Starting phenix.real_space_refine
on Wed Sep 17 03:03:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vha_21201/09_2025/6vha_21201.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vha_21201/09_2025/6vha_21201.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vha_21201/09_2025/6vha_21201.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vha_21201/09_2025/6vha_21201.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vha_21201/09_2025/6vha_21201.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vha_21201/09_2025/6vha_21201.cif"
  }
  resolution = 4.3
  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=   0.001
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       6      5.16       5
     C    1521      2.51       5
     N     453      2.21       5
     O     459      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2439
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "E"
      Number of atoms: 813
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 813
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 4, 'TRANS': 102}
  Restraints were copied for chains:
    F, G
  Time building chain proxies: 0.80, per 1000 atoms: 0.33
  Number of scatterers: 2439
  At special positions: 0
  Unit cell: (80.598, 106.05, 31.108, 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       6     16.00
     O     459      8.00
     N     453      7.00
     C    1521      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: 0.20
  Conformation dependent library (CDL) restraints added in 105.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  630 Ramachandran restraints generated.
    315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  564

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 67.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'E' and resid 275 through 282
      removed outlier: 6.993A  pdb=" N   GLN E 276 " --> pdb=" O   VAL F 275 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   ILE F 277 " --> pdb=" O   GLN E 276 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   ILE E 278 " --> pdb=" O   ILE F 277 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   ASN F 279 " --> pdb=" O   ILE E 278 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   LYS E 280 " --> pdb=" O   ASN F 279 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   LYS F 281 " --> pdb=" O   LYS E 280 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   GLN F 276 " --> pdb=" O   VAL G 275 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   ILE G 277 " --> pdb=" O   GLN F 276 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   ILE F 278 " --> pdb=" O   ILE G 277 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   ASN G 279 " --> pdb=" O   ILE F 278 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   LYS F 280 " --> pdb=" O   ASN G 279 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   LYS G 281 " --> pdb=" O   LYS F 280 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 285 through 299
      removed outlier: 8.876A  pdb=" N   ASN E 286 " --> pdb=" O   VAL F 287 " (cutoff:3.500A)
      removed outlier: 9.874A  pdb=" N   SER F 289 " --> pdb=" O   ASN E 286 " (cutoff:3.500A)
      removed outlier: 8.782A  pdb=" N   GLN E 288 " --> pdb=" O   SER F 289 " (cutoff:3.500A)
      removed outlier: 8.197A  pdb=" N   CYS F 291 " --> pdb=" O   GLN E 288 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   LYS E 290 " --> pdb=" O   CYS F 291 " (cutoff:3.500A)
      removed outlier: 5.284A  pdb=" N   SER F 293 " --> pdb=" O   LYS E 290 " (cutoff:3.500A)
      removed outlier: 7.677A  pdb=" N   GLY E 292 " --> pdb=" O   SER F 293 " (cutoff:3.500A)
      removed outlier: 8.467A  pdb=" N   ASP F 295 " --> pdb=" O   GLY E 292 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   LYS E 294 " --> pdb=" O   ASP F 295 " (cutoff:3.500A)
      removed outlier: 7.966A  pdb=" N   ILE F 297 " --> pdb=" O   LYS E 294 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   ASN E 296 " --> pdb=" O   ILE F 297 " (cutoff:3.500A)
      removed outlier: 7.900A  pdb=" N   HIS F 299 " --> pdb=" O   ASN E 296 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   LYS E 298 " --> pdb=" O   HIS F 299 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ASN F 286 " --> pdb=" O   SER G 285 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   VAL G 287 " --> pdb=" O   ASN F 286 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   GLN F 288 " --> pdb=" O   VAL G 287 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   SER G 289 " --> pdb=" O   GLN F 288 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   LYS F 290 " --> pdb=" O   SER G 289 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   SER G 293 " --> pdb=" O   GLY F 292 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   LYS F 294 " --> pdb=" O   SER G 293 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 303 through 310
      removed outlier: 6.741A  pdb=" N   GLY E 304 " --> pdb=" O   SER F 305 " (cutoff:3.500A)
      removed outlier: 8.172A  pdb=" N   GLN F 307 " --> pdb=" O   GLY E 304 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   VAL E 306 " --> pdb=" O   GLN F 307 " (cutoff:3.500A)
      removed outlier: 8.041A  pdb=" N   VAL F 309 " --> pdb=" O   VAL E 306 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ILE E 308 " --> pdb=" O   VAL F 309 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   GLY F 304 " --> pdb=" O   SER G 305 " (cutoff:3.500A)
      removed outlier: 8.162A  pdb=" N   GLN G 307 " --> pdb=" O   GLY F 304 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   VAL F 306 " --> pdb=" O   GLN G 307 " (cutoff:3.500A)
      removed outlier: 8.021A  pdb=" N   VAL G 309 " --> pdb=" O   VAL F 306 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ILE F 308 " --> pdb=" O   VAL G 309 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'E' and resid 313 through 321
