Starting phenix.real_space_refine
on Tue Mar  3 13:13:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vh7_21200/03_2026/6vh7_21200.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vh7_21200/03_2026/6vh7_21200.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vh7_21200/03_2026/6vh7_21200.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vh7_21200/03_2026/6vh7_21200.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vh7_21200/03_2026/6vh7_21200.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vh7_21200/03_2026/6vh7_21200.map"
  }
  resolution = 3.8
  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      12      5.16       5
     C    3042      2.51       5
     N     906      2.21       5
     O     918      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4878
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      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:
    B, C, E, F, G
  Time building chain proxies: 0.65, per 1000 atoms: 0.13
  Number of scatterers: 4878
  At special positions: 0
  Unit cell: (103.222, 193.718, 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      12     16.00
     O     918      8.00
     N     906      7.00
     C    3042      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: 0.38
  Conformation dependent library (CDL) restraints added in 431.5 milliseconds
  

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1128

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 16 sheets defined
      0.0% alpha, 67.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 275 through 282
      removed outlier: 6.993A  pdb=" N   GLN A 276 " --> pdb=" O   VAL B 275 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   ILE B 277 " --> pdb=" O   GLN A 276 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   ILE A 278 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   ASN B 279 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   LYS A 280 " --> pdb=" O   ASN B 279 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   LYS B 281 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   GLN B 276 " --> pdb=" O   VAL C 275 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   ILE C 277 " --> pdb=" O   GLN B 276 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   ILE B 278 " --> pdb=" O   ILE C 277 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   ASN C 279 " --> pdb=" O   ILE B 278 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   LYS B 280 " --> pdb=" O   ASN C 279 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   LYS C 281 " --> pdb=" O   LYS B 280 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 285 through 299
      removed outlier: 8.876A  pdb=" N   ASN A 286 " --> pdb=" O   VAL B 287 " (cutoff:3.500A)
      removed outlier: 9.875A  pdb=" N   SER B 289 " --> pdb=" O   ASN A 286 " (cutoff:3.500A)
      removed outlier: 8.782A  pdb=" N   GLN A 288 " --> pdb=" O   SER B 289 " (cutoff:3.500A)
      removed outlier: 8.197A  pdb=" N   CYS B 291 " --> pdb=" O   GLN A 288 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   LYS A 290 " --> pdb=" O   CYS B 291 " (cutoff:3.500A)
      removed outlier: 5.284A  pdb=" N   SER B 293 " --> pdb=" O   LYS A 290 " (cutoff:3.500A)
      removed outlier: 7.677A  pdb=" N   GLY A 292 " --> pdb=" O   SER B 293 " (cutoff:3.500A)
      removed outlier: 8.466A  pdb=" N   ASP B 295 " --> pdb=" O   GLY A 292 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   LYS A 294 " --> pdb=" O   ASP B 295 " (cutoff:3.500A)
      removed outlier: 7.966A  pdb=" N   ILE B 297 " --> pdb=" O   LYS A 294 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   ASN A 296 " --> pdb=" O   ILE B 297 " (cutoff:3.500A)
      removed outlier: 7.900A  pdb=" N   HIS B 299 " --> pdb=" O   ASN A 296 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   LYS A 298 " --> pdb=" O   HIS B 299 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   ASN B 286 " --> pdb=" O   SER C 285 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   VAL C 287 " --> pdb=" O   ASN B 286 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   GLN B 288 " --> pdb=" O   VAL C 287 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   SER C 289 " --> pdb=" O   GLN B 288 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   LYS B 290 " --> pdb=" O   SER C 289 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   SER C 293 " --> pdb=" O   GLY B 292 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   LYS B 294 " --> pdb=" O   SER C 293 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 303 through 310
      removed outlier: 6.740A  pdb=" N   GLY A 304 " --> pdb=" O   SER B 305 " (cutoff:3.500A)
      removed outlier: 8.171A  pdb=" N   GLN B 307 " --> pdb=" O   GLY A 304 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   VAL A 306 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
      removed outlier: 8.040A  pdb=" N   VAL B 309 " --> pdb=" O   VAL A 306 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ILE A 308 " --> pdb=" O   VAL B 309 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   GLY B 304 " --> pdb=" O   SER C 305 " (cutoff:3.500A)
      removed outlier: 8.161A  pdb=" N   GLN C 307 " --> pdb=" O   GLY B 304 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   VAL B 306 " --> pdb=" O   GLN C 307 " (cutoff:3.500A)
      removed outlier: 8.022A  pdb=" N   VAL C 309 " --> pdb=" O   VAL B 306 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   ILE B 308 " --> pdb=" O   VAL C 309 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 321
      removed outlier: 6.272A  pdb=" N   ASP A 314 " --> pdb=" O   LEU B 315 " (cutoff:3.500A)
