Starting phenix.real_space_refine
on Mon Jan 13 16:22:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gg1_51320/01_2025/9gg1_51320_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gg1_51320/01_2025/9gg1_51320.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gg1_51320/01_2025/9gg1_51320.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gg1_51320/01_2025/9gg1_51320.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gg1_51320/01_2025/9gg1_51320_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gg1_51320/01_2025/9gg1_51320_neut.cif"
  }
  resolution = 2.26
  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=   0.000 sd=   0.002
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       8      5.16       5
     C    2012      2.51       5
     N     604      2.21       5
     O     608      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 3232
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 808
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 3, 'TRANS': 103}
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 3.50, per 1000 atoms: 1.08
  Number of scatterers: 3232
  At special positions: 0
  Unit cell: (86.52, 106.296, 46.144, 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       8     16.00
     O     608      8.00
     N     604      7.00
     C    2012      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.06
  Conformation dependent library (CDL) restraints added in 397.4 milliseconds
  

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  744

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 11 sheets defined
      0.0% alpha, 59.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 274 through 279
      removed outlier: 6.538A  pdb=" N   VAL A 275 " --> pdb=" O   GLN C 276 " (cutoff:3.500A)
      removed outlier: 7.878A  pdb=" N   ILE C 278 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   ILE A 277 " --> pdb=" O   ILE C 278 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 282 through 283
      removed outlier: 6.546A  pdb=" N   LEU A 282 " --> pdb=" O   ASP B 283 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   LEU B 282 " --> pdb=" O   ASP D 283 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 286 through 302
      removed outlier: 6.812A  pdb=" N   LYS C 298 " --> pdb=" O   ILE A 297 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   HIS A 299 " --> pdb=" O   LYS C 298 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   ASN A 286 " --> pdb=" O   VAL B 287 " (cutoff:3.500A)
      removed outlier: 8.253A  pdb=" N   SER B 289 " --> pdb=" O   ASN A 286 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   GLN A 288 " --> pdb=" O   SER B 289 " (cutoff:3.500A)
      removed outlier: 8.047A  pdb=" N   CYS B 291 " --> pdb=" O   GLN A 288 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   LYS A 290 " --> pdb=" O   CYS B 291 " (cutoff:3.500A)
      removed outlier: 7.463A  pdb=" N   SER B 293 " --> pdb=" O   LYS A 290 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   GLY A 292 " --> pdb=" O   SER B 293 " (cutoff:3.500A)
      removed outlier: 8.017A  pdb=" N   ASP B 295 " --> pdb=" O   GLY A 292 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   LYS A 294 " --> pdb=" O   ASP B 295 " (cutoff:3.500A)
      removed outlier: 8.020A  pdb=" N   ILE B 297 " --> pdb=" O   LYS A 294 " (cutoff:3.500A)
      removed outlier: 8.134A  pdb=" N   ASN A 296 " --> pdb=" O   ILE B 297 " (cutoff:3.500A)
      removed outlier: 7.846A  pdb=" N   HIS B 299 " --> pdb=" O   ASN A 296 " (cutoff:3.500A)
      removed outlier: 6.130A  pdb=" N   LYS A 298 " --> pdb=" O   HIS B 299 " (cutoff:3.500A)
      removed outlier: 8.608A  pdb=" N   THR B 301 " --> pdb=" O   LYS A 298 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   VAL A 300 " --> pdb=" O   THR B 301 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   ASN B 286 " --> pdb=" O   VAL D 287 " (cutoff:3.500A)
      removed outlier: 8.254A  pdb=" N   SER D 289 " --> pdb=" O   ASN B 286 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   GLN B 288 " --> pdb=" O   SER D 289 " (cutoff:3.500A)