      removed outlier: 6.272A  pdb=" N   ASP E 314 " --> pdb=" O   LEU F 315 " (cutoff:3.500A)
      removed outlier: 8.098A  pdb=" N   LYS F 317 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   SER E 316 " --> pdb=" O   LYS F 317 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   THR F 319 " --> pdb=" O   SER E 316 " (cutoff:3.500A)
      removed outlier: 6.096A  pdb=" N   VAL E 318 " --> pdb=" O   THR F 319 " (cutoff:3.500A)
      removed outlier: 7.493A  pdb=" N   LYS F 321 " --> pdb=" O   VAL E 318 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   SER E 320 " --> pdb=" O   LYS F 321 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   ASP F 314 " --> pdb=" O   LEU G 315 " (cutoff:3.500A)
      removed outlier: 8.036A  pdb=" N   LYS G 317 " --> pdb=" O   ASP F 314 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   SER F 316 " --> pdb=" O   LYS G 317 " (cutoff:3.500A)
      removed outlier: 7.267A  pdb=" N   THR G 319 " --> pdb=" O   SER F 316 " (cutoff:3.500A)
      removed outlier: 6.029A  pdb=" N   VAL F 318 " --> pdb=" O   THR G 319 " (cutoff:3.500A)
      removed outlier: 7.431A  pdb=" N   LYS G 321 " --> pdb=" O   VAL F 318 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   SER F 320 " --> pdb=" O   LYS G 321 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'E' and resid 327 through 330
      removed outlier: 6.546A  pdb=" N   ILE E 328 " --> pdb=" O   HIS F 329 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   ILE F 328 " --> pdb=" O   HIS G 329 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 336 through 346
      removed outlier: 6.800A  pdb=" N   VAL F 337 " --> pdb=" O   GLN E 336 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   GLU E 338 " --> pdb=" O   VAL F 337 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   VAL F 339 " --> pdb=" O   GLU E 338 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   LYS E 340 " --> pdb=" O   VAL F 339 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   SER F 341 " --> pdb=" O   LYS E 340 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   GLU E 342 " --> pdb=" O   SER F 341 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   LYS F 343 " --> pdb=" O   GLU G 342 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   LEU G 344 " --> pdb=" O   LYS F 343 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   ASP F 345 " --> pdb=" O   LEU G 344 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   PHE G 346 " --> pdb=" O   ASP F 345 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 349 through 362
      removed outlier: 6.432A  pdb=" N   VAL E 350 " --> pdb=" O   GLN F 351 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   LYS F 353 " --> pdb=" O   VAL E 350 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   SER E 352 " --> pdb=" O   LYS F 353 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   GLY F 355 " --> pdb=" O   SER E 352 " (cutoff:3.500A)
      removed outlier: 8.275A  pdb=" N   ILE E 354 " --> pdb=" O   GLY F 355 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   LEU F 357 " --> pdb=" O   ILE E 354 " (cutoff:3.500A)
      removed outlier: 8.064A  pdb=" N   SER E 356 " --> pdb=" O   LEU F 357 " (cutoff:3.500A)
      removed outlier: 7.917A  pdb=" N   ASN F 359 " --> pdb=" O   SER E 356 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   ASP E 358 " --> pdb=" O   ASN F 359 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   THR F 361 " --> pdb=" O   ASP E 358 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   ILE E 360 " --> pdb=" O   THR F 361 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   SER F 356 " --> pdb=" O   GLY G 355 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   LEU G 357 " --> pdb=" O   SER F 356 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   ASP F 358 " --> pdb=" O   LEU G 357 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 369 through 379
      removed outlier: 6.035A  pdb=" N   LYS E 370 " --> pdb=" O   ILE F 371 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   THR F 373 " --> pdb=" O   LYS E 370 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   GLU E 372 " --> pdb=" O   THR F 373 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   LYS F 375 " --> pdb=" O   GLU E 372 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   HIS E 374 " --> pdb=" O   LYS F 375 " (cutoff:3.500A)
      removed outlier: 7.954A  pdb=" N   THR F 377 " --> pdb=" O   HIS E 374 " (cutoff:3.500A)
      removed outlier: 6.046A  pdb=" N   LEU E 376 " --> pdb=" O   THR F 377 " (cutoff:3.500A)
      removed outlier: 7.261A  pdb=" N   ARG F 379 " --> pdb=" O   LEU E 376 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   PHE E 378 " --> pdb=" O   ARG F 379 " (cutoff:3.500A)
      removed outlier: 5.990A  pdb=" N   LYS F 370 " --> pdb=" O   ILE G 371 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   THR G 373 " --> pdb=" O   LYS F 370 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   GLU F 372 " --> pdb=" O   THR G 373 " (cutoff:3.500A)
      removed outlier: 7.520A  pdb=" N   LYS G 375 " --> pdb=" O   GLU F 372 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   HIS F 374 " --> pdb=" O   LYS G 375 " (cutoff:3.500A)
      removed outlier: 7.902A  pdb=" N   THR G 377 " --> pdb=" O   HIS F 374 " (cutoff:3.500A)
      removed outlier: 5.982A  pdb=" N   LEU F 376 " --> pdb=" O   THR G 377 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   ARG G 379 " --> pdb=" O   LEU F 376 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   PHE F 378 " --> pdb=" O   ARG G 379 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    29 hydrogen bonds defined for protein.
    87 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: 0.31

