Starting phenix.real_space_refine
on Tue Feb 11 08:54:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vh7_21200/02_2025/6vh7_21200.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vh7_21200/02_2025/6vh7_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vh7_21200/02_2025/6vh7_21200.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vh7_21200/02_2025/6vh7_21200.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vh7_21200/02_2025/6vh7_21200.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vh7_21200/02_2025/6vh7_21200.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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:
    C, B, E, G, F
  Time building chain proxies: 2.38, per 1000 atoms: 0.49
  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: 1.24
  Conformation dependent library (CDL) restraints added in 644.4 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: 0.67
  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: 1.17

  Time building geometry restraints manager: 1.44 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'G'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.110
  Find NCS groups from input model:        0.120
  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:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.930
-------------------------------------------------------------------------------
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= 0.493
  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 : 28.35
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.78 (0.23), 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
 HIS   0.006   0.001   HIS G 374 
 PHE   0.003   0.001   PHE E 378 
 TYR   0.004   0.002   TYR E 310 
 ARG   0.001   0.000   ARG G 349 

*********************** 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  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  285 SER cc_start: 0.7274 (t) cc_final: 0.7066 (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: 0.7263 (mp)
REVERT: B  345 ASP cc_start: 0.7908 (p0) cc_final: 0.7590 (p0)
REVERT: C  278 ILE cc_start: 0.5867 (mt) cc_final: 0.5593 (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: 0.6817 (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: 0.2019
  time to fit residues: 43.0362
Evaluate side-chains
  93 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 90
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
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 50 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 30 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 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 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: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5030 r_free = 0.5030 target = 0.170210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4795 r_free = 0.4795 target = 0.148291 restraints weight = 13566.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4724 r_free = 0.4724 target = 0.146527 restraints weight = 10845.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4725 r_free = 0.4725 target = 0.146979 restraints weight = 9613.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.4658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6876
moved from start:          0.3926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4944  Z= 0.271
  Angle     :  0.788   7.324   6606  Z= 0.401
  Chirality :  0.052   0.147    744
  Planarity :  0.005   0.037    846
  Dihedral  :  7.820  59.092    658
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 18.44 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.53 (0.24), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.44 (0.18), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.017   0.002   HIS C 374 
 PHE   0.010   0.001   PHE G 378 
 TYR   0.010   0.002   TYR E 310 
 ARG   0.002   0.001   ARG E 379 

*********************** 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
  139 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.685 
Fit side-chains
REVERT: A  277 ILE cc_start: 0.8599 (mp) cc_final: 0.8300 (tp)
REVERT: A  285 SER cc_start: 0.8341 (t) cc_final: 0.8138 (m)
REVERT: G  317 LYS cc_start: 0.7122 (mttm) cc_final: 0.6815 (mttm)
REVERT: G  370 LYS cc_start: 0.6680 (mttt) cc_final: 0.6404 (pptt)
REVERT: G  378 PHE cc_start: 0.6321 (m-80) cc_final: 0.6112 (m-80)
  outliers start: 24
  outliers final: 13
  residues processed: 129
  average time/residue: 0.1469
  time to fit residues: 24.8140
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  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain B residue  371 ILE
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  337 VAL
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain F residue  374 HIS
Chi-restraints excluded: chain G residue  356 SER
Chi-restraints excluded: chain G residue  368 ASN
Chi-restraints excluded: chain G residue  374 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 59 optimal weight:    0.1980
   chunk 56 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 38 optimal weight:    0.2980
   chunk 6 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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
** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 330 HIS
** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 374 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4990 r_free = 0.4990 target = 0.168467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4728 r_free = 0.4728 target = 0.146034 restraints weight = 13798.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4671 r_free = 0.4671 target = 0.144485 restraints weight = 9512.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4673 r_free = 0.4673 target = 0.144781 restraints weight = 8589.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.4626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6959
moved from start:          0.4610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4944  Z= 0.224
  Angle     :  0.693   6.827   6606  Z= 0.352
  Chirality :  0.051   0.128    744
  Planarity :  0.004   0.035    846
  Dihedral  :  6.507  20.242    656
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.25 %
    Favored  : 91.75 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 20.57 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.44 (0.24), 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
 HIS   0.017   0.001   HIS G 374 
 PHE   0.009   0.002   PHE B 346 
 TYR   0.009   0.002   TYR E 310 
 ARG   0.001   0.000   ARG F 379 