      removed outlier: 8.048A  pdb=" N   CYS D 291 " --> pdb=" O   GLN B 288 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   LYS B 290 " --> pdb=" O   CYS D 291 " (cutoff:3.500A)
      removed outlier: 7.463A  pdb=" N   SER D 293 " --> pdb=" O   LYS B 290 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   GLY B 292 " --> pdb=" O   SER D 293 " (cutoff:3.500A)
      removed outlier: 8.017A  pdb=" N   ASP D 295 " --> pdb=" O   GLY B 292 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   LYS B 294 " --> pdb=" O   ASP D 295 " (cutoff:3.500A)
      removed outlier: 8.020A  pdb=" N   ILE D 297 " --> pdb=" O   LYS B 294 " (cutoff:3.500A)
      removed outlier: 8.134A  pdb=" N   ASN B 296 " --> pdb=" O   ILE D 297 " (cutoff:3.500A)
      removed outlier: 7.846A  pdb=" N   HIS D 299 " --> pdb=" O   ASN B 296 " (cutoff:3.500A)
      removed outlier: 6.130A  pdb=" N   LYS B 298 " --> pdb=" O   HIS D 299 " (cutoff:3.500A)
      removed outlier: 8.607A  pdb=" N   THR D 301 " --> pdb=" O   LYS B 298 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   VAL B 300 " --> pdb=" O   THR D 301 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 305 through 310
      removed outlier: 6.351A  pdb=" N   SER A 305 " --> pdb=" O   VAL C 306 " (cutoff:3.500A)
      removed outlier: 7.970A  pdb=" N   ILE C 308 " --> pdb=" O   SER A 305 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   GLN A 307 " --> pdb=" O   ILE C 308 " (cutoff:3.500A)
      removed outlier: 7.756A  pdb=" N   TYR C 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   VAL A 309 " --> pdb=" O   TYR C 310 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 313 through 314
      removed outlier: 6.943A  pdb=" N   VAL A 313 " --> pdb=" O   ASP B 314 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   VAL B 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 317 through 322
      removed outlier: 6.476A  pdb=" N   LYS A 317 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 8.182A  pdb=" N   SER B 320 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   THR A 319 " --> pdb=" O   SER B 320 " (cutoff:3.500A)
      removed outlier: 7.886A  pdb=" N   CYS B 322 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   LYS A 321 " --> pdb=" O   CYS B 322 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   LYS B 317 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
      removed outlier: 8.182A  pdb=" N   SER D 320 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   THR B 319 " --> pdb=" O   SER D 320 " (cutoff:3.500A)
      removed outlier: 7.886A  pdb=" N   CYS D 322 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   LYS B 321 " --> pdb=" O   CYS D 322 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 327 through 330
      removed outlier: 6.497A  pdb=" N   ASN A 327 " --> pdb=" O   ILE B 328 " (cutoff:3.500A)
      removed outlier: 7.764A  pdb=" N   HIS B 330 " --> pdb=" O   ASN A 327 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   HIS A 329 " --> pdb=" O   HIS B 330 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   ASN B 327 " --> pdb=" O   ILE D 328 " (cutoff:3.500A)
      removed outlier: 7.765A  pdb=" N   HIS D 330 " --> pdb=" O   ASN B 327 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   HIS B 329 " --> pdb=" O   HIS D 330 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 337 through 346
      removed outlier: 6.911A  pdb=" N   GLU A 338 " --> pdb=" O   VAL C 337 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   VAL C 339 " --> pdb=" O   GLU A 338 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   LYS A 340 " --> pdb=" O   VAL C 339 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   SER C 341 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   GLU A 342 " --> pdb=" O   SER C 341 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   LYS C 343 " --> pdb=" O   GLU A 342 " (cutoff:3.500A)
      removed outlier: 8.963A  pdb=" N   VAL A 337 " --> pdb=" O   GLU B 338 " (cutoff:3.500A)