  Time building geometry restraints manager: 0.27 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 813
        1.34 -     1.46: 309
        1.46 -     1.57: 1344
        1.57 -     1.69: 0
        1.69 -     1.80: 6
  Bond restraints: 2472
  Sorted by residual:
  bond pdb=" CA  LYS G 353 "
       pdb=" CB  LYS G 353 "
    ideal  model  delta    sigma   weight residual
    1.529  1.499  0.030 1.38e-02 5.25e+03 4.69e+00
  bond pdb=" CA  LYS E 353 "
       pdb=" CB  LYS E 353 "
    ideal  model  delta    sigma   weight residual
    1.529  1.499  0.030 1.38e-02 5.25e+03 4.58e+00
  bond pdb=" CA  LYS F 353 "
       pdb=" CB  LYS F 353 "
    ideal  model  delta    sigma   weight residual
    1.529  1.500  0.029 1.38e-02 5.25e+03 4.52e+00
  bond pdb=" C   LYS G 331 "
       pdb=" N   PRO G 332 "
    ideal  model  delta    sigma   weight residual
    1.334  1.296  0.038 2.34e-02 1.83e+03 2.67e+00
  bond pdb=" C   LYS F 331 "
       pdb=" N   PRO F 332 "
    ideal  model  delta    sigma   weight residual
    1.334  1.296  0.038 2.34e-02 1.83e+03 2.66e+00
  ... (remaining 2467 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 2867
        1.38 -     2.77: 363
        2.77 -     4.15: 55
        4.15 -     5.53: 12
        5.53 -     6.92: 6
  Bond angle restraints: 3303
  Sorted by residual:
  angle pdb=" C   LYS E 347 "
        pdb=" N   ASP E 348 "
        pdb=" CA  ASP E 348 "
      ideal   model   delta    sigma   weight residual
     122.17  115.25    6.92 1.54e+00 4.22e-01 2.02e+01
  angle pdb=" C   LYS G 347 "
        pdb=" N   ASP G 348 "
        pdb=" CA  ASP G 348 "
      ideal   model   delta    sigma   weight residual
     122.17  115.28    6.89 1.54e+00 4.22e-01 2.00e+01
  angle pdb=" C   LYS F 347 "
        pdb=" N   ASP F 348 "
        pdb=" CA  ASP F 348 "
      ideal   model   delta    sigma   weight residual
     122.17  115.29    6.88 1.54e+00 4.22e-01 2.00e+01
  angle pdb=" N   ASP E 348 "
        pdb=" CA  ASP E 348 "
        pdb=" C   ASP E 348 "
      ideal   model   delta    sigma   weight residual
     112.12  116.70   -4.58 1.34e+00 5.57e-01 1.17e+01
  angle pdb=" N   ASP F 348 "
        pdb=" CA  ASP F 348 "
        pdb=" C   ASP F 348 "
      ideal   model   delta    sigma   weight residual
     112.12  116.69   -4.57 1.34e+00 5.57e-01 1.16e+01
  ... (remaining 3298 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.25: 1328
       16.25 -    32.51: 157
       32.51 -    48.76: 27
       48.76 -    65.01: 12
       65.01 -    81.26: 3
  Dihedral angle restraints: 1527
    sinusoidal: 642
      harmonic: 885
  Sorted by residual:
  dihedral pdb=" CA  VAL G 313 "
           pdb=" C   VAL G 313 "
           pdb=" N   ASP G 314 "
           pdb=" CA  ASP G 314 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.23  -20.77     0      5.00e+00 4.00e-02 1.73e+01
  dihedral pdb=" CA  VAL F 313 "
           pdb=" C   VAL F 313 "
           pdb=" N   ASP F 314 "
           pdb=" CA  ASP F 314 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.26  -20.74     0      5.00e+00 4.00e-02 1.72e+01
  dihedral pdb=" CA  VAL E 313 "
           pdb=" C   VAL E 313 "
           pdb=" N   ASP E 314 "
           pdb=" CA  ASP E 314 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.27  -20.73     0      5.00e+00 4.00e-02 1.72e+01
  ... (remaining 1524 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 194
       0.035 -    0.071: 108
       0.071 -    0.106: 48
       0.106 -    0.141: 16
       0.141 -    0.177: 6
  Chirality restraints: 372
  Sorted by residual:
  chirality pdb=" CB  ILE F 277 "
            pdb=" CA  ILE F 277 "
            pdb=" CG1 ILE F 277 "
            pdb=" CG2 ILE F 277 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.79e-01
  chirality pdb=" CB  ILE E 277 "
            pdb=" CA  ILE E 277 "
            pdb=" CG1 ILE E 277 "
            pdb=" CG2 ILE E 277 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.73e-01
  chirality pdb=" CB  ILE G 277 "
            pdb=" CA  ILE G 277 "
            pdb=" CG1 ILE G 277 "
            pdb=" CG2 ILE G 277 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.71e-01
  ... (remaining 369 not shown)

