resid 13 through 35
    Processing helix  chain 'B' and resid 37 through 45
    Processing helix  chain 'B' and resid 45 through 59
      removed outlier: 3.740A  pdb=" N   GLY B  49 " --> pdb=" O   ILE B  45 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   LEU B  59 " --> pdb=" O   LEU B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 75
      removed outlier: 3.761A  pdb=" N   ILE B  75 " --> pdb=" O   GLY B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 109
      removed outlier: 4.056A  pdb=" N  ALYS B  86 " --> pdb=" O   ARG B  82 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   ARG B 107 " --> pdb=" O   LEU B 103 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   PHE B 109 " --> pdb=" O   VAL B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 139
      removed outlier: 3.528A  pdb=" N   THR B 135 " --> pdb=" O   SER B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 150
    Processing helix  chain 'B' and resid 152 through 171
      removed outlier: 3.762A  pdb=" N   VAL B 156 " --> pdb=" O   GLU B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 222
      removed outlier: 3.739A  pdb=" N   GLN B 205 " --> pdb=" O   GLY B 201 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   TYR B 206 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      Proline residue:  B 208  - end of helix
      removed outlier: 3.837A  pdb=" N   PHE B 212 " --> pdb=" O   PRO B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 257
      removed outlier: 3.702A  pdb=" N   VAL B 234 " --> pdb=" O   LEU B 230 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA B 236 " --> pdb=" O   LYS B 232 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLY B 240 " --> pdb=" O   ALA B 236 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   PHE B 250 " --> pdb=" O   VAL B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 278
      removed outlier: 5.672A  pdb=" N   ASP B 269 " --> pdb=" O   ARG B 265 " (cutoff:3.500A)
      removed outlier: 5.610A  pdb=" N   ALA B 270 " --> pdb=" O   LYS B 266 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   THR B 277 " --> pdb=" O   THR B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 294
      removed outlier: 3.891A  pdb=" N   GLU B 293 " --> pdb=" O   ARG B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 303
    Processing helix  chain 'B' and resid 304 through 310
    Processing helix  chain 'B' and resid 314 through 332
      removed outlier: 3.842A  pdb=" N   VAL B 323 " --> pdb=" O   LEU B 319 " (cutoff:3.500A)
      removed outlier: 5.016A  pdb=" N   LEU B 326 " --> pdb=" O   GLY B 322 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   PHE B 327 " --> pdb=" O   VAL B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 343 through 348
    Processing helix  chain 'B' and resid 360 through 373
      removed outlier: 3.530A  pdb=" N   SER B 372 " --> pdb=" O   MET B 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 393
      removed outlier: 3.712A  pdb=" N   LEU B 385 " --> pdb=" O   SER B 381 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ILE B 390 " --> pdb=" O   ALA B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 402
      removed outlier: 4.290A  pdb=" N   GLY B 400 " --> pdb=" O   ILE B 396 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   THR B 402 " --> pdb=" O   ASP B 398 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 420
    Processing helix  chain 'C' and resid 6 through 11
    Processing helix  chain 'C' and resid 16 through 34
    Processing helix  chain 'C' and resid 37 through 45
    Processing helix  chain 'C' and resid 45 through 76
      removed outlier: 3.938A  pdb=" N   GLY C  49 " --> pdb=" O   ILE C  45 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   LEU C  59 " --> pdb=" O   LEU C  55 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   VAL C  60 " --> pdb=" O   LEU C  56 " (cutoff:3.500A)
      removed outlier: 4.704A  pdb=" N   MET C  61 " --> pdb=" O   LYS C  57 " (cutoff:3.500A)
      Proline residue:  C  62  - end of helix
    Processing helix  chain 'C' and resid 81 through 108
      removed outlier: 3.882A  pdb=" N   VAL C  89 " --> pdb=" O   VAL C  85 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   TYR C  90 " --> pdb=" O   LYS C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 131 through 138
    Processing helix  chain 'C' and resid 143 through 150
    Processing helix  chain 'C' and resid 153 through 171
    Processing helix  chain 'C' and resid 175 through 223
      Proline residue:  C 208  - end of helix
      removed outlier: 4.156A  pdb=" N   GLN C 222 " --> pdb=" O   VAL C 218 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 226 through 234
    Processing helix  chain 'C' and resid 236 through 255
      removed outlier: 4.593A  pdb=" N   PHE C 250 " --> pdb=" O   VAL C 246 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   LEU C 253 " --> pdb=" O   TYR C 249 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 259 through 278
      removed outlier: 5.742A  pdb=" N   ASP C 269 " --> pdb=" O   ARG C 265 " (cutoff:3.500A)
      removed outlier: 5.568A  pdb=" N   ALA C 270 " --> pdb=" O   LYS C 266 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 283 through 294
      removed outlier: 3.649A  pdb=" N   GLU C 294 " --> pdb=" O   VAL C 290 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 298 through 313
      removed outlier: 5.347A  pdb=" N   PHE C 304 " --> pdb=" O   GLY C 300 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   LEU C 306 " --> pdb=" O   PHE C 302 " (cutoff:3.500A)
      Proline residue:  C 307  - end of helix
      removed outlier: 3.937A  pdb=" N   THR C 311 " --> pdb=" O   PRO C 307 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 315 through 333
      removed outlier: 4.229A  pdb=" N   GLN C 321 " --> pdb=" O   THR C 317 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLY C 322 " --> pdb=" O   ALA C 318 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   VAL C 325 " --> pdb=" O   GLN C 321 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   LEU C 326 " --> pdb=" O   GLY C 322 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ALA C 329 " --> pdb=" O   VAL C 325 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 339 through 351
      removed outlier: 3.550A  pdb=" N   VAL C 343 " --> pdb=" O   GLY C 339 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   VAL C 345 " --> pdb=" O   GLN C 341 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   VAL C 349 " --> pdb=" O   VAL C 345 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 357 through 362
      removed outlier: 3.590A  pdb=" N   ALA C 361 " --> pdb=" O   GLY C 357 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 363 through 374
      removed outlier: 3.771A  pdb=" N   ALA C 367 " --> pdb=" O   ALA C 363 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   GLN C 371 " --> pdb=" O   ALA C 367 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 381 through 393
      removed outlier: 3.594A  pdb=" N   LEU C 385 " --> pdb=" O   SER C 381 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   ILE C 390 " --> pdb=" O   ALA C 386 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 394 through 420
      removed outlier: 4.504A  pdb=" N   GLY C 400 " --> pdb=" O   ILE C 396 " (cutoff:3.500A)
      removed outlier: 5.062A  pdb=" N   MET C 403 " --> pdb=" O   MET C 399 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   VAL C 404 " --> pdb=" O   GLY C 400 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ASN C 405 " --> pdb=" O   ARG C 401 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   VAL C 406 " --> pdb=" O   THR C 402 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   THR C 407 " --> pdb=" O   MET C 403 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 424 through 428
      removed outlier: 3.537A  pdb=" N   LYS C 427 " --> pdb=" O   ASP C 424 " (cutoff:3.500A)