      removed outlier: 10.285A  pdb=" N   LYS B 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 9.005A  pdb=" N   VAL A 339 " --> pdb=" O   LYS B 340 " (cutoff:3.500A)
      removed outlier: 10.327A  pdb=" N   GLU B 342 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 8.960A  pdb=" N   SER A 341 " --> pdb=" O   GLU B 342 " (cutoff:3.500A)
      removed outlier: 9.240A  pdb=" N   LEU B 344 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   LYS A 343 " --> pdb=" O   LEU B 344 " (cutoff:3.500A)
      removed outlier: 7.969A  pdb=" N   PHE B 346 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   ASP A 345 " --> pdb=" O   PHE B 346 " (cutoff:3.500A)
      removed outlier: 8.962A  pdb=" N   VAL B 337 " --> pdb=" O   GLU D 338 " (cutoff:3.500A)
      removed outlier: 10.284A  pdb=" N   LYS D 340 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 9.004A  pdb=" N   VAL B 339 " --> pdb=" O   LYS D 340 " (cutoff:3.500A)
      removed outlier: 10.327A  pdb=" N   GLU D 342 " --> pdb=" O   VAL B 339 " (cutoff:3.500A)
      removed outlier: 8.960A  pdb=" N   SER B 341 " --> pdb=" O   GLU D 342 " (cutoff:3.500A)
      removed outlier: 9.240A  pdb=" N   LEU D 344 " --> pdb=" O   SER B 341 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   LYS B 343 " --> pdb=" O   LEU D 344 " (cutoff:3.500A)
      removed outlier: 7.968A  pdb=" N   PHE D 346 " --> pdb=" O   LYS B 343 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   ASP B 345 " --> pdb=" O   PHE D 346 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 350 through 354
      removed outlier: 6.431A  pdb=" N   VAL A 350 " --> pdb=" O   GLN C 351 " (cutoff:3.500A)
      removed outlier: 8.253A  pdb=" N   LYS C 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   SER A 352 " --> pdb=" O   LYS C 353 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 357 through 362
      removed outlier: 6.415A  pdb=" N   ASP A 358 " --> pdb=" O   ASN B 359 " (cutoff:3.500A)
      removed outlier: 7.615A  pdb=" N   THR B 361 " --> pdb=" O   ASP A 358 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   ILE A 360 " --> pdb=" O   THR B 361 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   ASP B 358 " --> pdb=" O   ASN D 359 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   THR D 361 " --> pdb=" O   ASP B 358 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   ILE B 360 " --> pdb=" O   THR D 361 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 368 through 378
      removed outlier: 6.465A  pdb=" N   LYS A 369 " --> pdb=" O   LYS B 370 " (cutoff:3.500A)
      removed outlier: 8.115A  pdb=" N   GLU B 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   ILE A 371 " --> pdb=" O   GLU B 372 " (cutoff:3.500A)
      removed outlier: 8.150A  pdb=" N   HIS B 374 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   THR A 373 " --> pdb=" O   HIS B 374 " (cutoff:3.500A)
      removed outlier: 8.111A  pdb=" N   LEU B 376 " --> pdb=" O   THR A 373 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   LYS A 375 " --> pdb=" O   LEU B 376 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   PHE B 378 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   THR A 377 " --> pdb=" O   PHE B 378 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   LYS B 369 " --> pdb=" O   LYS D 370 " (cutoff:3.500A)
      removed outlier: 8.114A  pdb=" N   GLU D 372 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ILE B 371 " --> pdb=" O   GLU D 372 " (cutoff:3.500A)
      removed outlier: 8.150A  pdb=" N   HIS D 374 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   THR B 373 " --> pdb=" O   HIS D 374 " (cutoff:3.500A)
      removed outlier: 8.112A  pdb=" N   LEU D 376 " --> pdb=" O   THR B 373 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   LYS B 375 " --> pdb=" O   LEU D 376 " (cutoff:3.500A)
      removed outlier: 7.844A  pdb=" N   PHE D 378 " --> pdb=" O   LYS B 375 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   THR B 377 " --> pdb=" O   PHE D 378 " (cutoff:3.500A)