  Planarity restraints: 423
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL G 363 "    0.034 5.00e-02 4.00e+02   5.18e-02 4.30e+00
        pdb=" N   PRO G 364 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO G 364 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO G 364 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL F 363 "    0.034 5.00e-02 4.00e+02   5.17e-02 4.28e+00
        pdb=" N   PRO F 364 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO F 364 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO F 364 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL E 363 "    0.034 5.00e-02 4.00e+02   5.13e-02 4.22e+00
        pdb=" N   PRO E 364 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO E 364 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO E 364 "    0.029 5.00e-02 4.00e+02
  ... (remaining 420 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 782
        2.83 -     3.35: 2275
        3.35 -     3.87: 4387
        3.87 -     4.38: 4326
        4.38 -     4.90: 8374
  Nonbonded interactions: 20144
  Sorted by model distance:
  nonbonded pdb=" N   GLU E 380 "
            pdb=" OE1 GLU E 380 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" N   GLU F 380 "
            pdb=" OE1 GLU F 380 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" N   GLU G 380 "
            pdb=" OE1 GLU G 380 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" O   GLU E 342 "
            pdb=" CB  LYS F 343 "
     model   vdw
     2.366 2.752
  nonbonded pdb=" O   SER G 324 "
            pdb=" OG  SER G 324 "
     model   vdw
     2.378 3.040
  ... (remaining 20139 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

