Starting phenix.real_space_refine
on Sat May  2 21:25:23 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9m7r_63691/05_2026/9m7r_63691.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9m7r_63691/05_2026/9m7r_63691.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9m7r_63691/05_2026/9m7r_63691.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9m7r_63691/05_2026/9m7r_63691.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9m7r_63691/05_2026/9m7r_63691.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9m7r_63691/05_2026/9m7r_63691.map"
  }
  resolution = 2.63
  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=   0.077
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    5817      2.51       5
     N    1362      2.21       5
     O    1404      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8631
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2877
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 358, 2877
          Classifications: {'peptide': 358}
          Link IDs: {'PTRANS': 22, 'TRANS': 335}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 2.44, per 1000 atoms: 0.28
  Number of scatterers: 8631
  At special positions: 0
  Unit cell: (100.488, 102.163, 76.2034, 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    1404      8.00
     N    1362      7.00
     C    5817      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: 0.96
  Conformation dependent library (CDL) restraints added in 409.4 milliseconds
  

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2040

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 3 sheets defined
      76.5% alpha, 0.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 222 through 229
      removed outlier: 3.574A  pdb=" N   TYR A 226 " --> pdb=" O   PRO A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 261
      No H-bonds generated for 'chain 'A' and resid 259 through 261'
    Processing helix  chain 'A' and resid 262 through 282
      removed outlier: 4.478A  pdb=" N   CYS A 266 " --> pdb=" O   THR A 262 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU A 267 " --> pdb=" O   PHE A 263 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   GLN A 272 " --> pdb=" O   GLY A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 289
      removed outlier: 3.684A  pdb=" N   LYS A 286 " --> pdb=" O   GLU A 283 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   PHE A 287 " --> pdb=" O   PRO A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 320
      removed outlier: 3.543A  pdb=" N   GLN A 296 " --> pdb=" O   LEU A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 329
    Processing helix  chain 'A' and resid 332 through 337
    Processing helix  chain 'A' and resid 338 through 350
    Processing helix  chain 'A' and resid 360 through 368
      removed outlier: 4.153A  pdb=" N   TRP A 364 " --> pdb=" O   PRO A 360 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   TYR A 365 " --> pdb=" O   HIS A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 383
      removed outlier: 3.862A  pdb=" N   LYS A 377 " --> pdb=" O   CYS A 373 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   GLY A 380 " --> pdb=" O   LEU A 376 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   MET A 383 " --> pdb=" O   TYR A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 395 through 397
      No H-bonds generated for 'chain 'A' and resid 395 through 397'
    Processing helix  chain 'A' and resid 398 through 416
      removed outlier: 3.708A  pdb=" N   VAL A 402 " --> pdb=" O   ASN A 398 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLY A 404 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   ASN A 405 " --> pdb=" O   SER A 401 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   PHE A 406 " --> pdb=" O   VAL A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 441
      removed outlier: 3.913A  pdb=" N   TYR A 440 " --> pdb=" O   PHE A 436 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLN A 441 " --> pdb=" O   VAL A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 457
    Processing helix  chain 'A' and resid 458 through 476
      removed outlier: 3.904A  pdb=" N   ALA A 462 " --> pdb=" O   PHE A 458 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   ALA A 463 " --> pdb=" O   LEU A 459 " (cutoff:3.500A)
      Proline residue:  A 464  - end of helix
      removed outlier: 3.512A  pdb=" N   MET A 469 " --> pdb=" O   SER A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 500
    Processing helix  chain 'A' and resid 509 through 515
    Processing helix  chain 'A' and resid 516 through 533
      removed outlier: 3.672A  pdb=" N   THR A 520 " --> pdb=" O   THR A 516 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   VAL A 532 " --> pdb=" O   ARG A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 565
    Processing helix  chain 'A' and resid 574 through 578
    Processing helix  chain 'B' and resid 222 through 229
      removed outlier: 3.572A  pdb=" N   TYR B 226 " --> pdb=" O   PRO B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 261
      No H-bonds generated for 'chain 'B' and resid 259 through 261'
    Processing helix  chain 'B' and resid 262 through 282
      removed outlier: 4.477A  pdb=" N   CYS B 266 " --> pdb=" O   THR B 262 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU B 267 " --> pdb=" O   PHE B 263 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   GLN B 272 " --> pdb=" O   GLY B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 289
      removed outlier: 3.684A  pdb=" N   LYS B 286 " --> pdb=" O   GLU B 283 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   PHE B 287 " --> pdb=" O   PRO B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 320
      removed outlier: 3.543A  pdb=" N   GLN B 296 " --> pdb=" O   LEU B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 320 through 329
    Processing helix  chain 'B' and resid 332 through 337
    Processing helix  chain 'B' and resid 338 through 350
    Processing helix  chain 'B' and resid 360 through 368
      removed outlier: 4.154A  pdb=" N   TRP B 364 " --> pdb=" O   PRO B 360 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   TYR B 365 " --> pdb=" O   HIS B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 368 through 383