      removed outlier: 8.097A  pdb=" N   LYS B 317 " --> pdb=" O   ASP A 314 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   SER A 316 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   THR B 319 " --> pdb=" O   SER A 316 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   VAL A 318 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 7.493A  pdb=" N   LYS B 321 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   SER A 320 " --> pdb=" O   LYS B 321 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   ASP B 314 " --> pdb=" O   LEU C 315 " (cutoff:3.500A)
      removed outlier: 8.035A  pdb=" N   LYS C 317 " --> pdb=" O   ASP B 314 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   SER B 316 " --> pdb=" O   LYS C 317 " (cutoff:3.500A)
      removed outlier: 7.268A  pdb=" N   THR C 319 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
      removed outlier: 6.029A  pdb=" N   VAL B 318 " --> pdb=" O   THR C 319 " (cutoff:3.500A)
      removed outlier: 7.431A  pdb=" N   LYS C 321 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   SER B 320 " --> pdb=" O   LYS C 321 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 327 through 330
      removed outlier: 6.547A  pdb=" N   ILE A 328 " --> pdb=" O   HIS B 329 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   ILE B 328 " --> pdb=" O   HIS C 329 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 336 through 346
      removed outlier: 6.801A  pdb=" N   VAL B 337 " --> pdb=" O   GLN A 336 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   GLU A 338 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   VAL B 339 " --> pdb=" O   GLU A 338 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   LYS A 340 " --> pdb=" O   VAL B 339 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   SER B 341 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   GLU A 342 " --> pdb=" O   SER B 341 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   LYS B 343 " --> pdb=" O   GLU C 342 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   LEU C 344 " --> pdb=" O   LYS B 343 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   ASP B 345 " --> pdb=" O   LEU C 344 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   PHE C 346 " --> pdb=" O   ASP B 345 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 349 through 362
      removed outlier: 6.433A  pdb=" N   VAL A 350 " --> pdb=" O   GLN B 351 " (cutoff:3.500A)
      removed outlier: 7.891A  pdb=" N   LYS B 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   SER A 352 " --> pdb=" O   LYS B 353 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   GLY B 355 " --> pdb=" O   SER A 352 " (cutoff:3.500A)
      removed outlier: 8.274A  pdb=" N   ILE A 354 " --> pdb=" O   GLY B 355 " (cutoff:3.500A)
      removed outlier: 7.173A  pdb=" N   LEU B 357 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
      removed outlier: 8.064A  pdb=" N   SER A 356 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
      removed outlier: 7.918A  pdb=" N   ASN B 359 " --> pdb=" O   SER A 356 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   ASP A 358 " --> pdb=" O   ASN B 359 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   THR B 361 " --> pdb=" O   ASP A 358 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   ILE A 360 " --> pdb=" O   THR B 361 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   SER B 356 " --> pdb=" O   GLY C 355 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   LEU C 357 " --> pdb=" O   SER B 356 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   ASP B 358 " --> pdb=" O   LEU C 357 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 379
      removed outlier: 6.034A  pdb=" N   LYS A 370 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   THR B 373 " --> pdb=" O   LYS A 370 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   GLU A 372 " --> pdb=" O   THR B 373 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   LYS B 375 " --> pdb=" O   GLU A 372 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   HIS A 374 " --> pdb=" O   LYS B 375 " (cutoff:3.500A)
      removed outlier: 7.954A  pdb=" N   THR B 377 " --> pdb=" O   HIS A 374 " (cutoff:3.500A)
      removed outlier: 6.046A  pdb=" N   LEU A 376 " --> pdb=" O   THR B 377 " (cutoff:3.500A)
      removed outlier: 7.261A  pdb=" N   ARG B 379 " --> pdb=" O   LEU A 376 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   PHE A 378 " --> pdb=" O   ARG B 379 " (cutoff:3.500A)
      removed outlier: 5.990A  pdb=" N   LYS B 370 " --> pdb=" O   ILE C 371 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   THR C 373 " --> pdb=" O   LYS B 370 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   GLU B 372 " --> pdb=" O   THR C 373 " (cutoff:3.500A)
      removed outlier: 7.519A  pdb=" N   LYS C 375 " --> pdb=" O   GLU B 372 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   HIS B 374 " --> pdb=" O   LYS C 375 " (cutoff:3.500A)
      removed outlier: 7.902A  pdb=" N   THR C 377 " --> pdb=" O   HIS B 374 " (cutoff:3.500A)
      removed outlier: 5.983A  pdb=" N   LEU B 376 " --> pdb=" O   THR C 377 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   ARG C 379 " --> pdb=" O   LEU B 376 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   PHE B 378 " --> pdb=" O   ARG C 379 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, 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=AB1, 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=AB2, 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=AB2
    Processing sheet with id=AB3, 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=AB3
    Processing sheet with id=AB4, 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=AB4
    Processing sheet with id=AB5, 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=AB6, 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=AB7, 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=AB7

    58 hydrogen bonds defined for protein.
    174 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: 0.75