    700 hydrogen bonds defined for protein.
    2086 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.99

  Time building geometry restraints manager: 2.91 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: 2975
        1.34 -     1.46: 1451
        1.46 -     1.57: 5223
        1.57 -     1.69: 0
        1.69 -     1.81: 96
  Bond restraints: 9745
  Sorted by residual:
  bond pdb=" CG  LEU C  68 "
       pdb=" CD1 LEU C  68 "
    ideal  model  delta    sigma   weight residual
    1.521  1.466  0.055 3.30e-02 9.18e+02 2.76e+00
  bond pdb=" C   ILE A  75 "
       pdb=" N   SER A  76 "
    ideal  model  delta    sigma   weight residual
    1.332  1.313  0.018 1.21e-02 6.83e+03 2.32e+00
  bond pdb=" CB  THR C 168 "
       pdb=" CG2 THR C 168 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 3.30e-02 9.18e+02 1.85e+00
  bond pdb=" CB  TRP A  20 "
       pdb=" CG  TRP A  20 "
    ideal  model  delta    sigma   weight residual
    1.498  1.456  0.042 3.10e-02 1.04e+03 1.82e+00
  bond pdb=" CB  VAL A 200 "
       pdb=" CG2 VAL A 200 "
    ideal  model  delta    sigma   weight residual
    1.521  1.477  0.044 3.30e-02 9.18e+02 1.80e+00
  ... (remaining 9740 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 12695
        1.59 -     3.18: 466
        3.18 -     4.77: 77
        4.77 -     6.36: 25
        6.36 -     7.95: 5
  Bond angle restraints: 13268
  Sorted by residual:
  angle pdb=" N   GLY C 235 "
        pdb=" CA  GLY C 235 "
        pdb=" C   GLY C 235 "
      ideal   model   delta    sigma   weight residual
     114.69  109.10    5.59 1.19e+00 7.06e-01 2.21e+01
  angle pdb=" C   VAL A 246 "
        pdb=" N   ILE A 247 "
        pdb=" CA  ILE A 247 "
      ideal   model   delta    sigma   weight residual
     122.97  119.16    3.81 9.80e-01 1.04e+00 1.51e+01
  angle pdb=" N   ILE B 301 "
        pdb=" CA  ILE B 301 "
        pdb=" C   ILE B 301 "
      ideal   model   delta    sigma   weight residual
     111.48  108.67    2.81 9.40e-01 1.13e+00 8.92e+00
  angle pdb=" N   THR B 378 "
        pdb=" CA  THR B 378 "
        pdb=" C   THR B 378 "
      ideal   model   delta    sigma   weight residual
     109.81  116.29   -6.48 2.21e+00 2.05e-01 8.61e+00
  angle pdb=" N   ALA C 207 "
        pdb=" CA  ALA C 207 "
        pdb=" C   ALA C 207 "
      ideal   model   delta    sigma   weight residual
     109.81  116.17   -6.36 2.21e+00 2.05e-01 8.27e+00
  ... (remaining 13263 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 5287
       18.00 -    36.00: 400
       36.00 -    53.99: 48
       53.99 -    71.99: 6
       71.99 -    89.99: 6
  Dihedral angle restraints: 5747
    sinusoidal: 2132
      harmonic: 3615
  Sorted by residual:
  dihedral pdb=" CA  LEU B 342 "
           pdb=" C   LEU B 342 "
           pdb=" N   VAL B 343 "
           pdb=" CA  VAL B 343 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.34   20.66     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CA  LEU C  59 "
           pdb=" C   LEU C  59 "
           pdb=" N   VAL C  60 "
           pdb=" CA  VAL C  60 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.48  -18.52     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  ASN C 110 "
           pdb=" C   ASN C 110 "
           pdb=" N   VAL C 111 "
           pdb=" CA  VAL C 111 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.62  -18.38     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 5744 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 814
       0.031 -    0.062: 585
       0.062 -    0.094: 177
       0.094 -    0.125: 61
       0.125 -    0.156: 13