      removed outlier: 3.862A  pdb=" N   LYS B 377 " --> pdb=" O   CYS B 373 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   GLY B 380 " --> pdb=" O   LEU B 376 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   MET B 383 " --> pdb=" O   TYR B 379 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 397
      No H-bonds generated for 'chain 'B' and resid 395 through 397'
    Processing helix  chain 'B' and resid 398 through 416
      removed outlier: 3.707A  pdb=" N   VAL B 402 " --> pdb=" O   ASN B 398 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLY B 404 " --> pdb=" O   LEU B 400 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   ASN B 405 " --> pdb=" O   SER B 401 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   PHE B 406 " --> pdb=" O   VAL B 402 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 418 through 441
      removed outlier: 3.912A  pdb=" N   TYR B 440 " --> pdb=" O   PHE B 436 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLN B 441 " --> pdb=" O   VAL B 437 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 457
    Processing helix  chain 'B' and resid 458 through 476
      removed outlier: 3.903A  pdb=" N   ALA B 462 " --> pdb=" O   PHE B 458 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   ALA B 463 " --> pdb=" O   LEU B 459 " (cutoff:3.500A)
      Proline residue:  B 464  - end of helix
      removed outlier: 3.512A  pdb=" N   MET B 469 " --> pdb=" O   SER B 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 479 through 500
    Processing helix  chain 'B' and resid 509 through 515
    Processing helix  chain 'B' and resid 516 through 533
      removed outlier: 3.671A  pdb=" N   THR B 520 " --> pdb=" O   THR B 516 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   VAL B 532 " --> pdb=" O   ARG B 528 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 535 through 565
    Processing helix  chain 'B' and resid 574 through 578
    Processing helix  chain 'C' and resid 222 through 229
      removed outlier: 3.572A  pdb=" N   TYR C 226 " --> pdb=" O   PRO C 222 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 259 through 261
      No H-bonds generated for 'chain 'C' and resid 259 through 261'
    Processing helix  chain 'C' and resid 262 through 282
      removed outlier: 4.479A  pdb=" N   CYS C 266 " --> pdb=" O   THR C 262 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU C 267 " --> pdb=" O   PHE C 263 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   GLN C 272 " --> pdb=" O   GLY C 268 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 283 through 289
      removed outlier: 3.685A  pdb=" N   LYS C 286 " --> pdb=" O   GLU C 283 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   PHE C 287 " --> pdb=" O   PRO C 284 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 292 through 320
      removed outlier: 3.543A  pdb=" N   GLN C 296 " --> pdb=" O   LEU C 292 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 320 through 329
    Processing helix  chain 'C' and resid 332 through 337
    Processing helix  chain 'C' and resid 338 through 350
    Processing helix  chain 'C' and resid 360 through 368
      removed outlier: 4.154A  pdb=" N   TRP C 364 " --> pdb=" O   PRO C 360 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   TYR C 365 " --> pdb=" O   HIS C 361 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 368 through 383
      removed outlier: 3.862A  pdb=" N   LYS C 377 " --> pdb=" O   CYS C 373 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   GLY C 380 " --> pdb=" O   LEU C 376 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   MET C 383 " --> pdb=" O   TYR C 379 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 395 through 397
      No H-bonds generated for 'chain 'C' and resid 395 through 397'
    Processing helix  chain 'C' and resid 398 through 416
      removed outlier: 3.708A  pdb=" N   VAL C 402 " --> pdb=" O   ASN C 398 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLY C 404 " --> pdb=" O   LEU C 400 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   ASN C 405 " --> pdb=" O   SER C 401 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   PHE C 406 " --> pdb=" O   VAL C 402 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 418 through 441
      removed outlier: 3.913A  pdb=" N   TYR C 440 " --> pdb=" O   PHE C 436 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLN C 441 " --> pdb=" O   VAL C 437 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 454 through 457
    Processing helix  chain 'C' and resid 458 through 476
      removed outlier: 3.903A  pdb=" N   ALA C 462 " --> pdb=" O   PHE C 458 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   ALA C 463 " --> pdb=" O   LEU C 459 " (cutoff:3.500A)
      Proline residue:  C 464  - end of helix
      removed outlier: 3.513A  pdb=" N   MET C 469 " --> pdb=" O   SER C 465 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 479 through 500
    Processing helix  chain 'C' and resid 509 through 515
    Processing helix  chain 'C' and resid 516 through 533
      removed outlier: 3.672A  pdb=" N   THR C 520 " --> pdb=" O   THR C 516 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   VAL C 532 " --> pdb=" O   ARG C 528 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 535 through 565
    Processing helix  chain 'C' and resid 574 through 578
    Processing sheet with id=AA1, first strand: chain 'A' and resid 230 through 231
      removed outlier: 3.540A  pdb=" N   THR A 237 " --> pdb=" O   GLU A 231 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 230 through 231
      removed outlier: 3.539A  pdb=" N   THR B 237 " --> pdb=" O   GLU B 231 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 230 through 231
      removed outlier: 3.538A  pdb=" N   THR C 237 " --> pdb=" O   GLU C 231 " (cutoff:3.500A)

    528 hydrogen bonds defined for protein.
    1476 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: 1.21

  Time building geometry restraints manager: 1.18 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: 2500
        1.34 -     1.46: 1533
        1.46 -     1.57: 4796
        1.57 -     1.69: 0
        1.69 -     1.81: 81
  Bond restraints: 8910
  Sorted by residual:
  bond pdb=" C   PHE A 517 "
       pdb=" N   PRO A 518 "
    ideal  model  delta    sigma   weight residual