    70 hydrogen bonds defined for protein.
    210 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: 0.82

  Time building geometry restraints manager: 1.19 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: 845
        1.34 -     1.46: 794
        1.46 -     1.58: 1625
        1.58 -     1.70: 0
        1.70 -     1.82: 8
  Bond restraints: 3272
  Sorted by residual:
  bond pdb=" CA  SER B 356 "
       pdb=" CB  SER B 356 "
    ideal  model  delta    sigma   weight residual
    1.533  1.495  0.038 1.72e-02 3.38e+03 4.91e+00
  bond pdb=" CA  SER A 356 "
       pdb=" CB  SER A 356 "
    ideal  model  delta    sigma   weight residual
    1.533  1.495  0.038 1.72e-02 3.38e+03 4.86e+00
  bond pdb=" CA  SER C 356 "
       pdb=" CB  SER C 356 "
    ideal  model  delta    sigma   weight residual
    1.533  1.496  0.038 1.72e-02 3.38e+03 4.85e+00
  bond pdb=" CA  SER C 341 "
       pdb=" CB  SER C 341 "
    ideal  model  delta    sigma   weight residual
    1.532  1.497  0.036 1.62e-02 3.81e+03 4.82e+00
  bond pdb=" CA  SER D 341 "
       pdb=" CB  SER D 341 "
    ideal  model  delta    sigma   weight residual
    1.532  1.497  0.035 1.62e-02 3.81e+03 4.75e+00
  ... (remaining 3267 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 3574
        1.56 -     3.13: 675
        3.13 -     4.69: 111
        4.69 -     6.25: 4
        6.25 -     7.82: 4
  Bond angle restraints: 4368
  Sorted by residual:
  angle pdb=" C   ARG D 349 "
        pdb=" CA  ARG D 349 "
        pdb=" CB  ARG D 349 "
      ideal   model   delta    sigma   weight residual
     109.54  101.72    7.82 1.84e+00 2.95e-01 1.81e+01
  angle pdb=" C   ARG C 349 "
        pdb=" CA  ARG C 349 "
        pdb=" CB  ARG C 349 "
      ideal   model   delta    sigma   weight residual
     109.54  101.72    7.82 1.84e+00 2.95e-01 1.80e+01
  angle pdb=" C   ARG B 349 "
        pdb=" CA  ARG B 349 "
        pdb=" CB  ARG B 349 "
      ideal   model   delta    sigma   weight residual
     109.54  101.75    7.79 1.84e+00 2.95e-01 1.79e+01
  angle pdb=" C   ARG A 349 "
        pdb=" CA  ARG A 349 "
        pdb=" CB  ARG A 349 "
      ideal   model   delta    sigma   weight residual
     109.54  101.75    7.79 1.84e+00 2.95e-01 1.79e+01
  angle pdb=" CA  ASP C 283 "
        pdb=" CB  ASP C 283 "
        pdb=" CG  ASP C 283 "
      ideal   model   delta    sigma   weight residual
     112.60  116.40   -3.80 1.00e+00 1.00e+00 1.44e+01
  ... (remaining 4363 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.50: 1754
       13.50 -    27.00: 174
       27.00 -    40.50: 48
       40.50 -    53.99: 16
       53.99 -    67.49: 16
  Dihedral angle restraints: 2008
    sinusoidal: 836
      harmonic: 1172
  Sorted by residual:
  dihedral pdb=" CA  GLN C 276 "
           pdb=" C   GLN C 276 "
           pdb=" N   ILE C 277 "
           pdb=" CA  ILE C 277 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.60   22.40     0      5.00e+00 4.00e-02 2.01e+01
  dihedral pdb=" CA  GLN D 276 "
           pdb=" C   GLN D 276 "
           pdb=" N   ILE D 277 "
           pdb=" CA  ILE D 277 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.61   22.39     0      5.00e+00 4.00e-02 2.01e+01
  dihedral pdb=" CA  GLN A 276 "
           pdb=" C   GLN A 276 "
           pdb=" N   ILE A 277 "
           pdb=" CA  ILE A 277 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.62   22.38     0      5.00e+00 4.00e-02 2.00e+01
  ... (remaining 2005 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.042: 160
       0.042 -    0.083: 161
       0.083 -    0.124: 137
       0.124 -    0.164: 30
       0.164 -    0.205: 8
  Chirality restraints: 496
  Sorted by residual:
  chirality pdb=" CA  GLN B 288 "
            pdb=" N   GLN B 288 "
            pdb=" C   GLN B 288 "
            pdb=" CB  GLN B 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.21 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CA  GLN C 288 "
            pdb=" N   GLN C 288 "
            pdb=" C   GLN C 288 "
            pdb=" CB  GLN C 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CA  GLN A 288 "
            pdb=" N   GLN A 288 "
            pdb=" C   GLN A 288 "
            pdb=" CB  GLN A 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.04e+00
  ... (remaining 493 not shown)