  Chirality restraints: 1650
  Sorted by residual:
  chirality pdb=" CA  THR B 378 "
            pdb=" N   THR B 378 "
            pdb=" C   THR B 378 "
            pdb=" CB  THR B 378 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.37    0.16 2.00e-01 2.50e+01 6.09e-01
  chirality pdb=" CB  VAL B 105 "
            pdb=" CA  VAL B 105 "
            pdb=" CG1 VAL B 105 "
            pdb=" CG2 VAL B 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 4.93e-01
  chirality pdb=" CA  PRO B  47 "
            pdb=" N   PRO B  47 "
            pdb=" C   PRO B  47 "
            pdb=" CB  PRO B  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.72e-01
  ... (remaining 1647 not shown)

  Planarity restraints: 1632
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  64 "   -0.011 2.00e-02 2.50e+03   2.14e-02 4.58e+00
        pdb=" C   VAL A  64 "    0.037 2.00e-02 2.50e+03
        pdb=" O   VAL A  64 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   LEU A  65 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 245 "    0.010 2.00e-02 2.50e+03   2.06e-02 4.23e+00
        pdb=" C   ILE A 245 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   ILE A 245 "    0.013 2.00e-02 2.50e+03
        pdb=" N   VAL A 246 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 381 "    0.032 5.00e-02 4.00e+02   4.87e-02 3.79e+00
        pdb=" N   PRO B 382 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO B 382 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 382 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1629 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 167
        2.68 -     3.23: 10503
        3.23 -     3.79: 15341
        3.79 -     4.34: 20170
        4.34 -     4.90: 33962
  Nonbonded interactions: 80143
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C 305 "
            pdb=" OG1 THR C 413 "
     model   vdw
     2.122 3.040
  nonbonded pdb=" O   THR A 283 "
            pdb=" OG1 THR A 287 "
     model   vdw
     2.183 3.040
  nonbonded pdb=" OH  TYR A 249 "
            pdb=" OD2 ASP A 315 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O   THR A 378 "
            pdb=" OG  SER A 381 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OH  TYR C 249 "
            pdb=" OD2 ASP C 315 "
     model   vdw
     2.224 3.040
  ... (remaining 80138 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 7 or resid 9 through 85 or resid 87 through 333  \ 
or resid 335 through 430))
  selection = (chain 'B' and (resid 5 through 7 or resid 9 through 85 or resid 87 through 333  \ 
or resid 335 through 430))
  selection = (chain 'C' and (resid 5 through 7 or resid 9 through 85 or resid 87 through 333  \ 
or resid 335 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.690
  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:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     31.180
  Find NCS groups from input model:        0.430
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
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      :  0.008   0.055   9745  Z= 0.539
  Angle     :  0.754   7.950  13268  Z= 0.406
  Chirality :  0.046   0.156   1650
  Planarity :  0.005   0.049   1632
  Dihedral  : 12.807  89.991   3455
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.71 (0.21), residues: 1281
  helix: -1.38 (0.15), residues: 997
  sheet:  None (None), residues: 0
  loop : -2.70 (0.34), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  20 
 HIS   0.002   0.001   HIS C  34 
 PHE   0.020   0.002   PHE A 302 
 TYR   0.016   0.002   TYR A 320 
 ARG   0.003   0.000   ARG A 107 