    1.335  1.375 -0.040 1.28e-02 6.10e+03 9.79e+00
  bond pdb=" C   PHE C 517 "
       pdb=" N   PRO C 518 "
    ideal  model  delta    sigma   weight residual
    1.335  1.374 -0.040 1.28e-02 6.10e+03 9.55e+00
  bond pdb=" C   PHE B 517 "
       pdb=" N   PRO B 518 "
    ideal  model  delta    sigma   weight residual
    1.335  1.374 -0.039 1.28e-02 6.10e+03 9.44e+00
  bond pdb=" C   VAL B 351 "
       pdb=" N   PRO B 352 "
    ideal  model  delta    sigma   weight residual
    1.329  1.363 -0.033 1.18e-02 7.18e+03 8.06e+00
  bond pdb=" C   VAL C 351 "
       pdb=" N   PRO C 352 "
    ideal  model  delta    sigma   weight residual
    1.329  1.362 -0.033 1.18e-02 7.18e+03 7.84e+00
  ... (remaining 8905 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 11986
        1.80 -     3.59: 143
        3.59 -     5.39: 27
        5.39 -     7.18: 0
        7.18 -     8.98: 3
  Bond angle restraints: 12159
  Sorted by residual:
  angle pdb=" N   ALA B 462 "
        pdb=" CA  ALA B 462 "
        pdb=" C   ALA B 462 "
      ideal   model   delta    sigma   weight residual
     111.07  115.86   -4.79 1.07e+00 8.73e-01 2.00e+01
  angle pdb=" N   ALA C 462 "
        pdb=" CA  ALA C 462 "
        pdb=" C   ALA C 462 "
      ideal   model   delta    sigma   weight residual
     111.07  115.82   -4.75 1.07e+00 8.73e-01 1.97e+01
  angle pdb=" N   ALA A 462 "
        pdb=" CA  ALA A 462 "
        pdb=" C   ALA A 462 "
      ideal   model   delta    sigma   weight residual
     111.07  115.81   -4.74 1.07e+00 8.73e-01 1.96e+01
  angle pdb=" C   PHE C 517 "
        pdb=" N   PRO C 518 "
        pdb=" CA  PRO C 518 "
      ideal   model   delta    sigma   weight residual
     119.28  114.62    4.66 1.10e+00 8.26e-01 1.79e+01
  angle pdb=" C   PHE B 517 "
        pdb=" N   PRO B 518 "
        pdb=" CA  PRO B 518 "
      ideal   model   delta    sigma   weight residual
     119.28  114.65    4.63 1.10e+00 8.26e-01 1.77e+01
  ... (remaining 12154 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.10: 4552
       14.10 -    28.20: 450
       28.20 -    42.29: 116
       42.29 -    56.39: 12
       56.39 -    70.49: 6
  Dihedral angle restraints: 5136
    sinusoidal: 1980
      harmonic: 3156
  Sorted by residual:
  dihedral pdb=" CA  PHE A 478 "
           pdb=" C   PHE A 478 "
           pdb=" N   ASP A 479 "
           pdb=" CA  ASP A 479 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.05  -16.95     0      5.00e+00 4.00e-02 1.15e+01
  dihedral pdb=" CA  PHE B 478 "
           pdb=" C   PHE B 478 "
           pdb=" N   ASP B 479 "
           pdb=" CA  ASP B 479 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.08  -16.92     0      5.00e+00 4.00e-02 1.15e+01
  dihedral pdb=" CA  PHE C 478 "
           pdb=" C   PHE C 478 "
           pdb=" N   ASP C 479 "
           pdb=" CA  ASP C 479 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.09  -16.91     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 5133 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 842
       0.029 -    0.058: 366
       0.058 -    0.088: 133
       0.088 -    0.117: 48
       0.117 -    0.146: 3
  Chirality restraints: 1392
  Sorted by residual:
  chirality pdb=" CA  ALA C 462 "
            pdb=" N   ALA C 462 "
            pdb=" C   ALA C 462 "
            pdb=" CB  ALA C 462 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.34    0.15 2.00e-01 2.50e+01 5.34e-01
  chirality pdb=" CA  ALA B 462 "
            pdb=" N   ALA B 462 "
            pdb=" C   ALA B 462 "
            pdb=" CB  ALA B 462 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.34    0.15 2.00e-01 2.50e+01 5.30e-01
  chirality pdb=" CA  ALA A 462 "
            pdb=" N   ALA A 462 "
            pdb=" C   ALA A 462 "
            pdb=" CB  ALA A 462 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.34    0.14 2.00e-01 2.50e+01 5.10e-01
  ... (remaining 1389 not shown)

  Planarity restraints: 1476
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 420 "    0.047 5.00e-02 4.00e+02   7.11e-02 8.09e+00
        pdb=" N   PRO B 421 "   -0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO B 421 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO B 421 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 420 "   -0.047 5.00e-02 4.00e+02   7.10e-02 8.07e+00
        pdb=" N   PRO A 421 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO A 421 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 421 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY C 420 "    0.047 5.00e-02 4.00e+02   7.09e-02 8.05e+00
        pdb=" N   PRO C 421 "   -0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO C 421 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO C 421 "    0.039 5.00e-02 4.00e+02
  ... (remaining 1473 not shown)

  Histogram of nonbonded interaction distances:
        2.42 -     2.91: 3438
        2.91 -     3.41: 8873
        3.41 -     3.91: 14651
        3.91 -     4.40: 17111
        4.40 -     4.90: 27935
  Nonbonded interactions: 72008
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS C 316 "
            pdb=" OE2 GLU C 327 "
     model   vdw
     2.416 3.120
  nonbonded pdb=" NZ  LYS B 316 "
            pdb=" OE2 GLU B 327 "
     model   vdw
     2.417 3.120
  nonbonded pdb=" NZ  LYS A 316 "
            pdb=" OE2 GLU A 327 "
     model   vdw
     2.417 3.120
  nonbonded pdb=" NH2 ARG A 499 "
            pdb=" O   SER C 384 "
     model   vdw
     2.426 3.120
  nonbonded pdb=" O   SER A 384 "
            pdb=" NH2 ARG B 499 "
     model   vdw
     2.427 3.120
  ... (remaining 72003 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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:             1.420
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.290
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8910  Z= 0.161
  Angle     :  0.544   8.981  12159  Z= 0.324
  Chirality :  0.038   0.146   1392
  Planarity :  0.007   0.071   1476
  Dihedral  : 12.177  70.489   3096
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.85 (0.26), residues: 1062
  helix:  0.82 (0.20), residues: 723
  sheet:  None (None), residues: 0
  loop :  0.26 (0.35), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 388 
 TYR   0.011   0.001   TYR B 313 
 PHE   0.011   0.001   PHE C 517 
 TRP   0.007   0.001   TRP C 293 