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 group one per residue
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:             1.350
  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:             0.000
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.850
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5593
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      :  0.007   0.039   2472  Z= 0.378
  Angle     :  1.025   6.915   3303  Z= 0.590
  Chirality :  0.054   0.177    372
  Planarity :  0.006   0.052    423
  Dihedral  : 15.141  81.261    963
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 27.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.38 %
    Favored  : 87.62 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 10.64 %
    Favored  : 87.23 %
  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 aren not related in a simple way.
  whole: -4.78 (0.33), residues: 315
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.64 (0.25), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G 349 
 TYR   0.004   0.002   TYR E 310 
 PHE   0.003   0.001   PHE E 378 
 HIS   0.006   0.001   HIS G 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00721 ( 2472)
  covalent geometry    : angle       1.02496 ( 3303)
  hydrogen bonds       : bond        0.07594 (   29)
  hydrogen bonds       : angle       9.25245 (   87)

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

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

  630 Ramachandran restraints generated.
    315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  630 Ramachandran restraints generated.
    315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.115 
Fit side-chains
REVERT: E  285 SER cc_start: 0.8035 (t) cc_final: 0.7808 (t)
REVERT: F  325 LEU cc_start: 0.9497 (mp) cc_final: 0.9098 (tp)
REVERT: G  319 THR cc_start: 0.8383 (m) cc_final: 0.8105 (p)
REVERT: G  325 LEU cc_start: 0.8703 (mp) cc_final: 0.8448 (tp)
  outliers start: 6
  outliers final: 0
  residues processed: 48
  average time/residue: 0.0309
  time to fit residues: 2.1145
Evaluate side-chains
  15 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 12 optimal weight:    0.5980
   chunk 24 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   chunk 13 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 8 optimal weight:    5.9990
   chunk 16 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0470
   chunk 25 optimal weight:    0.2980
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 362 HIS
** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 362 HIS
** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 359 ASN
G 362 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.070004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.059816 restraints weight = 22146.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.060600 restraints weight = 17789.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.061057 restraints weight = 15039.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.061521 restraints weight = 13218.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.061822 restraints weight = 12159.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6040
moved from start:          0.3167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2472  Z= 0.124
  Angle     :  0.665   5.397   3303  Z= 0.345
  Chirality :  0.055   0.183    372
  Planarity :  0.004   0.034    423
  Dihedral  :  6.789  18.808    327
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  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 aren not related in a simple way.
  whole: -4.37 (0.35), residues: 315
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.32 (0.27), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G 349 
 TYR   0.012   0.002   TYR F 310 
 PHE   0.007   0.001   PHE F 378 
 HIS   0.002   0.000   HIS E 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 2472)
  covalent geometry    : angle       0.66462 ( 3303)
  hydrogen bonds       : bond        0.01677 (   29)
  hydrogen bonds       : angle       7.18925 (   87)

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

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

  630 Ramachandran restraints generated.
    315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  630 Ramachandran restraints generated.
    315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.116 
Fit side-chains
REVERT: E  277 ILE cc_start: 0.8412 (tp) cc_final: 0.8188 (mp)
REVERT: F  325 LEU cc_start: 0.9279 (mp) cc_final: 0.8985 (tp)
REVERT: G  319 THR cc_start: 0.8864 (m) cc_final: 0.8488 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0272
  time to fit residues: 1.0630
Evaluate side-chains
  13 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 13 optimal weight:    8.9990
   chunk 15 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 12 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 10 optimal weight:    9.9990
   chunk 28 optimal weight:    2.9990
   chunk 21 optimal weight:    9.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 359 ASN
** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 359 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.066428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.056895 restraints weight = 23707.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.057557 restraints weight = 19503.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.058033 restraints weight = 16872.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.058408 restraints weight = 15049.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.058739 restraints weight = 13748.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6099
moved from start:          0.4317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   2472  Z= 0.159
  Angle     :  0.680  11.873   3303  Z= 0.336
  Chirality :  0.051   0.166    372
  Planarity :  0.004   0.031    423
  Dihedral  :  6.302  17.659    327
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  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 aren not related in a simple way.
  whole: -4.17 (0.35), residues: 315
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.17 (0.27), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 379 
 TYR   0.009   0.002   TYR E 310 
 PHE   0.004   0.001   PHE E 378 
 HIS   0.003   0.001   HIS F 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 2472)
  covalent geometry    : angle       0.68025 ( 3303)
  hydrogen bonds       : bond        0.01968 (   29)
  hydrogen bonds       : angle       6.18386 (   87)