  Planarity restraints: 556
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 297 "    0.008 2.00e-02 2.50e+03   1.60e-02 2.55e+00
        pdb=" C   ILE B 297 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   ILE B 297 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LYS B 298 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE D 297 "    0.008 2.00e-02 2.50e+03   1.58e-02 2.49e+00
        pdb=" C   ILE D 297 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   ILE D 297 "    0.010 2.00e-02 2.50e+03
        pdb=" N   LYS D 298 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 297 "    0.008 2.00e-02 2.50e+03   1.57e-02 2.48e+00
        pdb=" C   ILE A 297 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   ILE A 297 "    0.010 2.00e-02 2.50e+03
        pdb=" N   LYS A 298 "    0.009 2.00e-02 2.50e+03
  ... (remaining 553 not shown)

  Histogram of nonbonded interaction distances:
        2.61 -     3.07: 1922
        3.07 -     3.53: 2994
        3.53 -     3.98: 5077
        3.98 -     4.44: 5538
        4.44 -     4.90: 10879
  Nonbonded interactions: 26410
  Sorted by model distance:
  nonbonded pdb=" N   LEU B 315 "
            pdb=" O   ASP D 314 "
     model   vdw
     2.610 3.120
  nonbonded pdb=" N   LEU A 315 "
            pdb=" O   ASP B 314 "
     model   vdw
     2.610 3.120
  nonbonded pdb=" O   ASP A 314 "
            pdb=" N   LEU C 315 "
     model   vdw
     2.611 3.120
  nonbonded pdb=" OE1 GLN A 276 "
            pdb=" NE2 GLN B 276 "
     model   vdw
     2.617 3.120
  nonbonded pdb=" NE2 GLN A 276 "
            pdb=" OE1 GLN C 276 "
     model   vdw
     2.617 3.120
  ... (remaining 26405 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 'C'
  selection = chain 'B'
  selection = chain 'D'
}