 HIS   0.003   0.001   HIS A 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 8910)
  covalent geometry    : angle       0.54396 (12159)
  hydrogen bonds       : bond        0.15753 (  528)
  hydrogen bonds       : angle       6.37722 ( 1476)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.333 
Fit side-chains
REVERT: B  368 MET cc_start: 0.8333 (mmm) cc_final: 0.8004 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.4345
  time to fit residues: 72.9408
Evaluate side-chains
  118 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0870
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.1980
   chunk 62 optimal weight:    0.0870
   chunk 51 optimal weight:    0.6980
   chunk 100 optimal weight:    2.9990
   chunk 38 optimal weight:    9.9990
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.3536

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

Flipped N/Q/H residues before XYZ refinement:
B 563 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.213401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.171968 restraints weight = 9671.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.4073 rms_B_bonded: 1.93
r_work: 0.3982 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3875 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.1694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8910  Z= 0.098
  Angle     :  0.466   5.222  12159  Z= 0.236
  Chirality :  0.039   0.130   1392
  Planarity :  0.006   0.069   1476
  Dihedral  :  3.781  15.259   1161
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  6.84 %
    Favored  : 91.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.08 (0.26), residues: 1062
  helix:  1.76 (0.19), residues: 714
  sheet:  None (None), residues: 0
  loop :  0.77 (0.37), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 389 
 TYR   0.010   0.001   TYR A 432 
 PHE   0.014   0.001   PHE A 517 
 TRP   0.011   0.001   TRP B 276 
 HIS   0.003   0.001   HIS C 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 ( 8910)
  covalent geometry    : angle       0.46576 (12159)
  hydrogen bonds       : bond        0.03813 (  528)
  hydrogen bonds       : angle       3.74166 ( 1476)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.398 
Fit side-chains
REVERT: A  326 ARG cc_start: 0.8133 (mtt-85) cc_final: 0.7802 (mtp85)
REVERT: A  458 PHE cc_start: 0.7555 (m-80) cc_final: 0.6652 (t80)
REVERT: A  540 ILE cc_start: 0.7797 (mt) cc_final: 0.7587 (mm)
REVERT: A  577 ILE cc_start: 0.6345 (pt) cc_final: 0.6133 (pp)
REVERT: B  368 MET cc_start: 0.8728 (mmm) cc_final: 0.8111 (mmm)
REVERT: B  506 ILE cc_start: 0.7224 (OUTLIER) cc_final: 0.6487 (tp)
REVERT: B  537 MET cc_start: 0.6990 (OUTLIER) cc_final: 0.6332 (ttt)
REVERT: C  534 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7627 (mtpt)
REVERT: C  540 ILE cc_start: 0.7768 (mt) cc_final: 0.7536 (mm)
  outliers start: 16
  outliers final: 8
  residues processed: 126
  average time/residue: 0.4979
  time to fit residues: 67.7788
Evaluate side-chains
  122 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  509 SER
Chi-restraints excluded: chain A residue  537 MET
Chi-restraints excluded: chain A residue  553 VAL
Chi-restraints excluded: chain B residue  506 ILE
Chi-restraints excluded: chain B residue  509 SER
Chi-restraints excluded: chain B residue  537 MET
Chi-restraints excluded: chain B residue  553 VAL
Chi-restraints excluded: chain C residue  261 SER
Chi-restraints excluded: chain C residue  509 SER
Chi-restraints excluded: chain C residue  534 LYS
Chi-restraints excluded: chain C residue  553 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 80 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 91 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 37 optimal weight:    9.9990
   chunk 55 optimal weight:    0.9980
   chunk 102 optimal weight:    4.9990
   chunk 59 optimal weight:    0.7980
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
A 563 HIS
B 361 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.200677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.158055 restraints weight = 9757.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.3938 rms_B_bonded: 1.90
r_work: 0.3841 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3735 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   8910  Z= 0.202
  Angle     :  0.571   6.214  12159  Z= 0.296
  Chirality :  0.044   0.127   1392
  Planarity :  0.006   0.067   1476
  Dihedral  :  4.245  17.976   1161
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  :  7.93 %
    Favored  : 89.47 %
  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:  1.94 (0.26), residues: 1062
  helix:  1.66 (0.19), residues: 687
  sheet:  None (None), residues: 0
  loop :  0.79 (0.35), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 389 
 TYR   0.021   0.002   TYR A 258 
 PHE   0.021   0.002   PHE C 341 
 TRP   0.013   0.001   TRP C 276 
 HIS   0.006   0.002   HIS A 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 ( 8910)
  covalent geometry    : angle       0.57149 (12159)
  hydrogen bonds       : bond        0.05440 (  528)
  hydrogen bonds       : angle       4.21766 ( 1476)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A  326 ARG cc_start: 0.8270 (mtt-85) cc_final: 0.8007 (mtp85)
REVERT: A  458 PHE cc_start: 0.7581 (m-80) cc_final: 0.6676 (t80)
REVERT: A  494 PHE cc_start: 0.7048 (t80) cc_final: 0.6525 (m-10)
REVERT: A  534 LYS cc_start: 0.8283 (mtpt) cc_final: 0.8038 (mppt)
REVERT: B  494 PHE cc_start: 0.7150 (t80) cc_final: 0.6640 (m-10)
REVERT: B  551 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7490 (mm)
REVERT: C  326 ARG cc_start: 0.8253 (mtt-85) cc_final: 0.7952 (mtp85)
REVERT: C  479 ASP cc_start: 0.6451 (p0) cc_final: 0.6214 (p0)
REVERT: C  494 PHE cc_start: 0.7138 (t80) cc_final: 0.6600 (m-10)
REVERT: C  537 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6568 (ttt)
REVERT: C  539 GLN cc_start: 0.7148 (mt0) cc_final: 0.6902 (mt0)
  outliers start: 24
  outliers final: 14
  residues processed: 124
  average time/residue: 0.5166
  time to fit residues: 68.7780
Evaluate side-chains
  122 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  509 SER
Chi-restraints excluded: chain A residue  537 MET
Chi-restraints excluded: chain A residue  553 VAL
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  506 ILE