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

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

  630 Ramachandran restraints generated.
    315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  630 Ramachandran restraints generated.
    315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.113 
Fit side-chains
REVERT: F  278 ILE cc_start: 0.9133 (mm) cc_final: 0.8836 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 17
  average time/residue: 0.0264
  time to fit residues: 0.7933
Evaluate side-chains
  12 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 11 optimal weight:   10.0000
   chunk 3 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9980
   chunk 15 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 18 optimal weight:    9.9990
   chunk 28 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 359 ASN
** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 374 HIS
** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 288 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 = 0.4005 r_free = 0.4005 target = 0.068426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.059715 restraints weight = 24874.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.060367 restraints weight = 19814.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.060709 restraints weight = 16776.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.061152 restraints weight = 14872.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.061566 restraints weight = 13271.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6222
moved from start:          0.6234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   2472  Z= 0.265
  Angle     :  0.843   8.349   3303  Z= 0.433
  Chirality :  0.052   0.153    372
  Planarity :  0.005   0.030    423
  Dihedral  :  7.684  27.635    327
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 15.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.25 %
    Favored  : 91.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  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 aren not related in a simple way.
  whole: -4.30 (0.33), residues: 315
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.27 (0.25), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG G 379 
 TYR   0.010   0.003   TYR F 310 
 PHE   0.010   0.002   PHE E 378 
 HIS   0.006   0.002   HIS E 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 ( 2472)
  covalent geometry    : angle       0.84255 ( 3303)
  hydrogen bonds       : bond        0.02656 (   29)
  hydrogen bonds       : angle       5.45199 (   87)

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

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

  630 Ramachandran restraints generated.
    315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  630 Ramachandran restraints generated.
    315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.115 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0292
  time to fit residues: 0.6808
Evaluate side-chains
  8 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 8
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 9 optimal weight:    0.1980
   chunk 26 optimal weight:    0.6980
   chunk 14 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 17 optimal weight:    6.9990
   chunk 4 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    1.2982

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

Flipped N/Q/H residues before XYZ refinement:
** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 359 ASN
** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 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 = 0.3994 r_free = 0.3994 target = 0.068915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.060323 restraints weight = 24447.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.061000 restraints weight = 19326.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.061504 restraints weight = 16201.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 13)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.061737 restraints weight = 14077.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.062131 restraints weight = 12754.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6206
moved from start:          0.6589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2472  Z= 0.158
  Angle     :  0.707  11.559   3303  Z= 0.345
  Chirality :  0.052   0.173    372
  Planarity :  0.003   0.030    423
  Dihedral  :  6.564  23.799    327
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.17 (0.34), residues: 315
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.17 (0.26), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG G 349 
 TYR   0.007   0.002   TYR F 310 
 PHE   0.005   0.001   PHE F 346 
 HIS   0.003   0.001   HIS E 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 2472)
  covalent geometry    : angle       0.70681 ( 3303)
  hydrogen bonds       : bond        0.02248 (   29)
  hydrogen bonds       : angle       5.13633 (   87)

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

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

  630 Ramachandran restraints generated.
    315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  630 Ramachandran restraints generated.
    315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.144 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0294
  time to fit residues: 0.7908
Evaluate side-chains
  8 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 8
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 19 optimal weight:    9.9990
   chunk 20 optimal weight:    0.0570
   chunk 23 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 11 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 17 optimal weight:   10.0000
   chunk 29 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.1704