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 1.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 MET cc_start: 0.8686 (mmt) cc_final: 0.8448 (mmm)
REVERT: A  393 ILE cc_start: 0.9333 (tp) cc_final: 0.8994 (tp)
REVERT: B  259 ASP cc_start: 0.8312 (t0) cc_final: 0.8105 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.2117
  time to fit residues: 38.9617
Evaluate side-chains
  95 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 1.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    1.9990
   chunk 95 optimal weight:    8.9990
   chunk 52 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 64 optimal weight:    7.9990
   chunk 51 optimal weight:    0.7980
   chunk 98 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   chunk 73 optimal weight:    0.8980
   chunk 114 optimal weight:    4.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
A 138 ASN
B 321 GLN
B 340 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.079133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.058647 restraints weight = 82981.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.2877 rms_B_bonded: 5.63
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2878
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2878 r_free = 0.2878    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2878 r_free = 0.2878    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2878
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.1596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9745  Z= 0.221
  Angle     :  0.619   7.853  13268  Z= 0.312
  Chirality :  0.041   0.166   1650
  Planarity :  0.005   0.053   1632
  Dihedral  :  4.338  21.970   1369
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  9.65 %
    Favored  : 89.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.23), residues: 1281
  helix: -0.05 (0.16), residues: 1025
  sheet:  None (None), residues: 0
  loop : -1.89 (0.39), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  20 
 HIS   0.003   0.001   HIS A  34 
 PHE   0.024   0.001   PHE A 302 
 TYR   0.013   0.001   TYR B 320 
 ARG   0.004   0.000   ARG B 289 

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 127
  time to evaluate  : 1.041 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 ASN cc_start: 0.9345 (m110) cc_final: 0.9082 (m110)
REVERT: A  219 MET cc_start: 0.9021 (mmm) cc_final: 0.8807 (mmm)
REVERT: A  321 GLN cc_start: 0.8139 (mt0) cc_final: 0.7932 (mt0)
REVERT: A  365 MET cc_start: 0.9323 (ttm) cc_final: 0.9010 (ttt)
REVERT: A  393 ILE cc_start: 0.9111 (tp) cc_final: 0.8695 (tp)
REVERT: B   46 LYS cc_start: 0.8713 (tptt) cc_final: 0.8451 (tptp)
REVERT: B   50 ASP cc_start: 0.8598 (m-30) cc_final: 0.8214 (m-30)
REVERT: B  150 LYS cc_start: 0.9501 (mtmm) cc_final: 0.9157 (mtmm)
REVERT: B  259 ASP cc_start: 0.8643 (t0) cc_final: 0.8138 (t0)
REVERT: B  295 MET cc_start: 0.8439 (mmm) cc_final: 0.8137 (mmt)
REVERT: B  424 ASP cc_start: 0.8813 (t0) cc_final: 0.7826 (p0)
REVERT: C  340 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7633 (pm20)
REVERT: C  403 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.7169 (tpp)
  outliers start: 5
  outliers final: 1
  residues processed: 129
  average time/residue: 0.1938
  time to fit residues: 36.9718
Evaluate side-chains
  115 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 112
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   20 TRP
Chi-restraints excluded: chain C residue  340 GLN
Chi-restraints excluded: chain C residue  403 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 6 optimal weight:    0.4980
   chunk 17 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 112 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 49 optimal weight:    7.9990
   chunk 121 optimal weight:    0.5980
   chunk 118 optimal weight:    0.6980
   chunk 103 optimal weight:    0.6980
   chunk 67 optimal weight:    6.9990
   overall best weight:    0.6982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.080467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.059637 restraints weight = 91288.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.2904 rms_B_bonded: 5.97
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2906
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2906 r_free = 0.2906    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2906 r_free = 0.2906    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2906
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9745  Z= 0.184
  Angle     :  0.589   7.713  13268  Z= 0.296
  Chirality :  0.040   0.184   1650
  Planarity :  0.004   0.054   1632
  Dihedral  :  4.115  23.699   1369
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 12.74 %
    Favored  : 86.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.24), residues: 1281
  helix:  0.46 (0.17), residues: 1039
  sheet:  None (None), residues: 0
  loop : -1.71 (0.41), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  20 
 HIS   0.003   0.001   HIS B 334 
 PHE   0.019   0.001   PHE A 302 
 TYR   0.011   0.001   TYR B 320 
 ARG   0.003   0.000   ARG B 289 