  Time building geometry restraints manager: 0.53 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: 1626
        1.34 -     1.46: 626
        1.46 -     1.57: 2680
        1.57 -     1.69: 0
        1.69 -     1.80: 12
  Bond restraints: 4944
  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 C 353 "
       pdb=" CB  LYS C 353 "
    ideal  model  delta    sigma   weight residual
    1.529  1.499  0.030 1.38e-02 5.25e+03 4.66e+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 A 353 "
       pdb=" CB  LYS A 353 "
    ideal  model  delta    sigma   weight residual
    1.529  1.500  0.029 1.38e-02 5.25e+03 4.53e+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
  ... (remaining 4939 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 5735
        1.38 -     2.77: 724
        2.77 -     4.15: 111
        4.15 -     5.53: 24
        5.53 -     6.92: 12
  Bond angle restraints: 6606
  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 B 347 "
        pdb=" N   ASP B 348 "
        pdb=" CA  ASP B 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=" C   LYS C 347 "
        pdb=" N   ASP C 348 "
        pdb=" CA  ASP C 348 "
      ideal   model   delta    sigma   weight residual
     122.17  115.30    6.87 1.54e+00 4.22e-01 1.99e+01
  ... (remaining 6601 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.26: 2654
       16.26 -    32.52: 317
       32.52 -    48.77: 53
       48.77 -    65.03: 24
       65.03 -    81.29: 6
  Dihedral angle restraints: 3054
    sinusoidal: 1284
      harmonic: 1770
  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 A 313 "
           pdb=" C   VAL A 313 "
           pdb=" N   ASP A 314 "
           pdb=" CA  ASP A 314 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.25  -20.75     0      5.00e+00 4.00e-02 1.72e+01
  dihedral pdb=" CA  VAL B 313 "
           pdb=" C   VAL B 313 "
           pdb=" N   ASP B 314 "
           pdb=" CA  ASP B 314 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.25  -20.75     0      5.00e+00 4.00e-02 1.72e+01
  ... (remaining 3051 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 394
       0.036 -    0.073: 219
       0.073 -    0.109: 92
       0.109 -    0.145: 27
       0.145 -    0.181: 12
  Chirality restraints: 744
  Sorted by residual:
  chirality pdb=" CB  ILE B 277 "
            pdb=" CA  ILE B 277 "
            pdb=" CG1 ILE B 277 "
            pdb=" CG2 ILE B 277 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.21e-01
  chirality pdb=" CB  ILE A 277 "
            pdb=" CA  ILE A 277 "
            pdb=" CG1 ILE A 277 "
            pdb=" CG2 ILE A 277 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.80e-01
  chirality pdb=" CB  ILE C 277 "
            pdb=" CA  ILE C 277 "
            pdb=" CG1 ILE C 277 "
            pdb=" CG2 ILE C 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
  ... (remaining 741 not shown)

  Planarity restraints: 846
  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 A 363 "   -0.034 5.00e-02 4.00e+02   5.18e-02 4.29e+00
        pdb=" N   PRO A 364 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A 364 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 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
  ... (remaining 843 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 1567
        2.83 -     3.35: 4573
        3.35 -     3.87: 8817
        3.87 -     4.38: 8741
        4.38 -     4.90: 16812
  Nonbonded interactions: 40510
  Sorted by model distance:
  nonbonded pdb=" N   GLU C 380 "
            pdb=" OE1 GLU C 380 "
     model   vdw
     2.318 3.120
  nonbonded pdb=" N   GLU E 380 "
            pdb=" OE1 GLU E 380 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" N   GLU B 380 "
            pdb=" OE1 GLU B 380 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" N   GLU A 380 "
            pdb=" OE1 GLU A 380 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" N   GLU F 380 "
            pdb=" OE1 GLU F 380 "
     model   vdw
     2.319 3.120
  ... (remaining 40505 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = 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:             2.040
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.640
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6243
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   4944  Z= 0.378
  Angle     :  1.025   6.915   6606  Z= 0.590
  Chirality :  0.054   0.181    744
  Planarity :  0.006   0.052    846
  Dihedral  : 15.142  81.287   1926
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 28.45
  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 are not related in a simple way.
  whole: -4.78 (0.23), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.64 (0.18), residues: 630

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 ( 4944)
  covalent geometry    : angle       1.02503 ( 6606)
  hydrogen bonds       : bond        0.07591 (   58)
  hydrogen bonds       : angle       9.25201 (  174)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 166
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  285 SER cc_start: 0.7274 (t) cc_final: 0.7067 (t)
REVERT: B  277 ILE cc_start: 0.8449 (tp) cc_final: 0.8052 (mp)
REVERT: B  278 ILE cc_start: 0.7470 (mt) cc_final: 0.7262 (mp)
REVERT: B  337 VAL cc_start: 0.9057 (t) cc_final: 0.8822 (t)
REVERT: B  345 ASP cc_start: 0.7908 (p0) cc_final: 0.7587 (p0)
REVERT: C  278 ILE cc_start: 0.5867 (mt) cc_final: 0.5594 (mp)
REVERT: F  277 ILE cc_start: 0.8529 (tp) cc_final: 0.8186 (mp)
REVERT: F  278 ILE cc_start: 0.7084 (mt) cc_final: 0.6816 (mp)
REVERT: F  338 GLU cc_start: 0.6168 (mm-30) cc_final: 0.5582 (mm-30)
REVERT: F  345 ASP cc_start: 0.7216 (p0) cc_final: 0.6890 (p0)
REVERT: G  278 ILE cc_start: 0.5385 (mt) cc_final: 0.5111 (mp)
REVERT: G  370 LYS cc_start: 0.6726 (mttt) cc_final: 0.6511 (pptt)
  outliers start: 12
  outliers final: 3
  residues processed: 174
  average time/residue: 0.0765
  time to fit residues: 16.5811
Evaluate side-chains
  94 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 91
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  356 SER
Chi-restraints excluded: chain G residue  356 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0030
   chunk 48 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.7594