Chi-restraints excluded: chain B residue  509 SER
Chi-restraints excluded: chain B residue  537 MET
Chi-restraints excluded: chain B residue  551 LEU
Chi-restraints excluded: chain B residue  553 VAL
Chi-restraints excluded: chain C residue  261 SER
Chi-restraints excluded: chain C residue  509 SER
Chi-restraints excluded: chain C residue  511 SER
Chi-restraints excluded: chain C residue  537 MET
Chi-restraints excluded: chain C residue  553 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 63 optimal weight:    4.9990
   chunk 103 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 101 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 84 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 15 optimal weight:    0.4980
   chunk 13 optimal weight:    0.0470
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
C 563 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.206951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.166086 restraints weight = 9789.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3988 rms_B_bonded: 1.96
r_work: 0.3886 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3778 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.2742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8910  Z= 0.105
  Angle     :  0.458   5.796  12159  Z= 0.232
  Chirality :  0.039   0.130   1392
  Planarity :  0.006   0.065   1476
  Dihedral  :  3.871  16.167   1161
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  :  9.12 %
    Favored  : 87.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.04 (0.26), residues: 1062
  helix:  1.80 (0.19), residues: 714
  sheet:  None (None), residues: 0
  loop :  0.58 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 389 
 TYR   0.010   0.001   TYR A 432 
 PHE   0.018   0.001   PHE A 517 
 TRP   0.009   0.001   TRP C 276 
 HIS   0.004   0.001   HIS B 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 8910)
  covalent geometry    : angle       0.45837 (12159)
  hydrogen bonds       : bond        0.03902 (  528)
  hydrogen bonds       : angle       3.77013 ( 1476)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 108
  time to evaluate  : 0.397 
Fit side-chains
REVERT: A  458 PHE cc_start: 0.7525 (m-80) cc_final: 0.6846 (t80)
REVERT: A  494 PHE cc_start: 0.6755 (t80) cc_final: 0.6215 (m-10)
REVERT: A  540 ILE cc_start: 0.7787 (mt) cc_final: 0.7577 (mm)
REVERT: B  368 MET cc_start: 0.8586 (mmm) cc_final: 0.8079 (mmm)
REVERT: B  494 PHE cc_start: 0.6858 (t80) cc_final: 0.6291 (m-10)
REVERT: C  326 ARG cc_start: 0.8103 (mtt-85) cc_final: 0.7844 (mtp85)
REVERT: C  537 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6415 (ttt)
REVERT: C  539 GLN cc_start: 0.6974 (mt0) cc_final: 0.6736 (mt0)
REVERT: C  540 ILE cc_start: 0.7762 (mt) cc_final: 0.7508 (mm)
  outliers start: 31
  outliers final: 12
  residues processed: 127
  average time/residue: 0.5060
  time to fit residues: 69.1750
Evaluate side-chains
  115 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  509 SER
Chi-restraints excluded: chain A residue  537 MET
Chi-restraints excluded: chain A residue  553 VAL
Chi-restraints excluded: chain B residue  506 ILE
Chi-restraints excluded: chain B residue  509 SER
Chi-restraints excluded: chain B residue  553 VAL
Chi-restraints excluded: chain C residue  261 SER
Chi-restraints excluded: chain C residue  506 ILE
Chi-restraints excluded: chain C residue  509 SER
Chi-restraints excluded: chain C residue  511 SER
Chi-restraints excluded: chain C residue  537 MET
Chi-restraints excluded: chain C residue  553 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 51 optimal weight:    0.2980
   chunk 8 optimal weight:    0.6980
   chunk 99 optimal weight:    0.3980
   chunk 29 optimal weight:    0.4980
   chunk 63 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 75 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.4403 r_free = 0.4403 target = 0.206371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.165966 restraints weight = 9796.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.4002 rms_B_bonded: 2.07
r_work: 0.3899 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3791 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.2809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8910  Z= 0.100
  Angle     :  0.445   5.690  12159  Z= 0.226
  Chirality :  0.039   0.131   1392
  Planarity :  0.005   0.064   1476
  Dihedral  :  3.719  15.229   1161
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 10.31 %
    Favored  : 86.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.28 (0.26), residues: 1062
  helix:  1.98 (0.19), residues: 714
  sheet:  None (None), residues: 0
  loop :  0.65 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 389 
 TYR   0.011   0.001   TYR A 432 
 PHE   0.016   0.001   PHE A 517 
 TRP   0.009   0.001   TRP C 276 
 HIS   0.004   0.001   HIS B 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 8910)
  covalent geometry    : angle       0.44541 (12159)
  hydrogen bonds       : bond        0.03737 (  528)
  hydrogen bonds       : angle       3.61747 ( 1476)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 109
  time to evaluate  : 0.349 
Fit side-chains
REVERT: A  221 MET cc_start: 0.5712 (mtp) cc_final: 0.5095 (ttm)
REVERT: A  326 ARG cc_start: 0.8116 (mtp85) cc_final: 0.7905 (mtp85)
REVERT: A  458 PHE cc_start: 0.7461 (m-80) cc_final: 0.6837 (t80)
REVERT: A  494 PHE cc_start: 0.6714 (t80) cc_final: 0.6201 (m-10)
REVERT: A  540 ILE cc_start: 0.7766 (mt) cc_final: 0.7559 (mm)
REVERT: B  368 MET cc_start: 0.8601 (mmm) cc_final: 0.8098 (mmm)
REVERT: B  494 PHE cc_start: 0.6811 (t80) cc_final: 0.6304 (m-10)
REVERT: B  537 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.6559 (tmt)
REVERT: C  265 MET cc_start: 0.7549 (mtp) cc_final: 0.7316 (mtm)
REVERT: C  326 ARG cc_start: 0.8065 (mtt-85) cc_final: 0.7842 (mtp85)
REVERT: C  383 MET cc_start: 0.6974 (mtt) cc_final: 0.6452 (mtt)
REVERT: C  389 ARG cc_start: 0.6830 (mtp180) cc_final: 0.6452 (mtp180)
REVERT: C  539 GLN cc_start: 0.7007 (mt0) cc_final: 0.6767 (mt0)
REVERT: C  540 ILE cc_start: 0.7701 (mt) cc_final: 0.7468 (mm)
  outliers start: 28
  outliers final: 15
  residues processed: 126
  average time/residue: 0.5084
  time to fit residues: 68.9161
Evaluate side-chains