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

Flipped N/Q/H residues before XYZ refinement:
** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 374 HIS
** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 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 = 0.3976 r_free = 0.3976 target = 0.067580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.059617 restraints weight = 23625.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.060222 restraints weight = 18648.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.060685 restraints weight = 15617.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.060921 restraints weight = 13662.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.061240 restraints weight = 12558.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6164
moved from start:          0.7442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2472  Z= 0.131
  Angle     :  0.670  13.022   3303  Z= 0.321
  Chirality :  0.052   0.194    372
  Planarity :  0.003   0.026    423
  Dihedral  :  5.730  19.361    327
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  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 aren not related in a simple way.
  whole: -4.07 (0.35), residues: 315
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.10 (0.27), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G 379 
 TYR   0.006   0.002   TYR F 310 
 PHE   0.005   0.001   PHE G 346 
 HIS   0.004   0.001   HIS E 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 2472)
  covalent geometry    : angle       0.67036 ( 3303)
  hydrogen bonds       : bond        0.02763 (   29)
  hydrogen bonds       : angle       4.68534 (   87)

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

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

  630 Ramachandran restraints generated.
    315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  630 Ramachandran restraints generated.
    315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.106 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0240
  time to fit residues: 0.5664
Evaluate side-chains
  9 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 9
  time to evaluate  : 0.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 17 optimal weight:    7.9990
   chunk 4 optimal weight:    1.9990
   chunk 19 optimal weight:    9.9990
   chunk 20 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 29 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 359 ASN
** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 374 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.067427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.059529 restraints weight = 24417.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.059989 restraints weight = 18648.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.060683 restraints weight = 15640.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.060943 restraints weight = 13353.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.061275 restraints weight = 11770.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6183
moved from start:          0.8099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2472  Z= 0.164
  Angle     :  0.696   9.425   3303  Z= 0.346
  Chirality :  0.053   0.261    372
  Planarity :  0.004   0.027    423
  Dihedral  :  6.307  22.109    327
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  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 aren not related in a simple way.
  whole: -4.18 (0.35), residues: 315
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.18 (0.27), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 379 
 TYR   0.008   0.002   TYR F 310 
 PHE   0.009   0.002   PHE E 378 
 HIS   0.005   0.001   HIS E 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 2472)
  covalent geometry    : angle       0.69587 ( 3303)
  hydrogen bonds       : bond        0.02347 (   29)
  hydrogen bonds       : angle       4.45475 (   87)

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

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

  630 Ramachandran restraints generated.
    315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  630 Ramachandran restraints generated.
    315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  10 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.150 
Fit side-chains
REVERT: E  344 LEU cc_start: 0.8847 (mt) cc_final: 0.8331 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0285
  time to fit residues: 0.5499
Evaluate side-chains
  7 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 7
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 22 optimal weight:    4.9990
   chunk 26 optimal weight:    7.9990
   chunk 16 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 29 optimal weight:    0.0030
   chunk 28 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 18 optimal weight:    8.9990
   chunk 6 optimal weight:    0.6980
   chunk 7 optimal weight:    0.2980
   overall best weight:    1.1994

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

Flipped N/Q/H residues before XYZ refinement:
** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 374 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.067973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.060177 restraints weight = 24399.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.060779 restraints weight = 18934.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.061278 restraints weight = 15779.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.061581 restraints weight = 13714.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.061582 restraints weight = 11930.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6181
moved from start:          0.8363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   2472  Z= 0.131
  Angle     :  0.671  12.966   3303  Z= 0.321
  Chirality :  0.053   0.273    372
  Planarity :  0.003   0.026    423
  Dihedral  :  5.820  25.931    327
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.57 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  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 aren not related in a simple way.
  whole: -4.17 (0.36), residues: 315
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.17 (0.27), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 379 
 TYR   0.006   0.002   TYR F 310 
 PHE   0.005   0.001   PHE E 346 
 HIS   0.003   0.001   HIS G 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 2472)
  covalent geometry    : angle       0.67086 ( 3303)
  hydrogen bonds       : bond        0.02416 (   29)
  hydrogen bonds       : angle       4.51425 (   87)

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

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

  630 Ramachandran restraints generated.
    315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  630 Ramachandran restraints generated.
    315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  11 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.083 
Fit side-chains
REVERT: E  325 LEU cc_start: 0.8554 (pp) cc_final: 0.8307 (tp)
REVERT: E  344 LEU cc_start: 0.8970 (mt) cc_final: 0.8575 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 11
  average time/residue: 0.0208
  time to fit residues: 0.4314
Evaluate side-chains
  10 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 8 optimal weight:    8.9990
   chunk 18 optimal weight:    1.9990
   chunk 15 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0970
   chunk 22 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.1582