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

Flipped N/Q/H residues before XYZ refinement:
** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 362 HIS
B 279 ASN
** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 362 HIS
C 279 ASN
** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 362 HIS
C 368 ASN
C 374 HIS
** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 362 HIS
F 279 ASN
** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 362 HIS
G 279 ASN
G 362 HIS
G 374 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5000 r_free = 0.5000 target = 0.171004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4739 r_free = 0.4739 target = 0.144917 restraints weight = 12091.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4710 r_free = 0.4710 target = 0.143740 restraints weight = 8315.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4716 r_free = 0.4716 target = 0.144587 restraints weight = 7377.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4719 r_free = 0.4719 target = 0.144705 restraints weight = 6367.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4721 r_free = 0.4721 target = 0.144899 restraints weight = 5963.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.4680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6899
moved from start:          0.3717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4944  Z= 0.162
  Angle     :  0.777   6.865   6606  Z= 0.394
  Chirality :  0.052   0.134    744
  Planarity :  0.005   0.036    846
  Dihedral  :  7.825  58.185    658
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 19.86 %
    Favored  : 76.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.52 (0.24), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.44 (0.19), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 379 
 TYR   0.008   0.002   TYR E 310 
 PHE   0.010   0.001   PHE C 378 
 HIS   0.015   0.001   HIS C 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 4944)
  covalent geometry    : angle       0.77702 ( 6606)
  hydrogen bonds       : bond        0.01793 (   58)
  hydrogen bonds       : angle       7.28714 (  174)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 0.193 
Fit side-chains
REVERT: B  317 LYS cc_start: 0.7590 (mttt) cc_final: 0.7199 (mttm)
REVERT: C  317 LYS cc_start: 0.6905 (mttm) cc_final: 0.6554 (mttm)
REVERT: C  338 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7239 (mp0)
REVERT: F  317 LYS cc_start: 0.7548 (mttm) cc_final: 0.7321 (mttm)
REVERT: G  370 LYS cc_start: 0.6703 (mttt) cc_final: 0.6429 (pptt)
  outliers start: 22
  outliers final: 10
  residues processed: 130
  average time/residue: 0.0665
  time to fit residues: 11.2814
Evaluate side-chains
  98 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain B residue  374 HIS
Chi-restraints excluded: chain C residue  356 SER
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain F residue  277 ILE
Chi-restraints excluded: chain F residue  337 VAL
Chi-restraints excluded: chain F residue  374 HIS
Chi-restraints excluded: chain G residue  356 SER
Chi-restraints excluded: chain G residue  368 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 8 optimal weight:    8.9990
   chunk 9 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 329 HIS
A 330 HIS
** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 329 HIS
C 329 HIS
** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 329 HIS
E 330 HIS
** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 329 HIS
** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 329 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4935 r_free = 0.4935 target = 0.161948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4656 r_free = 0.4656 target = 0.139586 restraints weight = 13840.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4587 r_free = 0.4587 target = 0.137746 restraints weight = 12526.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4586 r_free = 0.4586 target = 0.138086 restraints weight = 10401.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4591 r_free = 0.4591 target = 0.138543 restraints weight = 9411.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4590 r_free = 0.4590 target = 0.138533 restraints weight = 8310.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.4537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7045
moved from start:          0.5056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   4944  Z= 0.305
  Angle     :  0.883  11.601   6606  Z= 0.447
  Chirality :  0.053   0.139    744
  Planarity :  0.005   0.046    846
  Dihedral  :  7.493  24.383    656
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 15.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.89 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 21.28 %
    Favored  : 74.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.62 (0.22), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.52 (0.17), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG F 349 
 TYR   0.010   0.003   TYR C 310 
 PHE   0.010   0.002   PHE B 346 
 HIS   0.008   0.001   HIS F 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00641 ( 4944)
  covalent geometry    : angle       0.88263 ( 6606)
  hydrogen bonds       : bond        0.02791 (   58)
  hydrogen bonds       : angle       6.37090 (  174)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.205 
Fit side-chains
REVERT: E  378 PHE cc_start: 0.7687 (m-80) cc_final: 0.7461 (m-80)
REVERT: G  370 LYS cc_start: 0.6731 (mttt) cc_final: 0.6406 (pptt)
  outliers start: 24
  outliers final: 18
  residues processed: 116
  average time/residue: 0.0636
  time to fit residues: 9.7208
Evaluate side-chains
  106 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  374 HIS
Chi-restraints excluded: chain C residue  314 ASP
Chi-restraints excluded: chain C residue  337 VAL
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain E residue  343 LYS
Chi-restraints excluded: chain E residue  354 ILE
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain F residue  337 VAL
Chi-restraints excluded: chain F residue  356 SER
Chi-restraints excluded: chain F residue  374 HIS
Chi-restraints excluded: chain G residue  337 VAL
Chi-restraints excluded: chain G residue  358 ASP
Chi-restraints excluded: chain G residue  368 ASN
Chi-restraints excluded: chain G residue  374 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 50 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0570
   chunk 10 optimal weight:    0.0770
   chunk 31 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 30 optimal weight:    8.9990
   chunk 47 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 288 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 = 0.4997 r_free = 0.4997 target = 0.168582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4759 r_free = 0.4759 target = 0.146663 restraints weight = 13442.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4688 r_free = 0.4688 target = 0.145167 restraints weight = 11387.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4688 r_free = 0.4688 target = 0.145470 restraints weight = 9920.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4692 r_free = 0.4692 target = 0.145960 restraints weight = 8873.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4691 r_free = 0.4691 target = 0.145926 restraints weight = 8040.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.4648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6900
moved from start:          0.5417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4944  Z= 0.126
  Angle     :  0.728  12.345   6606  Z= 0.356
  Chirality :  0.052   0.144    744
  Planarity :  0.004   0.039    846
  Dihedral  :  6.445  21.127    654
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 23.76 %
    Favored  : 73.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.48 (0.23), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.41 (0.18), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 349 
 TYR   0.011   0.002   TYR E 310 
 PHE   0.018   0.002   PHE C 378 
 HIS   0.003   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 4944)
  covalent geometry    : angle       0.72819 ( 6606)
  hydrogen bonds       : bond        0.02525 (   58)
  hydrogen bonds       : angle       5.85349 (  174)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.213 
Fit side-chains
REVERT: B  277 ILE cc_start: 0.8528 (mp) cc_final: 0.8112 (tp)
REVERT: E  378 PHE cc_start: 0.7914 (m-80) cc_final: 0.7691 (m-80)
REVERT: F  315 LEU cc_start: 0.8006 (mp) cc_final: 0.7428 (tt)
REVERT: F  317 LYS cc_start: 0.7821 (mttm) cc_final: 0.7602 (mttm)
REVERT: G  315 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7064 (tt)
REVERT: G  370 LYS cc_start: 0.6614 (mttt) cc_final: 0.6293 (pptt)
  outliers start: 16
  outliers final: 9
  residues processed: 112
  average time/residue: 0.0548
  time to fit residues: 8.4952
Evaluate side-chains
  104 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain C residue  337 VAL
Chi-restraints excluded: chain E residue  285 SER
Chi-restraints excluded: chain E residue  354 ILE
Chi-restraints excluded: chain F residue  337 VAL
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain G residue  314 ASP
Chi-restraints excluded: chain G residue  315 LEU
Chi-restraints excluded: chain G residue  368 ASN
Chi-restraints excluded: chain G residue  374 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 8 optimal weight:    0.0030
   chunk 14 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 5 optimal weight:    6.9990
   chunk 17 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0040
   chunk 39 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 58 optimal weight:    4.9990
   chunk 9 optimal weight:    0.0670
   chunk 56 optimal weight:    2.9990
   overall best weight:    1.2144