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 125
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
REVERT: A  365 MET cc_start: 0.9317 (ttm) cc_final: 0.8923 (ttm)
REVERT: A  393 ILE cc_start: 0.9043 (tp) cc_final: 0.8631 (tp)
REVERT: B   46 LYS cc_start: 0.8712 (tptt) cc_final: 0.8412 (tptp)
REVERT: B   50 ASP cc_start: 0.8624 (m-30) cc_final: 0.8210 (m-30)
REVERT: B  150 LYS cc_start: 0.9440 (OUTLIER) cc_final: 0.8998 (mtmm)
REVERT: B  238 TYR cc_start: 0.8846 (m-80) cc_final: 0.8643 (m-80)
REVERT: B  259 ASP cc_start: 0.8559 (t0) cc_final: 0.8216 (t0)
REVERT: C  340 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7639 (pm20)
REVERT: C  403 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.7128 (tpp)
  outliers start: 8
  outliers final: 3
  residues processed: 128
  average time/residue: 0.1886
  time to fit residues: 35.5288
Evaluate side-chains
  111 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  150 LYS
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain C residue   20 TRP
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  340 GLN
Chi-restraints excluded: chain C residue  403 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 83 optimal weight:    4.9990
   chunk 107 optimal weight:    0.3980
   chunk 1 optimal weight:    1.9990
   chunk 78 optimal weight:    0.0570
   chunk 25 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 116 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9980
   chunk 35 optimal weight:    0.1980
   overall best weight:    0.4298

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

Flipped N/Q/H residues before XYZ refinement:
B 134 GLN
B 138 ASN
** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.081674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.061502 restraints weight = 73555.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 5.46
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2944
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2944 r_free = 0.2944    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2944 r_free = 0.2944    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2944
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.2535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9745  Z= 0.170
  Angle     :  0.585   7.786  13268  Z= 0.292
  Chirality :  0.040   0.153   1650
  Planarity :  0.004   0.054   1632
  Dihedral  :  4.073  27.637   1369
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 13.73 %
    Favored  : 85.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.24), residues: 1281
  helix:  0.76 (0.17), residues: 1036
  sheet:  None (None), residues: 0
  loop : -1.46 (0.41), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  20 
 HIS   0.004   0.001   HIS B 334 
 PHE   0.026   0.001   PHE B 242 
 TYR   0.013   0.001   TYR B 320 
 ARG   0.004   0.000   ARG A 289 

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 1.147 
Fit side-chains
   revert: symmetry clash
REVERT: A  365 MET cc_start: 0.9114 (ttm) cc_final: 0.8588 (ttt)
REVERT: A  393 ILE cc_start: 0.9042 (tp) cc_final: 0.8646 (tp)
REVERT: B   46 LYS cc_start: 0.8741 (tptt) cc_final: 0.8379 (tptp)
REVERT: B   50 ASP cc_start: 0.8727 (m-30) cc_final: 0.8274 (m-30)
REVERT: B  150 LYS cc_start: 0.9417 (OUTLIER) cc_final: 0.8977 (mtmm)
REVERT: B  238 TYR cc_start: 0.8821 (m-80) cc_final: 0.8553 (m-80)
REVERT: B  259 ASP cc_start: 0.8538 (t0) cc_final: 0.8163 (t0)
REVERT: C  314 MET cc_start: 0.8505 (mtp) cc_final: 0.8023 (mtm)
REVERT: C  340 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7530 (pm20)
REVERT: C  403 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.6990 (tpp)
  outliers start: 8
  outliers final: 3
  residues processed: 117
  average time/residue: 0.1768
  time to fit residues: 31.5813
Evaluate side-chains
  113 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 107
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  150 LYS
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain C residue   20 TRP
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  340 GLN
Chi-restraints excluded: chain C residue  403 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 96 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 116 optimal weight:    1.9990
   chunk 108 optimal weight:    7.9990
   chunk 94 optimal weight:    5.9990
   chunk 123 optimal weight:    0.0980
   chunk 14 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.4186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.079739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.059280 restraints weight = 78883.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.2897 rms_B_bonded: 5.50
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2899
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2899 r_free = 0.2899    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2899 r_free = 0.2899    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2899
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.2413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9745  Z= 0.236
  Angle     :  0.594   7.468  13268  Z= 0.298
  Chirality :  0.041   0.177   1650
  Planarity :  0.004   0.052   1632
  Dihedral  :  4.028  27.585   1369
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 15.12 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.24), residues: 1281
  helix:  0.91 (0.17), residues: 1038
  sheet:  None (None), residues: 0
  loop : -1.36 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  20 
 HIS   0.003   0.001   HIS B 334 
 PHE   0.018   0.001   PHE A 302 
 TYR   0.013   0.001   TYR B 320 
 ARG   0.002   0.000   ARG B 401 