  117 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  509 SER
Chi-restraints excluded: chain A residue  534 LYS
Chi-restraints excluded: chain A residue  537 MET
Chi-restraints excluded: chain A residue  553 VAL
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  265 MET
Chi-restraints excluded: chain B residue  506 ILE
Chi-restraints excluded: chain B residue  509 SER
Chi-restraints excluded: chain B residue  537 MET
Chi-restraints excluded: chain B residue  553 VAL
Chi-restraints excluded: chain C residue  261 SER
Chi-restraints excluded: chain C residue  506 ILE
Chi-restraints excluded: chain C residue  509 SER
Chi-restraints excluded: chain C residue  553 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 62 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 77 optimal weight:    4.9990
   chunk 1 optimal weight:    4.9990
   chunk 22 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 37 optimal weight:   10.0000
   chunk 46 optimal weight:    2.9990
   chunk 35 optimal weight:   10.0000
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
C 361 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.199796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.157053 restraints weight = 9752.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.3929 rms_B_bonded: 1.91
r_work: 0.3832 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3726 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.3098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8910  Z= 0.179
  Angle     :  0.534   6.076  12159  Z= 0.278
  Chirality :  0.043   0.128   1392
  Planarity :  0.006   0.064   1476
  Dihedral  :  4.110  17.321   1161
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 10.75 %
    Favored  : 85.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.03 (0.25), residues: 1062
  helix:  1.75 (0.19), residues: 687
  sheet:  None (None), residues: 0
  loop :  0.78 (0.34), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 389 
 TYR   0.018   0.002   TYR A 258 
 PHE   0.019   0.002   PHE C 341 
 TRP   0.011   0.001   TRP C 276 
 HIS   0.006   0.001   HIS B 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 8910)
  covalent geometry    : angle       0.53417 (12159)
  hydrogen bonds       : bond        0.05006 (  528)
  hydrogen bonds       : angle       4.04827 ( 1476)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 105
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A  221 MET cc_start: 0.5913 (mtp) cc_final: 0.5245 (mtt)
REVERT: A  326 ARG cc_start: 0.8241 (mtp85) cc_final: 0.8025 (mtp85)
REVERT: A  494 PHE cc_start: 0.6950 (t80) cc_final: 0.6416 (m-10)
REVERT: B  473 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7666 (mptt)
REVERT: B  494 PHE cc_start: 0.6997 (t80) cc_final: 0.6446 (m-10)
REVERT: B  537 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6475 (ttt)
REVERT: B  551 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7456 (mm)
REVERT: C  326 ARG cc_start: 0.8215 (mtt-85) cc_final: 0.7996 (mtp85)
REVERT: C  383 MET cc_start: 0.7314 (mtt) cc_final: 0.7046 (mtt)
REVERT: C  479 ASP cc_start: 0.6401 (p0) cc_final: 0.6199 (p0)
REVERT: C  537 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6357 (ttt)
REVERT: C  539 GLN cc_start: 0.7113 (mt0) cc_final: 0.6825 (mt0)
  outliers start: 30
  outliers final: 14
  residues processed: 120
  average time/residue: 0.5075
  time to fit residues: 65.4287
Evaluate side-chains
  120 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  509 SER
Chi-restraints excluded: chain A residue  537 MET
Chi-restraints excluded: chain A residue  553 VAL
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  473 LYS
Chi-restraints excluded: chain B residue  506 ILE
Chi-restraints excluded: chain B residue  509 SER
Chi-restraints excluded: chain B residue  537 MET
Chi-restraints excluded: chain B residue  551 LEU
Chi-restraints excluded: chain B residue  553 VAL
Chi-restraints excluded: chain C residue  261 SER
Chi-restraints excluded: chain C residue  509 SER
Chi-restraints excluded: chain C residue  511 SER
Chi-restraints excluded: chain C residue  537 MET
Chi-restraints excluded: chain C residue  553 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 91 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 37 optimal weight:    8.9990
   chunk 49 optimal weight:    1.9990
   chunk 27 optimal weight:    7.9990
   chunk 99 optimal weight:    2.9990
   overall best weight:    1.7588

-------------------------------------------------------------------------------
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 = 0.4347 r_free = 0.4347 target = 0.199664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.157388 restraints weight = 9784.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3927 rms_B_bonded: 1.94
r_work: 0.3829 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3722 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.3287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8910  Z= 0.183
  Angle     :  0.537   6.078  12159  Z= 0.279
  Chirality :  0.042   0.126   1392
  Planarity :  0.006   0.064   1476
  Dihedral  :  4.228  17.182   1161
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 10.75 %
    Favored  : 86.10 %
  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:  1.79 (0.25), residues: 1062
  helix:  1.61 (0.19), residues: 681
  sheet:  None (None), residues: 0
  loop :  0.57 (0.33), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 389 
 TYR   0.018   0.002   TYR A 258 
 PHE   0.019   0.002   PHE C 341 
 TRP   0.011   0.001   TRP C 276 
 HIS   0.006   0.001   HIS A 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 8910)
  covalent geometry    : angle       0.53672 (12159)
  hydrogen bonds       : bond        0.04937 (  528)
  hydrogen bonds       : angle       4.06063 ( 1476)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 99
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A  221 MET cc_start: 0.5982 (mtp) cc_final: 0.5183 (mtt)
REVERT: A  326 ARG cc_start: 0.8255 (mtp85) cc_final: 0.8050 (mtp85)
REVERT: A  458 PHE cc_start: 0.7562 (m-80) cc_final: 0.6896 (t80)
REVERT: A  494 PHE cc_start: 0.6941 (t80) cc_final: 0.6325 (m-10)
REVERT: B  473 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7668 (mptt)
REVERT: B  494 PHE cc_start: 0.6932 (t80) cc_final: 0.6390 (m-10)