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

Flipped N/Q/H residues before XYZ refinement:
** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 288 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 = 0.4971 r_free = 0.4971 target = 0.165789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4727 r_free = 0.4727 target = 0.144233 restraints weight = 13919.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4652 r_free = 0.4652 target = 0.142696 restraints weight = 12031.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4652 r_free = 0.4652 target = 0.143066 restraints weight = 11514.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4656 r_free = 0.4656 target = 0.143490 restraints weight = 9592.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4654 r_free = 0.4654 target = 0.143458 restraints weight = 8773.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.4619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6934
moved from start:          0.5764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4944  Z= 0.184
  Angle     :  0.749  11.762   6606  Z= 0.371
  Chirality :  0.052   0.167    744
  Planarity :  0.004   0.036    846
  Dihedral  :  6.500  22.143    654
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.27 %
    Favored  : 88.73 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 25.71 %
    Favored  : 71.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.48 (0.23), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.41 (0.18), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 349 
 TYR   0.008   0.002   TYR C 310 
 PHE   0.017   0.002   PHE G 378 
 HIS   0.003   0.001   HIS F 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 4944)
  covalent geometry    : angle       0.74896 ( 6606)
  hydrogen bonds       : bond        0.02584 (   58)
  hydrogen bonds       : angle       5.56367 (  174)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.141 
Fit side-chains
REVERT: B  277 ILE cc_start: 0.8570 (mp) cc_final: 0.8137 (tp)
REVERT: E  378 PHE cc_start: 0.7952 (m-80) cc_final: 0.7599 (m-80)
REVERT: F  315 LEU cc_start: 0.7996 (mp) cc_final: 0.7528 (tt)
REVERT: G  315 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7363 (tt)
REVERT: G  370 LYS cc_start: 0.6594 (mttt) cc_final: 0.6289 (pptt)
  outliers start: 17
  outliers final: 12
  residues processed: 109
  average time/residue: 0.0608
  time to fit residues: 8.8231
Evaluate side-chains
  101 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain C residue  314 ASP
Chi-restraints excluded: chain C residue  337 VAL
Chi-restraints excluded: chain E residue  285 SER
Chi-restraints excluded: chain E residue  343 LYS
Chi-restraints excluded: chain E residue  354 ILE
Chi-restraints excluded: chain F residue  285 SER
Chi-restraints excluded: chain F residue  337 VAL
Chi-restraints excluded: chain G residue  314 ASP
Chi-restraints excluded: chain G residue  315 LEU
Chi-restraints excluded: chain G residue  368 ASN
Chi-restraints excluded: chain G residue  374 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0040
   chunk 13 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 59 optimal weight:    0.6980
   chunk 58 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 288 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 = 0.5025 r_free = 0.5025 target = 0.171528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4818 r_free = 0.4818 target = 0.150736 restraints weight = 13952.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4725 r_free = 0.4725 target = 0.148310 restraints weight = 9900.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4728 r_free = 0.4728 target = 0.148886 restraints weight = 11189.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4733 r_free = 0.4733 target = 0.149384 restraints weight = 8357.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4734 r_free = 0.4734 target = 0.149558 restraints weight = 7737.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.4742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6898
moved from start:          0.6012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4944  Z= 0.118
  Angle     :  0.693  11.273   6606  Z= 0.337
  Chirality :  0.053   0.189    744
  Planarity :  0.004   0.033    846
  Dihedral  :  5.950  20.411    654
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.37 %
    Favored  : 90.63 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 25.00 %
    Favored  : 72.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.44 (0.23), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.38 (0.18), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 379 
 TYR   0.007   0.001   TYR C 310 
 PHE   0.019   0.002   PHE G 378 
 HIS   0.003   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 4944)
  covalent geometry    : angle       0.69318 ( 6606)
  hydrogen bonds       : bond        0.02497 (   58)
  hydrogen bonds       : angle       5.44259 (  174)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A  277 ILE cc_start: 0.8269 (tp) cc_final: 0.7985 (tp)
REVERT: A  343 LYS cc_start: 0.6739 (OUTLIER) cc_final: 0.6378 (pttm)
REVERT: B  277 ILE cc_start: 0.8594 (mp) cc_final: 0.8258 (tp)
REVERT: B  348 ASP cc_start: 0.6534 (t0) cc_final: 0.6331 (t0)
REVERT: E  343 LYS cc_start: 0.6982 (OUTLIER) cc_final: 0.6502 (pttm)
REVERT: E  372 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8331 (mm-30)
