Starting phenix.real_space_refine (version: dev)
on Tue Nov 29 11:49:43 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vha_21201/11_2022/6vha_21201.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vha_21201/11_2022/6vha_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vha_21201/11_2022/6vha_21201.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vha_21201/11_2022/6vha_21201.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vha_21201/11_2022/6vha_21201.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vha_21201/11_2022/6vha_21201.pdb"
  }
  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
-------------------------------------------------------------------------------
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
Convert atoms to be neutral
Process input model

  Symmetric amino acids flipped
    Residue "E TYR  310": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ASP  345": "OD1" <-> "OD2"
    Residue "E PHE  346": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  378": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  310": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ASP  345": "OD1" <-> "OD2"
    Residue "F PHE  346": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  378": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G TYR  310": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G ASP  345": "OD1" <-> "OD2"
    Residue "G PHE  346": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G PHE  378": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib"
  Total number of atoms: 2439
  Number of models: 1
  Model: ""
    Number of chains: 3
    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}
    Chain: "F"
      Number of atoms: 813
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 813
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 4, 'TRANS': 102}
    Chain: "G"
      Number of atoms: 813
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 813
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 4, 'TRANS': 102}
  Time building chain proxies: 1.84, per 1000 atoms: 0.75
  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  - 3.50
        Amino acid           : False - 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: 1.04
  Conformation dependent library (CDL) restraints added in 388.6 milliseconds
  

  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: 0.15
  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: 0.55

  Time building geometry restraints manager: 1.12 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:
      102.01 -   107.87: 181
      107.87 -   113.73: 1408
      113.73 -   119.58: 565
      119.58 -   125.44: 1122
      125.44 -   131.29: 27
  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 2.520
  nonbonded pdb=" N   GLU F 380 "
            pdb=" OE1 GLU F 380 "
     model   vdw
     2.319 2.520
  nonbonded pdb=" N   GLU G 380 "
            pdb=" OE1 GLU G 380 "
     model   vdw
     2.319 2.520
  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 2.440
  ... (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
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
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.
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:             1.000
  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:          4.010
  Check model and map are aligned:         0.040
  Convert atoms to be neutral:             0.020
  Process input model:                     12.520
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Set scattering table:                    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:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5426
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= 0.489
  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 : 26.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.38 %
    Favored  : 87.62 %
  Rotamer Outliers :  2.13 %
  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: -4.78 (0.33), residues: 315
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.64 (0.25), residues: 315

*********************** 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 fitting.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.349 
Fit side-chains
  outliers start: 6
  outliers final: 0
  residues processed: 48
  average time/residue: 0.0782
  time to fit residues: 5.1869
Evaluate side-chains
  13 residues out of total 282 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.324 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.4347
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 12 optimal weight:    4.9990
   chunk 7 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 9 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    1.5588

-------------------------------------------------------------------------------
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 329 HIS
E 359 ASN
E 362 HIS
** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 276 GLN
** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 359 ASN
F 362 HIS
** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 359 ASN
G 362 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5540
moved from start:          0.4001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.037   2472  Z= 0.284
  Angle     :  0.749   7.821   3303  Z= 0.383
  Chirality :  0.052   0.169    372
  Planarity :  0.005   0.041    423
  Dihedral  :  7.047  21.349    327
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 14.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer Outliers :  0.35 %
  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: -4.28 (0.34), residues: 315
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.26 (0.26), residues: 315

*********************** 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
  14 residues out of total 282 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 13
  time to evaluate  : 0.331 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 14
  average time/residue: 0.0725
  time to fit residues: 1.7908
Evaluate side-chains
  7 residues out of total 282 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 7
  time to evaluate  : 0.336 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.4401
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 18 optimal weight:   10.0000
   chunk 7 optimal weight:    6.9990
   chunk 27 optimal weight:    4.9990
   chunk 29 optimal weight:    8.9990
   chunk 24 optimal weight:    4.9990
   chunk 9 optimal weight:    0.0050
   chunk 21 optimal weight:    6.9990
   chunk 26 optimal weight:    0.8980
   chunk 20 optimal weight:    8.9990
   chunk 14 optimal weight:    5.9990
   overall best weight:    3.1800

-------------------------------------------------------------------------------
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
E 374 HIS
** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 359 ASN
F 374 HIS
** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 359 ASN
G 374 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5682
moved from start:          0.6698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.041   2472  Z= 0.435
  Angle     :  0.951   8.005   3303  Z= 0.493
  Chirality :  0.058   0.309    372
  Planarity :  0.005   0.042    423
  Dihedral  :  8.425  27.831    327
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 21.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.43 %
    Favored  : 88.57 %
  Rotamer Outliers :  1.06 %
  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: -4.52 (0.32), residues: 315
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.44 (0.24), residues: 315

*********************** 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
  14 residues out of total 282 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 11
  time to evaluate  : 0.329 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 14
  average time/residue: 0.0702
  time to fit residues: 1.7628
Evaluate side-chains
  10 residues out of total 282 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 8
  time to evaluate  : 0.346 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0284
  time to fit residues: 0.5571
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 18 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 28 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0570
   chunk 24 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    1.3904

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5614
moved from start:          0.6985

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= 0.214
  Angle     :  0.666   6.806   3303  Z= 0.340
  Chirality :  0.053   0.262    372
  Planarity :  0.004   0.035    423
  Dihedral  :  6.698  20.516    327
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.28 (0.34), residues: 315
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.25 (0.26), residues: 315

*********************** 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
  15 residues out of total 282 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.342 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0851
  time to fit residues: 2.1015
Evaluate side-chains
  8 residues out of total 282 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 8
  time to evaluate  : 0.324 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.5400
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 14 optimal weight:    0.8980
   chunk 26 optimal weight:    4.9990
   chunk 7 optimal weight:    5.9990
   chunk 9 optimal weight:    7.9990
   chunk 5 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.5384