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.067699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.060184 restraints weight = 24792.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.060824 restraints weight = 18759.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.061226 restraints weight = 15484.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.061698 restraints weight = 13119.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.061982 restraints weight = 11710.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.3839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6168
moved from start:          0.8942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2472  Z= 0.126
  Angle     :  0.623   7.731   3303  Z= 0.308
  Chirality :  0.053   0.205    372
  Planarity :  0.003   0.029    423
  Dihedral  :  5.645  21.393    327
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.21 %
    Favored  : 90.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  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 aren not related in a simple way.
  whole: -4.20 (0.36), residues: 315
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.20 (0.27), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG E 379 
 TYR   0.006   0.001   TYR F 310 
 PHE   0.006   0.001   PHE E 378 
 HIS   0.005   0.001   HIS E 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 2472)
  covalent geometry    : angle       0.62282 ( 3303)
  hydrogen bonds       : bond        0.02395 (   29)
  hydrogen bonds       : angle       4.50773 (   87)

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

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

  630 Ramachandran restraints generated.
    315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  630 Ramachandran restraints generated.
    315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  9 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 9
  time to evaluate  : 0.094 
Fit side-chains
REVERT: E  344 LEU cc_start: 0.8974 (mt) cc_final: 0.8460 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 9
  average time/residue: 0.0192
  time to fit residues: 0.4030
Evaluate side-chains
  9 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 9
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 5 optimal weight:    0.0670
   chunk 2 optimal weight:    0.6980
   chunk 27 optimal weight:    6.9990
   chunk 29 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    1.1322

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.067669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.060159 restraints weight = 25136.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.060846 restraints weight = 19248.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.061359 restraints weight = 15992.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.061624 restraints weight = 13761.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.061893 restraints weight = 12502.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6166
moved from start:          0.9160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2472  Z= 0.121
  Angle     :  0.616   7.772   3303  Z= 0.302
  Chirality :  0.052   0.224    372
  Planarity :  0.003   0.030    423
  Dihedral  :  5.536  21.726    327
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.25 %
    Favored  : 91.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  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 aren not related in a simple way.
  whole: -4.13 (0.37), residues: 315
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.14 (0.28), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G 379 
 TYR   0.007   0.001   TYR F 310 
 PHE   0.005   0.001   PHE E 346 
 HIS   0.004   0.001   HIS G 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 2472)
  covalent geometry    : angle       0.61627 ( 3303)
  hydrogen bonds       : bond        0.02334 (   29)
  hydrogen bonds       : angle       4.39865 (   87)

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

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

  630 Ramachandran restraints generated.
    315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  630 Ramachandran restraints generated.
    315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  10 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.102 
Fit side-chains
REVERT: E  325 LEU cc_start: 0.9198 (tp) cc_final: 0.8952 (pp)
REVERT: E  344 LEU cc_start: 0.9022 (mt) cc_final: 0.8573 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0233
  time to fit residues: 0.4815
Evaluate side-chains
  8 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 8
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 19 optimal weight:    7.9990
   chunk 18 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 374 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.067052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.059570 restraints weight = 25022.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.060244 restraints weight = 19512.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.060780 restraints weight = 16179.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.061063 restraints weight = 13931.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.061421 restraints weight = 12210.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6223
moved from start:          0.9723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   2472  Z= 0.219
  Angle     :  0.745   6.988   3303  Z= 0.384
  Chirality :  0.054   0.192    372
  Planarity :  0.004   0.030    423
  Dihedral  :  6.711  25.289    327
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 14.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.75 %
    Favored  : 88.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.39 (0.35), residues: 315
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.34 (0.27), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 379 
 TYR   0.009   0.002   TYR F 310 
 PHE   0.010   0.002   PHE G 378 
 HIS   0.006   0.002   HIS G 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 2472)
  covalent geometry    : angle       0.74496 ( 3303)
  hydrogen bonds       : bond        0.02909 (   29)
  hydrogen bonds       : angle       4.42059 (   87)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 703.07 seconds
wall clock time: 12 minutes 46.53 seconds (766.53 seconds total)