REVERT: E  378 PHE cc_start: 0.7979 (m-80) cc_final: 0.7578 (m-80)
REVERT: F  372 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7745 (mm-30)
REVERT: G  370 LYS cc_start: 0.6646 (mttt) cc_final: 0.6312 (pptt)
  outliers start: 15
  outliers final: 7
  residues processed: 109
  average time/residue: 0.0673
  time to fit residues: 9.5439
Evaluate side-chains
  98 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain C residue  337 VAL
Chi-restraints excluded: chain E residue  343 LYS
Chi-restraints excluded: chain F residue  314 ASP
Chi-restraints excluded: chain F residue  337 VAL
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain G residue  314 ASP
Chi-restraints excluded: chain G residue  368 ASN
Chi-restraints excluded: chain G residue  374 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 35 optimal weight:    0.0870
   chunk 14 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 53 optimal weight:    0.3980
   chunk 59 optimal weight:    0.6980
   chunk 57 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 48 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
** A 288 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 = 0.4944 r_free = 0.4944 target = 0.169612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4632 r_free = 0.4632 target = 0.138080 restraints weight = 11389.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4649 r_free = 0.4649 target = 0.139557 restraints weight = 8045.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4657 r_free = 0.4657 target = 0.140405 restraints weight = 6475.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4661 r_free = 0.4661 target = 0.140896 restraints weight = 5731.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4663 r_free = 0.4663 target = 0.141222 restraints weight = 5328.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.4610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6821
moved from start:          0.6332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4944  Z= 0.118
  Angle     :  0.694  10.745   6606  Z= 0.338
  Chirality :  0.053   0.211    744
  Planarity :  0.004   0.034    846
  Dihedral  :  5.790  19.906    654
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 26.77 %
    Favored  : 71.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.39 (0.24), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.34 (0.18), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 349 
 TYR   0.020   0.003   TYR E 310 
 PHE   0.020   0.002   PHE G 378 
 HIS   0.003   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 4944)
  covalent geometry    : angle       0.69446 ( 6606)
  hydrogen bonds       : bond        0.02446 (   58)
  hydrogen bonds       : angle       5.28417 (  174)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A  343 LYS cc_start: 0.6854 (OUTLIER) cc_final: 0.6414 (pttm)
REVERT: A  349 ARG cc_start: 0.6824 (mtt-85) cc_final: 0.5469 (ptt-90)
REVERT: A  372 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8250 (mp0)
REVERT: E  343 LYS cc_start: 0.6762 (OUTLIER) cc_final: 0.6306 (pttm)
REVERT: E  349 ARG cc_start: 0.6927 (mtt-85) cc_final: 0.5460 (ptt-90)
REVERT: E  372 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8051 (mm-30)
REVERT: E  378 PHE cc_start: 0.7729 (m-80) cc_final: 0.7358 (m-80)
REVERT: F  372 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7612 (mm-30)
REVERT: G  370 LYS cc_start: 0.6720 (mttt) cc_final: 0.6342 (pptt)
  outliers start: 12
  outliers final: 7
  residues processed: 107
  average time/residue: 0.0746
  time to fit residues: 10.3569
Evaluate side-chains
  100 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain A residue  375 LYS
Chi-restraints excluded: chain C residue  314 ASP
Chi-restraints excluded: chain C residue  337 VAL
Chi-restraints excluded: chain E residue  343 LYS
Chi-restraints excluded: chain F residue  337 VAL
Chi-restraints excluded: chain F residue  344 LEU
Chi-restraints excluded: chain G residue  314 ASP
Chi-restraints excluded: chain G residue  374 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 44 optimal weight:    0.4980
   chunk 13 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0970
   chunk 31 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0570
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
** A 288 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 = 0.4966 r_free = 0.4966 target = 0.171652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4655 r_free = 0.4655 target = 0.140909 restraints weight = 11667.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4676 r_free = 0.4676 target = 0.142549 restraints weight = 7907.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4687 r_free = 0.4687 target = 0.143501 restraints weight = 6218.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4693 r_free = 0.4693 target = 0.144124 restraints weight = 5402.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4696 r_free = 0.4696 target = 0.144482 restraints weight = 4959.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.4642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6783
moved from start:          0.6494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4944  Z= 0.114
  Angle     :  0.698  10.494   6606  Z= 0.340
  Chirality :  0.053   0.261    744
  Planarity :  0.004   0.038    846
  Dihedral  :  5.645  19.161    654
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.25 %