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:             2.880
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     14.470
  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:13.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8854
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   0.038   3272  Z= 0.534
  Angle     :  1.278   7.818   4368  Z= 0.827
  Chirality :  0.079   0.205    496
  Planarity :  0.006   0.037    556
  Dihedral  : 14.087  67.492   1264
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 1.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.57 (0.34), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.95 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.003   HIS C 362 
 PHE   0.015   0.004   PHE A 346 
 TYR   0.011   0.004   TYR B 310 
 ARG   0.005   0.002   ARG C 379 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.427 
Fit side-chains
REVERT: A  348 ASP cc_start: 0.9017 (t0) cc_final: 0.8817 (t0)
REVERT: A  351 GLN cc_start: 0.8559 (pt0) cc_final: 0.8302 (pt0)
REVERT: A  372 GLU cc_start: 0.8611 (tt0) cc_final: 0.8410 (tt0)
REVERT: D  379 ARG cc_start: 0.7451 (mtt180) cc_final: 0.6897 (mtm180)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 1.2265
  time to fit residues: 108.4273
Evaluate side-chains
  78 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 31 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    0.4980
   chunk 36 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 288 GLN
A 296 ASN
B 296 ASN
D 276 GLN
D 296 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.117667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.098199 restraints weight = 3380.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 1.42
r_work: 0.3329 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3228 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8823
moved from start:          0.1304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   3272  Z= 0.136
  Angle     :  0.576   8.008   4368  Z= 0.287
  Chirality :  0.051   0.140    496
  Planarity :  0.003   0.024    556
  Dihedral  :  5.633  18.253    436
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 2.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  :  9.68 %
    Favored  : 88.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.44 (0.33), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.85 (0.25), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS C 330 
 PHE   0.003   0.001   PHE A 346 
 TYR   0.004   0.001   TYR B 310 
 ARG   0.003   0.001   ARG D 349 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.383 
Fit side-chains
REVERT: A  285 SER cc_start: 0.8414 (p) cc_final: 0.8085 (p)
REVERT: B  356 SER cc_start: 0.9193 (p) cc_final: 0.8983 (p)
REVERT: C  282 LEU cc_start: 0.8400 (tt) cc_final: 0.8173 (tp)
REVERT: C  285 SER cc_start: 0.8526 (p) cc_final: 0.8277 (p)
REVERT: C  286 ASN cc_start: 0.8351 (t0) cc_final: 0.8135 (t0)
  outliers start: 6
  outliers final: 2
  residues processed: 86
  average time/residue: 1.1345
  time to fit residues: 100.4467
Evaluate side-chains
  84 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 82
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain B residue  316 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 38 optimal weight:    7.9990
   chunk 6 optimal weight:    0.8980
   chunk 37 optimal weight:    5.9990
   chunk 7 optimal weight:    6.9990
   chunk 34 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 26 optimal weight:    0.2980
   chunk 4 optimal weight:    9.9990
   chunk 17 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
A 286 ASN
B 276 GLN
B 359 ASN
D 276 GLN
D 359 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.113220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.094016 restraints weight = 3385.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 1.40
r_work: 0.3274 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3171 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8866
moved from start:          0.1555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3272  Z= 0.244
  Angle     :  0.613   7.263   4368  Z= 0.314
  Chirality :  0.052   0.137    496
  Planarity :  0.003   0.020    556
  Dihedral  :  5.472  18.145    436
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 11.83 %
    Favored  : 86.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.37 (0.33), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.79 (0.25), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C 330 
 PHE   0.005   0.001   PHE A 378 
 TYR   0.002   0.001   TYR B 310 
 ARG   0.005   0.001   ARG B 349 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.431 
Fit side-chains
REVERT: B  379 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.6635 (mpp80)
REVERT: C  349 ARG cc_start: 0.8593 (mtt90) cc_final: 0.7172 (mmp-170)
  outliers start: 6
  outliers final: 3
  residues processed: 83
  average time/residue: 1.1364
  time to fit residues: 97.0633
Evaluate side-chains
  82 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  379 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 8 optimal weight:   10.0000
   chunk 21 optimal weight:    7.9990
   chunk 34 optimal weight:   10.0000
   chunk 26 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 37 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 288 GLN
A 359 ASN
B 276 GLN
B 359 ASN
C 276 GLN
C 286 ASN
C 288 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.113859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.094327 restraints weight = 3387.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 1.41
r_work: 0.3278 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 3.04 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8886
moved from start:          0.1768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035   3272  Z= 0.373
  Angle     :  0.687   7.453   4368  Z= 0.354
  Chirality :  0.053   0.143    496
  Planarity :  0.003   0.022    556
  Dihedral  :  5.623  19.058    436
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  5.00 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 11.56 %
    Favored  : 86.83 %
  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: -2.40 (0.33), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.82 (0.25), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 299 
 PHE   0.007   0.001   PHE C 378 
 TYR   0.003   0.001   TYR D 310 
 ARG   0.005   0.001   ARG B 349 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.428 
Fit side-chains
REVERT: B  379 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.6840 (mpp80)
REVERT: C  349 ARG cc_start: 0.8580 (mtt90) cc_final: 0.7117 (mmp-170)
  outliers start: 6
  outliers final: 3
  residues processed: 83
  average time/residue: 1.1813
  time to fit residues: 100.9654
Evaluate side-chains
  81 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  379 ARG
Chi-restraints excluded: chain D residue  342 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 7 optimal weight:    8.9990
   chunk 24 optimal weight:    6.9990
   chunk 33 optimal weight:    0.0020
   chunk 21 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   chunk 30 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 25 optimal weight:   10.0000
   overall best weight:    1.9792