REVERT: B  551 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7491 (mm)
REVERT: C  383 MET cc_start: 0.7253 (mtt) cc_final: 0.7024 (mtt)
REVERT: C  506 ILE cc_start: 0.6614 (OUTLIER) cc_final: 0.6269 (tp)
REVERT: C  537 MET cc_start: 0.6999 (OUTLIER) cc_final: 0.6233 (ttt)
REVERT: C  539 GLN cc_start: 0.7091 (mt0) cc_final: 0.6763 (mt0)
  outliers start: 29
  outliers final: 13
  residues processed: 118
  average time/residue: 0.4849
  time to fit residues: 61.7845
Evaluate side-chains
  116 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  509 SER
Chi-restraints excluded: chain A residue  537 MET
Chi-restraints excluded: chain A residue  553 VAL
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  473 LYS
Chi-restraints excluded: chain B residue  506 ILE
Chi-restraints excluded: chain B residue  509 SER
Chi-restraints excluded: chain B residue  551 LEU
Chi-restraints excluded: chain B residue  553 VAL
Chi-restraints excluded: chain C residue  261 SER
Chi-restraints excluded: chain C residue  506 ILE
Chi-restraints excluded: chain C residue  509 SER
Chi-restraints excluded: chain C residue  511 SER
Chi-restraints excluded: chain C residue  537 MET
Chi-restraints excluded: chain C residue  553 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 75 optimal weight:    0.6980
   chunk 18 optimal weight:    4.9990
   chunk 23 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 25 optimal weight:    0.4980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.4381 r_free = 0.4381 target = 0.203770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.161823 restraints weight = 9649.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3971 rms_B_bonded: 1.94
r_work: 0.3877 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3770 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.3264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8910  Z= 0.110
  Angle     :  0.465   5.844  12159  Z= 0.237
  Chirality :  0.039   0.130   1392
  Planarity :  0.005   0.063   1476
  Dihedral  :  3.897  16.202   1161
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 11.83 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.20 (0.25), residues: 1062
  helix:  1.97 (0.19), residues: 693
  sheet:  None (None), residues: 0
  loop :  0.61 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 389 
 TYR   0.011   0.001   TYR A 432 
 PHE   0.018   0.001   PHE A 517 
 TRP   0.009   0.001   TRP C 276 
 HIS   0.005   0.001   HIS C 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 8910)
  covalent geometry    : angle       0.46487 (12159)
  hydrogen bonds       : bond        0.03949 (  528)
  hydrogen bonds       : angle       3.74789 ( 1476)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 102
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A  221 MET cc_start: 0.5910 (mtp) cc_final: 0.5602 (tpt)
REVERT: A  494 PHE cc_start: 0.6819 (t80) cc_final: 0.6219 (m-10)
REVERT: B  221 MET cc_start: 0.5986 (mtp) cc_final: 0.5141 (mtt)
REVERT: B  368 MET cc_start: 0.8610 (mmm) cc_final: 0.8086 (mmm)
REVERT: B  494 PHE cc_start: 0.6851 (t80) cc_final: 0.6279 (m-10)
REVERT: B  506 ILE cc_start: 0.7434 (OUTLIER) cc_final: 0.7168 (pp)
REVERT: C  377 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7834 (ttmm)
REVERT: C  383 MET cc_start: 0.7221 (mtt) cc_final: 0.6795 (mtt)
REVERT: C  506 ILE cc_start: 0.6392 (OUTLIER) cc_final: 0.6150 (tp)
REVERT: C  537 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6304 (ttt)
REVERT: C  539 GLN cc_start: 0.6986 (mt0) cc_final: 0.6686 (mt0)
REVERT: C  540 ILE cc_start: 0.7714 (mt) cc_final: 0.7460 (mm)
  outliers start: 24
  outliers final: 11
  residues processed: 115
  average time/residue: 0.4952
  time to fit residues: 61.3004
Evaluate side-chains
  112 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  509 SER
Chi-restraints excluded: chain A residue  534 LYS
Chi-restraints excluded: chain A residue  537 MET
Chi-restraints excluded: chain A residue  553 VAL
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  506 ILE
Chi-restraints excluded: chain B residue  509 SER
Chi-restraints excluded: chain B residue  553 VAL
Chi-restraints excluded: chain C residue  261 SER
Chi-restraints excluded: chain C residue  377 LYS
Chi-restraints excluded: chain C residue  506 ILE
Chi-restraints excluded: chain C residue  511 SER
Chi-restraints excluded: chain C residue  537 MET
Chi-restraints excluded: chain C residue  553 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   chunk 56 optimal weight:    0.5980
   chunk 53 optimal weight:    0.5980
   chunk 31 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.4370 r_free = 0.4370 target = 0.202396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.160378 restraints weight = 9702.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.3956 rms_B_bonded: 1.93
r_work: 0.3860 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3753 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.3313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8910  Z= 0.129
  Angle     :  0.487   6.035  12159  Z= 0.250
  Chirality :  0.040   0.128   1392
  Planarity :  0.005   0.063   1476
  Dihedral  :  3.947  16.122   1161
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 12.05 %
    Favored  : 85.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.16 (0.25), residues: 1062
  helix:  1.94 (0.19), residues: 693
  sheet:  None (None), residues: 0
  loop :  0.60 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 389 
 TYR   0.014   0.001   TYR A 432 
 PHE   0.016   0.001   PHE A 517 
 TRP   0.010   0.001   TRP B 276 
 HIS   0.005   0.001   HIS A 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8910)
  covalent geometry    : angle       0.48687 (12159)
  hydrogen bonds       : bond        0.04264 (  528)
  hydrogen bonds       : angle       3.82117 ( 1476)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 97
  time to evaluate  : 0.363 
Fit side-chains
REVERT: A  221 MET cc_start: 0.5886 (mtp) cc_final: 0.5575 (tpt)
REVERT: A  494 PHE cc_start: 0.6901 (t80) cc_final: 0.6311 (m-10)
REVERT: B  221 MET cc_start: 0.5920 (mtp) cc_final: 0.5222 (ttm)
REVERT: B  368 MET cc_start: 0.8584 (mmm) cc_final: 0.8014 (mmm)
REVERT: B  494 PHE cc_start: 0.6885 (t80) cc_final: 0.6305 (m-10)
REVERT: B  509 SER cc_start: 0.8182 (OUTLIER) cc_final: 0.7212 (p)