    Favored  : 91.75 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 27.48 %
    Favored  : 70.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.35 (0.24), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.31 (0.18), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG C 349 
 TYR   0.025   0.003   TYR A 310 
 PHE   0.019   0.002   PHE G 378 
 HIS   0.002   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 4944)
  covalent geometry    : angle       0.69789 ( 6606)
  hydrogen bonds       : bond        0.02352 (   58)
  hydrogen bonds       : angle       5.16289 (  174)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.198 
Fit side-chains
REVERT: A  343 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.6958 (pttm)
REVERT: A  349 ARG cc_start: 0.6903 (mtt-85) cc_final: 0.5500 (ptt-90)
REVERT: A  372 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8409 (mp0)
REVERT: E  343 LYS cc_start: 0.6784 (OUTLIER) cc_final: 0.6395 (pttm)
REVERT: E  349 ARG cc_start: 0.6885 (mtt-85) cc_final: 0.5431 (ptt-90)
REVERT: E  372 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8133 (mm-30)
REVERT: E  378 PHE cc_start: 0.7770 (m-80) cc_final: 0.7358 (m-80)
REVERT: F  372 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7671 (mm-30)
REVERT: G  370 LYS cc_start: 0.6730 (mttt) cc_final: 0.6332 (pptt)
  outliers start: 12
  outliers final: 7
  residues processed: 105
  average time/residue: 0.0730
  time to fit residues: 9.9543
Evaluate side-chains
  101 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain A residue  375 LYS
Chi-restraints excluded: chain C residue  314 ASP
Chi-restraints excluded: chain E residue  343 LYS
Chi-restraints excluded: chain F residue  285 SER
Chi-restraints excluded: chain F residue  337 VAL
Chi-restraints excluded: chain F residue  344 LEU
Chi-restraints excluded: chain G residue  314 ASP
Chi-restraints excluded: chain G residue  374 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 288 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 = 0.4944 r_free = 0.4944 target = 0.170496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4635 r_free = 0.4635 target = 0.140282 restraints weight = 11774.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4661 r_free = 0.4661 target = 0.141735 restraints weight = 8023.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4668 r_free = 0.4668 target = 0.142533 restraints weight = 6437.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4673 r_free = 0.4673 target = 0.142989 restraints weight = 5697.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4677 r_free = 0.4677 target = 0.143356 restraints weight = 5330.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.4608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6838
moved from start:          0.6646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4944  Z= 0.132
  Angle     :  0.712  10.065   6606  Z= 0.348
  Chirality :  0.053   0.222    744
  Planarity :  0.004   0.040    846
  Dihedral  :  5.712  19.910    654
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.48 %
    Favored  : 89.52 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 26.77 %
    Favored  : 70.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.35 (0.24), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.31 (0.18), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 349 
 TYR   0.018   0.003   TYR E 310 
 PHE   0.019   0.002   PHE F 378 
 HIS   0.002   0.001   HIS G 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 4944)
  covalent geometry    : angle       0.71183 ( 6606)
  hydrogen bonds       : bond        0.02403 (   58)
  hydrogen bonds       : angle       5.07449 (  174)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.222 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.6903 (mtt-85) cc_final: 0.5498 (ptt-90)
REVERT: A  372 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8513 (mp0)
REVERT: E  310 TYR cc_start: 0.8431 (t80) cc_final: 0.8198 (t80)
REVERT: E  343 LYS cc_start: 0.6682 (OUTLIER) cc_final: 0.6239 (pttm)
REVERT: E  349 ARG cc_start: 0.6858 (mtt-85) cc_final: 0.5450 (ptt-90)
REVERT: E  372 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8070 (mm-30)
REVERT: E  378 PHE cc_start: 0.7653 (m-80) cc_final: 0.7236 (m-80)
REVERT: F  372 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7630 (mm-30)
REVERT: G  368 ASN cc_start: 0.7293 (OUTLIER) cc_final: 0.6983 (m110)
REVERT: G  370 LYS cc_start: 0.6732 (mttt) cc_final: 0.6334 (pptt)
  outliers start: 15
  outliers final: 10
  residues processed: 104
  average time/residue: 0.0731
  time to fit residues: 9.7719
Evaluate side-chains
  105 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain A residue  375 LYS
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain C residue  314 ASP
Chi-restraints excluded: chain E residue  343 LYS
Chi-restraints excluded: chain F residue  285 SER
Chi-restraints excluded: chain F residue  344 LEU
Chi-restraints excluded: chain F residue  356 SER
Chi-restraints excluded: chain G residue  314 ASP
Chi-restraints excluded: chain G residue  368 ASN
Chi-restraints excluded: chain G residue  374 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0010
   chunk 26 optimal weight:    2.9990
   chunk 35 optimal weight:    0.1980
   chunk 40 optimal weight:    6.9990
   chunk 36 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0050
   chunk 27 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.3800