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

Flipped N/Q/H residues before XYZ refinement:
A 276 GLN
A 286 ASN
B 276 GLN
B 296 ASN
C 276 GLN
C 288 GLN
D 359 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.113740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.094491 restraints weight = 3415.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 1.41
r_work: 0.3291 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3188 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8874
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3272  Z= 0.240
  Angle     :  0.594   8.492   4368  Z= 0.311
  Chirality :  0.052   0.142    496
  Planarity :  0.002   0.021    556
  Dihedral  :  5.479  18.312    436
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.95 %
    Allowed  :  3.81 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 12.63 %
    Favored  : 86.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.41 (0.33), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.83 (0.25), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D 374 
 PHE   0.006   0.001   PHE C 378 
 TYR   0.002   0.001   TYR B 310 
 ARG   0.006   0.001   ARG B 349 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 0.457 
Fit side-chains
REVERT: B  379 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.6859 (mpp80)
REVERT: C  349 ARG cc_start: 0.8600 (mtt90) cc_final: 0.7059 (mmp-170)
  outliers start: 3
  outliers final: 1
  residues processed: 76
  average time/residue: 1.2530
  time to fit residues: 97.8836
Evaluate side-chains
  76 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  379 ARG
Chi-restraints excluded: chain D residue  342 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 36 optimal weight:    7.9990
   chunk 30 optimal weight:    6.9990
   chunk 31 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 12 optimal weight:    4.9990
   chunk 13 optimal weight:    6.9990
   chunk 19 optimal weight:    8.9990
   chunk 15 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 9 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 276 GLN
C 276 GLN
C 288 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.111362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.091970 restraints weight = 3446.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 1.42
r_work: 0.3238 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3134 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8897
moved from start:          0.1872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   3272  Z= 0.418
  Angle     :  0.694   8.302   4368  Z= 0.365
  Chirality :  0.054   0.151    496
  Planarity :  0.003   0.021    556
  Dihedral  :  5.640  18.859    436
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.95 %
    Allowed  :  3.57 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 12.63 %
    Favored  : 86.02 %
  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: -2.35 (0.33), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.25), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 299 
 PHE   0.010   0.001   PHE C 378 
 TYR   0.003   0.001   TYR D 310 
 ARG   0.006   0.001   ARG D 349 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.446 
Fit side-chains
REVERT: B  379 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7324 (mpp80)
REVERT: C  349 ARG cc_start: 0.8582 (mtt90) cc_final: 0.7038 (mmp-170)
  outliers start: 5
  outliers final: 3
  residues processed: 81
  average time/residue: 1.1898
  time to fit residues: 99.1276
Evaluate side-chains
  83 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  379 ARG
Chi-restraints excluded: chain D residue  342 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 18 optimal weight:    8.9990
   chunk 33 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0060
   chunk 28 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.7596

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

Flipped N/Q/H residues before XYZ refinement:
** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 286 ASN
** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 288 GLN
** D 276 GLN ** 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 = 0.3750 r_free = 0.3750 target = 0.116370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.097111 restraints weight = 3337.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 1.41
r_work: 0.3327 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3225 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8851
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   3272  Z= 0.143
  Angle     :  0.614  11.980   4368  Z= 0.302
  Chirality :  0.052   0.146    496
  Planarity :  0.002   0.019    556
  Dihedral  :  5.515  20.509    436
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.95 %
    Allowed  :  3.81 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 13.71 %
    Favored  : 85.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.39 (0.33), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.82 (0.25), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS D 374 
 PHE   0.004   0.001   PHE A 378 
 TYR   0.002   0.000   TYR B 310 
 ARG   0.007   0.001   ARG D 349 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
REVERT: A  352 SER cc_start: 0.8908 (t) cc_final: 0.8691 (p)
REVERT: B  379 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.6981 (mpp80)
REVERT: C  349 ARG cc_start: 0.8614 (mtt90) cc_final: 0.7089 (mmp-170)
  outliers start: 4
  outliers final: 2
  residues processed: 76
  average time/residue: 1.2217
  time to fit residues: 95.5544
Evaluate side-chains
  74 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 71
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  379 ARG
Chi-restraints excluded: chain C residue  282 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 29 optimal weight:    6.9990
   chunk 5 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 23 optimal weight:    0.0470
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 21 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 13 optimal weight:   10.0000
   overall best weight:    3.8084

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

Flipped N/Q/H residues before XYZ refinement:
** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 288 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.111437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.092159 restraints weight = 3383.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 1.40
r_work: 0.3242 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8896
moved from start:          0.1967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   3272  Z= 0.419
  Angle     :  0.731  11.092   4368  Z= 0.373
  Chirality :  0.055   0.152    496
  Planarity :  0.003   0.020    556
  Dihedral  :  5.640  22.804    436
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.95 %
    Allowed  :  3.81 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 13.98 %
    Favored  : 84.95 %
  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: -2.35 (0.33), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 299 
 PHE   0.010   0.001   PHE C 378 
 TYR   0.003   0.001   TYR D 310 
 ARG   0.007   0.001   ARG D 349 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 0.395 
Fit side-chains
REVERT: C  349 ARG cc_start: 0.8595 (mtt90) cc_final: 0.7107 (mmp-170)
  outliers start: 4
  outliers final: 4
  residues processed: 77
  average time/residue: 1.1363
  time to fit residues: 90.0929
Evaluate side-chains
  78 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  379 ARG
Chi-restraints excluded: chain D residue  342 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 5 optimal weight:    9.9990
   chunk 35 optimal weight:    0.0970
   chunk 34 optimal weight:    6.9990
   chunk 30 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    2.5984