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 110
  time to evaluate  : 1.210 
Fit side-chains
   revert: symmetry clash
REVERT: A  365 MET cc_start: 0.9105 (ttm) cc_final: 0.8582 (ttt)
REVERT: A  393 ILE cc_start: 0.9109 (tp) cc_final: 0.8673 (tp)
REVERT: B   46 LYS cc_start: 0.8794 (tptt) cc_final: 0.8369 (tppt)
REVERT: B   50 ASP cc_start: 0.8761 (m-30) cc_final: 0.8388 (m-30)
REVERT: B  150 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.8936 (mtmm)
REVERT: B  238 TYR cc_start: 0.8877 (m-80) cc_final: 0.8593 (m-80)
REVERT: B  259 ASP cc_start: 0.8637 (t0) cc_final: 0.8286 (t0)
REVERT: B  396 ILE cc_start: 0.8718 (mt) cc_final: 0.8472 (mt)
REVERT: C  314 MET cc_start: 0.8608 (mtp) cc_final: 0.8398 (mtt)
REVERT: C  340 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7449 (pm20)
REVERT: C  403 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7081 (tpp)
  outliers start: 8
  outliers final: 3
  residues processed: 114
  average time/residue: 0.1826
  time to fit residues: 31.3627
Evaluate side-chains
  109 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 103
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  150 LYS
Chi-restraints excluded: chain C residue   20 TRP
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  340 GLN
Chi-restraints excluded: chain C residue  403 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 110 optimal weight:   10.0000
   chunk 47 optimal weight:    0.7980
   chunk 88 optimal weight:    0.8980
   chunk 102 optimal weight:    0.6980
   chunk 108 optimal weight:    1.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
B 138 ASN
B 321 GLN
** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.080446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.059652 restraints weight = 88956.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.2907 rms_B_bonded: 5.86
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2909
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2909
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.2587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9745  Z= 0.204
  Angle     :  0.594   7.904  13268  Z= 0.295
  Chirality :  0.041   0.203   1650
  Planarity :  0.004   0.052   1632
  Dihedral  :  4.022  27.245   1369
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 16.12 %
    Favored  : 82.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.24), residues: 1281
  helix:  1.03 (0.17), residues: 1037
  sheet:  None (None), residues: 0
  loop : -1.32 (0.41), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  20 
 HIS   0.003   0.001   HIS B 334 
 PHE   0.020   0.001   PHE B 242 
 TYR   0.013   0.001   TYR B 320 
 ARG   0.002   0.000   ARG B 289 

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 109
  time to evaluate  : 1.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  219 MET cc_start: 0.9112 (mmm) cc_final: 0.8775 (mmm)
REVERT: A  365 MET cc_start: 0.8951 (ttm) cc_final: 0.8556 (ttm)
REVERT: A  393 ILE cc_start: 0.9084 (tp) cc_final: 0.8661 (tp)
REVERT: B   46 LYS cc_start: 0.8765 (tptt) cc_final: 0.8409 (tptp)
REVERT: B  150 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.8663 (mtmm)
REVERT: B  238 TYR cc_start: 0.8865 (m-80) cc_final: 0.8584 (m-80)
REVERT: B  259 ASP cc_start: 0.8641 (t0) cc_final: 0.8290 (t0)
REVERT: B  396 ILE cc_start: 0.8618 (mt) cc_final: 0.8338 (mt)
REVERT: C  314 MET cc_start: 0.8676 (mtp) cc_final: 0.8433 (mtp)
REVERT: C  340 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7487 (pm20)
REVERT: C  403 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.7026 (tpp)
  outliers start: 10
  outliers final: 4
  residues processed: 112
  average time/residue: 0.1788
  time to fit residues: 30.1162
Evaluate side-chains
  111 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  150 LYS
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain C residue   20 TRP
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  340 GLN
Chi-restraints excluded: chain C residue  403 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 62 optimal weight:    0.8980
   chunk 99 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 57 optimal weight:    0.6980
   chunk 92 optimal weight:    0.1980
   chunk 124 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 125 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.080863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.060264 restraints weight = 79866.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.2920 rms_B_bonded: 5.58
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2922
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2922 r_free = 0.2922    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2922 r_free = 0.2922    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2922
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.2720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9745  Z= 0.194
  Angle     :  0.599   9.941  13268  Z= 0.295
  Chirality :  0.041   0.339   1650
  Planarity :  0.004   0.051   1632
  Dihedral  :  3.996  28.094   1369
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 16.62 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.24), residues: 1281
  helix:  1.10 (0.17), residues: 1038
  sheet:  None (None), residues: 0
  loop : -1.27 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP C  20 
 HIS   0.003   0.001   HIS B 334 
 PHE   0.016   0.001   PHE A 302 
 TYR   0.012   0.001   TYR B 320 
 ARG   0.002   0.000   ARG B 289 