*********************** 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
  122 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.579 
Fit side-chains
REVERT: A  277 ILE cc_start: 0.8647 (mp) cc_final: 0.8331 (tp)
REVERT: A  285 SER cc_start: 0.8485 (t) cc_final: 0.8269 (m)
REVERT: G  317 LYS cc_start: 0.7112 (mttm) cc_final: 0.6849 (mttt)
REVERT: G  370 LYS cc_start: 0.6600 (mttt) cc_final: 0.6302 (pptt)
  outliers start: 19
  outliers final: 11
  residues processed: 115
  average time/residue: 0.1540
  time to fit residues: 23.3323
Evaluate side-chains
  103 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain B 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  358 ASP
Chi-restraints excluded: chain F residue  337 VAL
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain F residue  374 HIS
Chi-restraints excluded: chain G residue  319 THR
Chi-restraints excluded: chain G residue  358 ASP
Chi-restraints excluded: chain G residue  368 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 27 optimal weight:    0.4980
   chunk 19 optimal weight:    7.9990
   chunk 42 optimal weight:    0.9980
   chunk 30 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 54 optimal weight:    0.8980
   chunk 35 optimal weight:    7.9990
   chunk 11 optimal weight:    5.9990
   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**
A 329 HIS
** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 329 HIS
** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4968 r_free = 0.4968 target = 0.167662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4652 r_free = 0.4652 target = 0.138102 restraints weight = 12192.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4674 r_free = 0.4674 target = 0.139248 restraints weight = 8687.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4681 r_free = 0.4681 target = 0.139950 restraints weight = 7189.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.4620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6963
moved from start:          0.5218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4944  Z= 0.212
  Angle     :  0.662   6.289   6606  Z= 0.334
  Chirality :  0.051   0.125    744
  Planarity :  0.004   0.033    846
  Dihedral  :  6.130  21.023    654
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 20.57 %
    Favored  : 75.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.37 (0.23), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.32 (0.18), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS G 374 
 PHE   0.018   0.002   PHE C 378 
 TYR   0.010   0.002   TYR A 310 
 ARG   0.002   0.000   ARG F 379 

*********************** 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
  127 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.613 
Fit side-chains
REVERT: A  344 LEU cc_start: 0.8729 (mt) cc_final: 0.8493 (mp)
REVERT: G  315 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7138 (tt)
REVERT: G  370 LYS cc_start: 0.6652 (mttt) cc_final: 0.6329 (pptt)
  outliers start: 24
  outliers final: 15
  residues processed: 121
  average time/residue: 0.1428
  time to fit residues: 22.7667
Evaluate side-chains
  107 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B 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  314 ASP
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain E residue  285 SER
Chi-restraints excluded: chain E residue  343 LYS
Chi-restraints excluded: chain F residue  356 SER
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain F residue  374 HIS
Chi-restraints excluded: chain G residue  314 ASP
Chi-restraints excluded: chain G residue  315 LEU
Chi-restraints excluded: chain G residue  358 ASP
Chi-restraints excluded: chain G residue  368 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 10 optimal weight:    0.4980
   chunk 7 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 56 optimal weight:    0.7980
   chunk 45 optimal weight:    7.9990
   chunk 12 optimal weight:    4.9990
   chunk 9 optimal weight:   10.0000
   chunk 19 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    1.2586

-------------------------------------------------------------------------------
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 = 0.4956 r_free = 0.4956 target = 0.165772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4634 r_free = 0.4634 target = 0.136487 restraints weight = 12042.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4656 r_free = 0.4656 target = 0.137700 restraints weight = 8499.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4662 r_free = 0.4662 target = 0.138320 restraints weight = 6869.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.4590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6986
moved from start:          0.5548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   4944  Z= 0.276
  Angle     :  0.711   6.020   6606  Z= 0.362
  Chirality :  0.052   0.159    744
  Planarity :  0.004   0.034    846
  Dihedral  :  6.293  22.675    654
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 22.87 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.46 (0.23), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.39 (0.18), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS G 330 
 PHE   0.014   0.002   PHE F 378 
 TYR   0.008   0.002   TYR G 310 
 ARG   0.002   0.001   ARG G 349 

*********************** 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
  119 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.639 
Fit side-chains
REVERT: C  317 LYS cc_start: 0.7318 (mttm) cc_final: 0.6917 (mttt)
REVERT: F  317 LYS cc_start: 0.8068 (mttm) cc_final: 0.7832 (mttm)
REVERT: G  370 LYS cc_start: 0.6661 (mttt) cc_final: 0.6322 (pptt)
  outliers start: 21
  outliers final: 16
  residues processed: 112
  average time/residue: 0.1499
  time to fit residues: 22.0342
Evaluate side-chains
  105 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  358 ASP
Chi-restraints excluded: chain C residue  337 VAL
Chi-restraints excluded: chain C residue  354 ILE
Chi-restraints excluded: chain C residue  358 ASP
Chi-restraints excluded: chain E residue  285 SER
Chi-restraints excluded: chain E residue  343 LYS
Chi-restraints excluded: chain F residue  314 ASP
Chi-restraints excluded: chain F residue  344 LEU
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain G residue  314 ASP
Chi-restraints excluded: chain G residue  358 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 59 optimal weight:    0.0050
   chunk 20 optimal weight:    6.9990
   chunk 42 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.8596