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5646
moved from start:          0.7483

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= 0.232
  Angle     :  0.704  12.509   3303  Z= 0.346
  Chirality :  0.051   0.166    372
  Planarity :  0.004   0.033    423
  Dihedral  :  6.517  23.689    327
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.57 %
    Favored  : 91.43 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.26 (0.35), residues: 315
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.24 (0.26), residues: 315

*********************** 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
  12 residues out of total 282 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.334 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 12
  average time/residue: 0.0908
  time to fit residues: 1.8615
Evaluate side-chains
  9 residues out of total 282 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 9
  time to evaluate  : 0.337 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.4531
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 29 optimal weight:    8.9990
   chunk 24 optimal weight:    0.2980
   chunk 13 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 9 optimal weight:    0.1980
   chunk 15 optimal weight:    5.9990
   chunk 27 optimal weight:    7.9990
   chunk 3 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 21 optimal weight:    8.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5639
moved from start:          0.7874

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= 0.203
  Angle     :  0.666   9.071   3303  Z= 0.334
  Chirality :  0.053   0.215    372
  Planarity :  0.003   0.030    423
  Dihedral  :  6.263  26.319    327
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.18 (0.35), residues: 315
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.18 (0.27), residues: 315

*********************** 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
  11 residues out of total 282 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.335 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 11
  average time/residue: 0.0589
  time to fit residues: 1.2306
Evaluate side-chains
  7 residues out of total 282 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 7
  time to evaluate  : 0.262 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.3507
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 28 optimal weight:    8.9990
   chunk 18 optimal weight:    0.8980
   chunk 17 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   chunk 11 optimal weight:    7.9990
   chunk 8 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 19 optimal weight:   10.0000
   chunk 14 optimal weight:    0.8980
   overall best weight:    1.5584

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5651
moved from start:          0.8376

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= 0.226
  Angle     :  0.674   6.893   3303  Z= 0.340
  Chirality :  0.053   0.229    372
  Planarity :  0.003   0.030    423
  Dihedral  :  6.359  27.451    327
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.84 %
    Favored  : 90.16 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.21 (0.35), residues: 315
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.20 (0.27), residues: 315

*********************** 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 fitting.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.350 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0629
  time to fit residues: 1.3282
Evaluate side-chains
  8 residues out of total 282 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 8
  time to evaluate  : 0.330 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.4405
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 11 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9990
   chunk 8 optimal weight:    6.9990
   chunk 24 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    2.3990

-------------------------------------------------------------------------------
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 329 HIS ** 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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5648
moved from start:          0.9173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.028   2472  Z= 0.317
  Angle     :  0.793  12.714   3303  Z= 0.401
  Chirality :  0.055   0.193    372
  Planarity :  0.004   0.031    423
  Dihedral  :  7.327  29.540    327
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 18.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.48 %
    Favored  : 89.52 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.53 (0.34), residues: 315
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.44 (0.26), residues: 315

*********************** 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
  8 residues out of total 282 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 8
  time to evaluate  : 0.339 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 8
  average time/residue: 0.0605
  time to fit residues: 1.1701
Evaluate side-chains
  6 residues out of total 282 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 6
  time to evaluate  : 0.337 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.4511
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 17 optimal weight:   10.0000
   chunk 13 optimal weight:    0.6980
   chunk 19 optimal weight:   10.0000
   chunk 29 optimal weight:    3.9990
   chunk 27 optimal weight:    0.1980
   chunk 23 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.9786

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5601
moved from start:          0.9243

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= 0.170
  Angle     :  0.628   5.654   3303  Z= 0.313
  Chirality :  0.054   0.216    372
  Planarity :  0.003   0.031    423
  Dihedral  :  6.174  24.939    327
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.52 %
    Favored  : 90.48 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.34 (0.35), residues: 315
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.30 (0.27), residues: 315

*********************** 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
  10 residues out of total 282 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.272 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0656
  time to fit residues: 1.3494
Evaluate side-chains
  7 residues out of total 282 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 7
  time to evaluate  : 0.339 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.4537
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 6 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   chunk 9 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 20 optimal weight:    0.2980
   chunk 1 optimal weight:    0.0170
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.5418

-------------------------------------------------------------------------------
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 374 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5599
moved from start:          0.9364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2472  Z= 0.141
  Angle     :  0.617   9.325   3303  Z= 0.299
  Chirality :  0.055   0.318    372
  Planarity :  0.003   0.030    423
  Dihedral  :  5.564  20.227    327
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.22 (0.35), residues: 315
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.21 (0.27), residues: 315

********************** 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 fitting.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.364 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0651
  time to fit residues: 1.3954
Evaluate side-chains
  7 residues out of total 282 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 7
  time to evaluate  : 0.339 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.4494
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    8.9990
   chunk 16 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 19 optimal weight:   10.0000
   chunk 18 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.5588

-------------------------------------------------------------------------------
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 = 0.3895 r_free = 0.3895 target = 0.065807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.058699 restraints weight = 24073.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.059387 restraints weight = 18950.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.059877 restraints weight = 15641.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6037
moved from start:          0.9695

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= 0.213
  Angle     :  0.647   5.091   3303  Z= 0.329
  Chirality :  0.053   0.153    372
  Planarity :  0.003   0.029    423
  Dihedral  :  6.068  22.118    327
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 14.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.84 %
    Favored  : 90.16 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.32 (0.35), residues: 315
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.28 (0.27), residues: 315

===============================================================================
Job complete
usr+sys time: 980.42 seconds
wall clock time: 19 minutes 2.90 seconds (1142.90 seconds total)