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

Flipped N/Q/H residues before XYZ refinement:
C 288 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.113543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.094249 restraints weight = 3398.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 1.40
r_work: 0.3277 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3175 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8883
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   3272  Z= 0.306
  Angle     :  0.687   9.451   4368  Z= 0.346
  Chirality :  0.053   0.151    496
  Planarity :  0.002   0.022    556
  Dihedral  :  5.649  21.071    436
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.95 %
    Allowed  :  3.33 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 14.78 %
    Favored  : 83.87 %
  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: -2.33 (0.33), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.77 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D 374 
 PHE   0.008   0.001   PHE C 378 
 TYR   0.002   0.001   TYR B 310 
 ARG   0.007   0.001   ARG D 349 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.428 
Fit side-chains
REVERT: B  349 ARG cc_start: 0.8539 (mtt90) cc_final: 0.8337 (mtt-85)
REVERT: C  349 ARG cc_start: 0.8588 (mtt90) cc_final: 0.7070 (mmp-170)
  outliers start: 5
  outliers final: 4
  residues processed: 77
  average time/residue: 1.1800
  time to fit residues: 93.4671
Evaluate side-chains
  76 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  379 ARG
Chi-restraints excluded: chain D residue  342 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 11 optimal weight:    7.9990
   chunk 39 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 15 optimal weight:    8.9990
   chunk 8 optimal weight:   10.0000
   chunk 19 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 3 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    2.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 276 GLN
C 288 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.112874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.093497 restraints weight = 3354.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 1.41
r_work: 0.3267 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8880
moved from start:          0.2014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3272  Z= 0.289
  Angle     :  0.709  13.992   4368  Z= 0.346
  Chirality :  0.053   0.150    496
  Planarity :  0.002   0.022    556
  Dihedral  :  5.626  21.534    436
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.95 %
    Allowed  :  2.86 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 14.52 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.32 (0.33), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.76 (0.25), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D 374 
 PHE   0.008   0.001   PHE C 378 
 TYR   0.003   0.001   TYR B 310 
 ARG   0.007   0.001   ARG D 349 

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.412 
Fit side-chains
REVERT: C  349 ARG cc_start: 0.8595 (mtt90) cc_final: 0.7061 (mmp-170)
  outliers start: 5
  outliers final: 4
  residues processed: 78
  average time/residue: 1.1594
  time to fit residues: 93.1669
Evaluate side-chains
  78 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  379 ARG
Chi-restraints excluded: chain D residue  342 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 3 optimal weight:    7.9990
   chunk 36 optimal weight:    3.9990
   chunk 28 optimal weight:    0.1980
   chunk 32 optimal weight:    0.5980
   chunk 25 optimal weight:    9.9990
   chunk 31 optimal weight:    3.9990
   chunk 6 optimal weight:    7.9990
   chunk 2 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 18 optimal weight:    8.9990
   chunk 21 optimal weight:    9.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 276 GLN
** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.114100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.094799 restraints weight = 3357.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 1.40
r_work: 0.3289 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3189 rms_B_bonded: 2.97 restraints_weight: 0.2500
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8874
moved from start:          0.2043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3272  Z= 0.266
  Angle     :  0.705  13.069   4368  Z= 0.341
  Chirality :  0.053   0.148    496
  Planarity :  0.003   0.033    556
  Dihedral  :  5.591  20.352    436
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.95 %
    Allowed  :  3.10 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 15.59 %
    Favored  : 83.33 %
  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: -2.31 (0.33), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.75 (0.25), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D 374 
 PHE   0.007   0.001   PHE C 378 
 TYR   0.003   0.001   TYR B 310 
 ARG   0.008   0.001   ARG D 349 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3474.24 seconds
wall clock time: 63 minutes 4.03 seconds (3784.03 seconds total)