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

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 = 0.168786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4734 r_free = 0.4734 target = 0.142756 restraints weight = 11991.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4694 r_free = 0.4694 target = 0.141850 restraints weight = 8102.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4701 r_free = 0.4701 target = 0.142603 restraints weight = 7224.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.4637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6910
moved from start:          0.5817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4944  Z= 0.209
  Angle     :  0.682   9.120   6606  Z= 0.340
  Chirality :  0.052   0.189    744
  Planarity :  0.004   0.032    846
  Dihedral  :  5.986  21.341    654
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.25 %
    Favored  : 91.75 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 24.11 %
    Favored  : 72.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.47 (0.23), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.40 (0.18), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 362 
 PHE   0.016   0.002   PHE F 378 
 TYR   0.019   0.002   TYR E 310 
 ARG   0.001   0.000   ARG B 379 

*********************** 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
  120 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.474 
Fit side-chains
REVERT: A  310 TYR cc_start: 0.7998 (t80) cc_final: 0.7748 (t80)
REVERT: A  315 LEU cc_start: 0.7619 (mp) cc_final: 0.7371 (tt)
REVERT: A  344 LEU cc_start: 0.8718 (mt) cc_final: 0.8476 (mp)
REVERT: C  317 LYS cc_start: 0.7249 (mttm) cc_final: 0.6891 (mttt)
REVERT: E  372 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7674 (mm-30)
REVERT: F  317 LYS cc_start: 0.7952 (mttm) cc_final: 0.7620 (mttm)
REVERT: G  370 LYS cc_start: 0.6656 (mttt) cc_final: 0.6308 (pptt)
  outliers start: 19
  outliers final: 16
  residues processed: 113
  average time/residue: 0.1608
  time to fit residues: 23.4180
Evaluate side-chains
  110 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  358 ASP
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 F residue  285 SER
Chi-restraints excluded: chain F residue  344 LEU
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain F residue  374 HIS
Chi-restraints excluded: chain G residue  314 ASP
Chi-restraints excluded: chain G residue  368 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 56 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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**
B 329 HIS
** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4938 r_free = 0.4938 target = 0.167247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4609 r_free = 0.4609 target = 0.138026 restraints weight = 11586.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4631 r_free = 0.4631 target = 0.139138 restraints weight = 8571.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.4637 r_free = 0.4637 target = 0.139758 restraints weight = 6996.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.4591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6907
moved from start:          0.6100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4944  Z= 0.213
  Angle     :  0.695   8.094   6606  Z= 0.348
  Chirality :  0.053   0.255    744
  Planarity :  0.004   0.033    846
  Dihedral  :  5.905  21.276    654
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.68 %
    Favored  : 90.32 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 25.35 %
    Favored  : 71.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.43 (0.23), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.37 (0.18), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C 330 
 PHE   0.018   0.002   PHE F 378 
 TYR   0.024   0.002   TYR E 310 
 ARG   0.002   0.000   ARG C 349 

*********************** 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
  117 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.585 
Fit side-chains
REVERT: A  310 TYR cc_start: 0.8036 (t80) cc_final: 0.7773 (t80)
REVERT: A  315 LEU cc_start: 0.7587 (mp) cc_final: 0.7374 (tt)
REVERT: A  344 LEU cc_start: 0.8763 (mt) cc_final: 0.8474 (mp)
REVERT: A  372 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8117 (mm-30)
REVERT: B  315 LEU cc_start: 0.7803 (mp) cc_final: 0.7115 (tp)
REVERT: B  372 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7549 (mm-30)
REVERT: C  317 LYS cc_start: 0.7216 (mttm) cc_final: 0.6853 (mttt)
REVERT: E  285 SER cc_start: 0.7898 (OUTLIER) cc_final: 0.7631 (p)
REVERT: E  315 LEU cc_start: 0.7500 (mp) cc_final: 0.7270 (tt)
REVERT: F  317 LYS cc_start: 0.7963 (mttm) cc_final: 0.7728 (mttm)
REVERT: G  370 LYS cc_start: 0.6698 (mttt) cc_final: 0.6334 (pptt)
  outliers start: 17
  outliers final: 13
  residues processed: 111
  average time/residue: 0.1711
  time to fit residues: 24.0856
Evaluate side-chains
  107 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain A residue  375 LYS
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  344 LEU
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 F residue  285 SER
Chi-restraints excluded: chain F residue  344 LEU
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain F residue  374 HIS
Chi-restraints excluded: chain G residue  314 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 15 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 5 optimal weight:    0.2980
   chunk 56 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0770
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.6340