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

Flipped N/Q/H residues before XYZ refinement:
** A 288 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 = 0.4980 r_free = 0.4980 target = 0.172296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4676 r_free = 0.4676 target = 0.141503 restraints weight = 11583.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4700 r_free = 0.4700 target = 0.143202 restraints weight = 7774.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4710 r_free = 0.4710 target = 0.144188 restraints weight = 6109.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.4715 r_free = 0.4715 target = 0.144628 restraints weight = 5314.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4718 r_free = 0.4718 target = 0.145019 restraints weight = 4955.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.4661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6754
moved from start:          0.6817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4944  Z= 0.105
  Angle     :  0.690  10.363   6606  Z= 0.336
  Chirality :  0.053   0.223    744
  Planarity :  0.004   0.046    846
  Dihedral  :  5.529  18.794    654
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.25 %
    Favored  : 91.75 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 27.13 %
    Favored  : 71.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.31 (0.24), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.28 (0.18), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 349 
 TYR   0.030   0.003   TYR A 310 
 PHE   0.020   0.002   PHE F 378 
 HIS   0.002   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 4944)
  covalent geometry    : angle       0.68958 ( 6606)
  hydrogen bonds       : bond        0.02393 (   58)
  hydrogen bonds       : angle       5.07992 (  174)

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

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

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1260 Ramachandran restraints generated.
    630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A  343 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.6801 (pttm)
REVERT: A  349 ARG cc_start: 0.6841 (mtt-85) cc_final: 0.5438 (ptt-90)
REVERT: A  372 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8511 (mp0)
REVERT: C  288 GLN cc_start: 0.7613 (mp10) cc_final: 0.5001 (tp40)
REVERT: E  343 LYS cc_start: 0.6639 (OUTLIER) cc_final: 0.5794 (pttm)
REVERT: E  349 ARG cc_start: 0.6793 (mtt-85) cc_final: 0.5372 (ptt-90)
REVERT: E  372 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8149 (mm-30)
REVERT: E  378 PHE cc_start: 0.7588 (m-80) cc_final: 0.7191 (m-80)
REVERT: F  372 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7732 (mm-30)
REVERT: G  370 LYS cc_start: 0.6732 (mttt) cc_final: 0.6339 (pptt)
  outliers start: 10
  outliers final: 5
  residues processed: 107
  average time/residue: 0.0735
  time to fit residues: 10.1770
Evaluate side-chains
  104 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 LYS
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain C residue  314 ASP
Chi-restraints excluded: chain E residue  343 LYS
Chi-restraints excluded: chain F residue  344 LEU
Chi-restraints excluded: chain G residue  314 ASP
Chi-restraints excluded: chain G residue  374 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9980
   chunk 35 optimal weight:    0.1980
   chunk 36 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 288 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 = 0.4950 r_free = 0.4950 target = 0.170845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4651 r_free = 0.4651 target = 0.140702 restraints weight = 11747.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4672 r_free = 0.4672 target = 0.142246 restraints weight = 8003.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4682 r_free = 0.4682 target = 0.143191 restraints weight = 6283.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4688 r_free = 0.4688 target = 0.143717 restraints weight = 5485.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.4691 r_free = 0.4691 target = 0.144020 restraints weight = 5065.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.4620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6823
moved from start:          0.6934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4944  Z= 0.138
  Angle     :  0.720   9.795   6606  Z= 0.350
  Chirality :  0.053   0.183    744
  Planarity :  0.005   0.050    846
  Dihedral  :  5.672  19.633    654
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.27 %
    Favored  : 88.73 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 27.66 %
    Favored  : 70.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.31 (0.24), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.28 (0.18), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 349 
 TYR   0.031   0.004   TYR A 310 
 PHE   0.019   0.002   PHE F 378 
 HIS   0.003   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4944)
  covalent geometry    : angle       0.71951 ( 6606)
  hydrogen bonds       : bond        0.02490 (   58)
  hydrogen bonds       : angle       4.98880 (  174)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1073.60 seconds
wall clock time: 19 minutes 15.18 seconds (1155.18 seconds total)