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 114
  time to evaluate  : 1.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  219 MET cc_start: 0.9104 (mmm) cc_final: 0.8778 (mmm)
REVERT: A  365 MET cc_start: 0.8975 (ttm) cc_final: 0.8694 (ttm)
REVERT: A  393 ILE cc_start: 0.9064 (tp) cc_final: 0.8638 (tp)
REVERT: B   46 LYS cc_start: 0.8666 (tptt) cc_final: 0.8411 (tptp)
REVERT: B  150 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.8639 (mtmm)
REVERT: B  238 TYR cc_start: 0.8835 (m-80) cc_final: 0.8552 (m-80)
REVERT: B  259 ASP cc_start: 0.8668 (t0) cc_final: 0.8304 (t0)
REVERT: B  396 ILE cc_start: 0.8622 (mt) cc_final: 0.8349 (mt)
REVERT: C  340 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7464 (pm20)
REVERT: C  403 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.6999 (tpp)
  outliers start: 8
  outliers final: 4
  residues processed: 118
  average time/residue: 0.1790
  time to fit residues: 32.2971
Evaluate side-chains
  115 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 108
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  150 LYS
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain C residue   20 TRP
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  340 GLN
Chi-restraints excluded: chain C residue  403 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 124 optimal weight:    0.9990
   chunk 122 optimal weight:    0.9980
   chunk 98 optimal weight:    0.0870
   chunk 43 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   chunk 121 optimal weight:    0.0970
   chunk 119 optimal weight:    0.0770
   overall best weight:    0.4314

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

Flipped N/Q/H residues before XYZ refinement:
B 138 ASN
** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 341 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.082791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.062438 restraints weight = 67380.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.2970 rms_B_bonded: 5.25
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2970
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2970 r_free = 0.2970    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2970 r_free = 0.2970    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2970
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.3051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9745  Z= 0.164
  Angle     :  0.592  12.287  13268  Z= 0.290
  Chirality :  0.041   0.400   1650
  Planarity :  0.004   0.051   1632
  Dihedral  :  3.963  28.446   1369
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 17.51 %
    Favored  : 81.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.24), residues: 1281
  helix:  1.20 (0.17), residues: 1038
  sheet:  None (None), residues: 0
  loop : -1.14 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP C  20 
 HIS   0.004   0.001   HIS B 334 
 PHE   0.021   0.001   PHE B 242 
 TYR   0.011   0.001   TYR B 320 
 ARG   0.002   0.000   ARG B 289 

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 133
  time to evaluate  : 1.072 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  365 MET cc_start: 0.8961 (ttm) cc_final: 0.8601 (ttm)
REVERT: A  393 ILE cc_start: 0.9009 (tp) cc_final: 0.8564 (tp)
REVERT: B  150 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8647 (mtmm)
REVERT: B  238 TYR cc_start: 0.8790 (m-80) cc_final: 0.8575 (m-80)
REVERT: B  396 ILE cc_start: 0.8674 (mt) cc_final: 0.8388 (mt)
REVERT: C  314 MET cc_start: 0.8698 (mtp) cc_final: 0.8209 (mtm)
REVERT: C  340 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7540 (pm20)
  outliers start: 7
  outliers final: 2
  residues processed: 135
  average time/residue: 0.1970
  time to fit residues: 39.0131
Evaluate side-chains
  124 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 120
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  150 LYS
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain C residue   20 TRP
Chi-restraints excluded: chain C residue  340 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 86 optimal weight:    5.9990
   chunk 99 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   chunk 104 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 71 optimal weight:    0.6980
   chunk 74 optimal weight:    3.9990
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.082340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.061499 restraints weight = 93182.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.2950 rms_B_bonded: 6.02
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2951
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2951 r_free = 0.2951    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2951 r_free = 0.2951    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2951
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.3129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9745  Z= 0.183
  Angle     :  0.614  12.662  13268  Z= 0.299
  Chirality :  0.042   0.404   1650
  Planarity :  0.004   0.050   1632
  Dihedral  :  3.988  27.982   1369
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 18.41 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.24), residues: 1281
  helix:  1.20 (0.17), residues: 1038
  sheet:  None (None), residues: 0
  loop : -1.17 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP C  20 
 HIS   0.003   0.001   HIS B 334 
 PHE   0.016   0.001   PHE B 302 
 TYR   0.013   0.001   TYR A 197 
 ARG   0.002   0.000   ARG B 289 