REVERT: C  383 MET cc_start: 0.7266 (mtt) cc_final: 0.6792 (mtt)
REVERT: C  506 ILE cc_start: 0.6374 (OUTLIER) cc_final: 0.6089 (tp)
REVERT: C  537 MET cc_start: 0.7007 (OUTLIER) cc_final: 0.6285 (ttt)
REVERT: C  539 GLN cc_start: 0.7036 (mt0) cc_final: 0.6729 (mt0)
  outliers start: 25
  outliers final: 17
  residues processed: 112
  average time/residue: 0.4736
  time to fit residues: 57.3836
Evaluate side-chains
  117 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  509 SER
Chi-restraints excluded: chain A residue  534 LYS
Chi-restraints excluded: chain A residue  537 MET
Chi-restraints excluded: chain A residue  553 VAL
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  397 THR
Chi-restraints excluded: chain B residue  506 ILE
Chi-restraints excluded: chain B residue  509 SER
Chi-restraints excluded: chain B residue  553 VAL
Chi-restraints excluded: chain C residue  261 SER
Chi-restraints excluded: chain C residue  265 MET
Chi-restraints excluded: chain C residue  397 THR
Chi-restraints excluded: chain C residue  506 ILE
Chi-restraints excluded: chain C residue  511 SER
Chi-restraints excluded: chain C residue  534 LYS
Chi-restraints excluded: chain C residue  537 MET
Chi-restraints excluded: chain C residue  553 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 61 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 94 optimal weight:    3.9990
   chunk 69 optimal weight:   10.0000
   chunk 56 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.4361 r_free = 0.4361 target = 0.201586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.159645 restraints weight = 9797.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3959 rms_B_bonded: 1.95
r_work: 0.3863 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3757 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.3348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8910  Z= 0.121
  Angle     :  0.481   8.952  12159  Z= 0.245
  Chirality :  0.040   0.129   1392
  Planarity :  0.005   0.063   1476
  Dihedral  :  3.907  15.653   1161
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 12.27 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.24 (0.25), residues: 1062
  helix:  1.99 (0.19), residues: 693
  sheet:  None (None), residues: 0
  loop :  0.65 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 389 
 TYR   0.013   0.001   TYR A 432 
 PHE   0.017   0.001   PHE A 517 
 TRP   0.010   0.001   TRP B 276 
 HIS   0.005   0.001   HIS A 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 8910)
  covalent geometry    : angle       0.48071 (12159)
  hydrogen bonds       : bond        0.04091 (  528)
  hydrogen bonds       : angle       3.77876 ( 1476)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A  221 MET cc_start: 0.5848 (mtp) cc_final: 0.5552 (tpt)
REVERT: A  494 PHE cc_start: 0.6838 (t80) cc_final: 0.6243 (m-10)
REVERT: B  221 MET cc_start: 0.5887 (mtp) cc_final: 0.5018 (ttm)
REVERT: B  368 MET cc_start: 0.8582 (mmm) cc_final: 0.8039 (mmm)
REVERT: B  494 PHE cc_start: 0.6858 (t80) cc_final: 0.6321 (m-10)
REVERT: B  509 SER cc_start: 0.8158 (OUTLIER) cc_final: 0.7256 (p)
REVERT: C  377 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7856 (ttmm)
REVERT: C  383 MET cc_start: 0.7162 (mtt) cc_final: 0.6803 (mtt)
REVERT: C  389 ARG cc_start: 0.6888 (mtp85) cc_final: 0.6595 (mtp85)
REVERT: C  506 ILE cc_start: 0.6334 (OUTLIER) cc_final: 0.6042 (tp)
REVERT: C  537 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6262 (ttt)
REVERT: C  539 GLN cc_start: 0.6993 (mt0) cc_final: 0.6677 (mt0)
  outliers start: 20
  outliers final: 16
  residues processed: 106
  average time/residue: 0.4982
  time to fit residues: 56.9964
Evaluate side-chains
  118 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  509 SER
Chi-restraints excluded: chain A residue  534 LYS
Chi-restraints excluded: chain A residue  537 MET
Chi-restraints excluded: chain A residue  553 VAL
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  397 THR
Chi-restraints excluded: chain B residue  506 ILE
Chi-restraints excluded: chain B residue  509 SER
Chi-restraints excluded: chain B residue  553 VAL
Chi-restraints excluded: chain C residue  261 SER
Chi-restraints excluded: chain C residue  377 LYS
Chi-restraints excluded: chain C residue  397 THR
Chi-restraints excluded: chain C residue  506 ILE
Chi-restraints excluded: chain C residue  511 SER
Chi-restraints excluded: chain C residue  534 LYS
Chi-restraints excluded: chain C residue  537 MET
Chi-restraints excluded: chain C residue  553 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 94 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 59 optimal weight:    0.5980
   chunk 100 optimal weight:    0.8980
   chunk 73 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 72 optimal weight:    8.9990
   chunk 82 optimal weight:    0.6980
   chunk 15 optimal weight:    0.5980
   chunk 101 optimal weight:    2.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.4368 r_free = 0.4368 target = 0.202159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.159982 restraints weight = 9716.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3951 rms_B_bonded: 1.95
r_work: 0.3855 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3749 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.3370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8910  Z= 0.125
  Angle     :  0.479   5.950  12159  Z= 0.246
  Chirality :  0.040   0.128   1392
  Planarity :  0.005   0.063   1476
  Dihedral  :  3.912  15.993   1161
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 11.83 %
    Favored  : 85.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.24 (0.25), residues: 1062
  helix:  1.98 (0.19), residues: 693
  sheet:  None (None), residues: 0
  loop :  0.66 (0.34), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 389 
 TYR   0.014   0.001   TYR A 432 
 PHE   0.016   0.001   PHE A 517 
 TRP   0.010   0.001   TRP B 276 
 HIS   0.005   0.001   HIS A 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 8910)
  covalent geometry    : angle       0.47900 (12159)
  hydrogen bonds       : bond        0.04165 (  528)
  hydrogen bonds       : angle       3.77535 ( 1476)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3242.86 seconds
wall clock time: 55 minutes 55.95 seconds (3355.95 seconds total)