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 123
  time to evaluate  : 1.052 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  365 MET cc_start: 0.9015 (ttm) cc_final: 0.8580 (ttt)
REVERT: B  150 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8602 (mtmm)
REVERT: B  238 TYR cc_start: 0.8806 (m-80) cc_final: 0.8575 (m-80)
REVERT: B  259 ASP cc_start: 0.8641 (t0) cc_final: 0.8270 (t0)
REVERT: B  396 ILE cc_start: 0.8652 (mt) cc_final: 0.8381 (mt)
REVERT: C  314 MET cc_start: 0.8690 (mtp) cc_final: 0.8440 (mtp)
REVERT: C  340 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7419 (pm20)
REVERT: C  365 MET cc_start: 0.6107 (tpp) cc_final: 0.5821 (tpp)
REVERT: C  403 MET cc_start: 0.7490 (tpp) cc_final: 0.7257 (tpp)
  outliers start: 5
  outliers final: 2
  residues processed: 126
  average time/residue: 0.1668
  time to fit residues: 32.4651
Evaluate side-chains
  125 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 121
  time to evaluate  : 1.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  150 LYS
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain C residue   20 TRP
Chi-restraints excluded: chain C residue  340 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 4 optimal weight:    0.3980
   chunk 65 optimal weight:    2.9990
   chunk 107 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 89 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.082356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.061719 restraints weight = 85844.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.2955 rms_B_bonded: 5.77
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2955
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2955 r_free = 0.2955    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2955 r_free = 0.2955    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2955
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.3200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9745  Z= 0.183
  Angle     :  0.609  12.066  13268  Z= 0.298
  Chirality :  0.041   0.403   1650
  Planarity :  0.004   0.050   1632
  Dihedral  :  3.994  28.078   1369
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  : 18.31 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.24), residues: 1281
  helix:  1.21 (0.17), residues: 1040
  sheet:  None (None), residues: 0
  loop : -0.99 (0.42), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP C  20 
 HIS   0.003   0.001   HIS B 334 
 PHE   0.019   0.001   PHE B 242 
 TYR   0.012   0.001   TYR A 197 
 ARG   0.003   0.000   ARG B 289 

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 123
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  365 MET cc_start: 0.9016 (ttm) cc_final: 0.8584 (ttt)
REVERT: B  150 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8560 (mtmm)
REVERT: B  190 ASP cc_start: 0.9050 (t0) cc_final: 0.8784 (t0)
REVERT: B  238 TYR cc_start: 0.8820 (m-80) cc_final: 0.8560 (m-80)
REVERT: B  298 ASP cc_start: 0.7536 (t0) cc_final: 0.7332 (t0)
REVERT: B  365 MET cc_start: 0.8970 (tpp) cc_final: 0.8229 (tpp)
REVERT: B  396 ILE cc_start: 0.8699 (mt) cc_final: 0.8427 (mt)
REVERT: C  314 MET cc_start: 0.8689 (mtp) cc_final: 0.8454 (mtp)
REVERT: C  340 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7404 (pm20)
REVERT: C  365 MET cc_start: 0.6145 (tpp) cc_final: 0.5848 (tpp)
REVERT: C  403 MET cc_start: 0.7464 (tpp) cc_final: 0.7239 (tpp)
  outliers start: 4
  outliers final: 2
  residues processed: 125
  average time/residue: 0.1796
  time to fit residues: 34.5985
Evaluate side-chains
  124 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 120
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  150 LYS
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain C residue   20 TRP
Chi-restraints excluded: chain C residue  340 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 80 optimal weight:    0.0370
   chunk 70 optimal weight:    0.8980
   chunk 103 optimal weight:    4.9990
   chunk 99 optimal weight:    0.7980
   chunk 71 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.082403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.061769 restraints weight = 95365.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.2957 rms_B_bonded: 6.03
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2957
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2957
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.3235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9745  Z= 0.181
  Angle     :  0.611  12.604  13268  Z= 0.299
  Chirality :  0.041   0.403   1650
  Planarity :  0.004   0.050   1632
  Dihedral  :  3.959  27.418   1369
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  : 18.51 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.24), residues: 1281
  helix:  1.25 (0.17), residues: 1040
  sheet:  None (None), residues: 0
  loop : -0.95 (0.42), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP C  20 
 HIS   0.003   0.001   HIS B 334 
 PHE   0.016   0.001   PHE B 302 
 TYR   0.012   0.001   TYR A 197 
 ARG   0.003   0.000   ARG B 289 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3896.34 seconds
wall clock time: 70 minutes 4.11 seconds (4204.11 seconds total)