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4959 r_free = 0.4959 target = 0.170165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4644 r_free = 0.4644 target = 0.140663 restraints weight = 11682.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4666 r_free = 0.4666 target = 0.141884 restraints weight = 8496.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4672 r_free = 0.4672 target = 0.142586 restraints weight = 6979.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.4625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6848
moved from start:          0.6369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4944  Z= 0.187
  Angle     :  0.682   7.391   6606  Z= 0.339
  Chirality :  0.052   0.231    744
  Planarity :  0.004   0.036    846
  Dihedral  :  5.682  20.029    654
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 25.18 %
    Favored  : 71.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.36 (0.24), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.32 (0.18), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 362 
 PHE   0.019   0.002   PHE G 378 
 TYR   0.008   0.001   TYR F 310 
 ARG   0.003   0.000   ARG G 349 

*********************** 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
  120 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.628 
Fit side-chains
REVERT: A  310 TYR cc_start: 0.7954 (t80) cc_final: 0.7719 (t80)
REVERT: A  315 LEU cc_start: 0.7629 (mp) cc_final: 0.7354 (tt)
REVERT: A  344 LEU cc_start: 0.8752 (mt) cc_final: 0.8473 (mp)
REVERT: A  349 ARG cc_start: 0.6875 (mtt-85) cc_final: 0.5514 (ptt-90)
REVERT: B  372 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7450 (mp0)
REVERT: C  317 LYS cc_start: 0.7042 (mttm) cc_final: 0.6694 (mttt)
REVERT: E  349 ARG cc_start: 0.6901 (mtt-85) cc_final: 0.5456 (ptt-90)
REVERT: F  317 LYS cc_start: 0.7850 (mttm) cc_final: 0.7601 (mttm)
REVERT: F  372 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7341 (mp0)
REVERT: G  370 LYS cc_start: 0.6712 (mttt) cc_final: 0.6333 (pptt)
  outliers start: 17
  outliers final: 13
  residues processed: 112
  average time/residue: 0.1731
  time to fit residues: 24.5232
Evaluate side-chains
  112 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  358 ASP
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  285 SER
Chi-restraints excluded: chain F residue  344 LEU
Chi-restraints excluded: chain F residue  358 ASP
Chi-restraints excluded: chain G residue  314 ASP
Chi-restraints excluded: chain G residue  368 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   overall best weight:    1.3784

-------------------------------------------------------------------------------
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**
C 276 GLN
C 329 HIS
** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 329 HIS
G 329 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4883 r_free = 0.4883 target = 0.165262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.136054 restraints weight = 12384.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4562 r_free = 0.4562 target = 0.136906 restraints weight = 9811.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4568 r_free = 0.4568 target = 0.137475 restraints weight = 8204.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.4551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6957
moved from start:          0.6577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4944  Z= 0.287
  Angle     :  0.768  12.158   6606  Z= 0.385
  Chirality :  0.053   0.214    744
  Planarity :  0.004   0.035    846
  Dihedral  :  6.182  22.235    654
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.75 %
    Favored  : 88.25 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 25.71 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.50 (0.23), residues: 630
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.42 (0.18), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 374 
 PHE   0.018   0.002   PHE F 378 
 TYR   0.023   0.003   TYR E 310 
 ARG   0.005   0.001   ARG C 349 

*********************** 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
  122 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.559 
Fit side-chains
REVERT: A  310 TYR cc_start: 0.8027 (t80) cc_final: 0.7564 (t80)
REVERT: A  315 LEU cc_start: 0.7889 (mp) cc_final: 0.7616 (tt)
REVERT: A  372 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7919 (mp0)
REVERT: B  315 LEU cc_start: 0.7868 (mp) cc_final: 0.7475 (tp)
REVERT: B  372 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7295 (mm-30)
REVERT: C  317 LYS cc_start: 0.7552 (mttm) cc_final: 0.7335 (mttt)
REVERT: E  349 ARG cc_start: 0.6960 (mtt-85) cc_final: 0.5514 (ptt-90)
REVERT: F  315 LEU cc_start: 0.7728 (mp) cc_final: 0.7288 (tp)
REVERT: F  317 LYS cc_start: 0.8221 (mttm) cc_final: 0.7925 (mttm)
REVERT: G  370 LYS cc_start: 0.6715 (mttt) cc_final: 0.6326 (pptt)
  outliers start: 18
  outliers final: 16
  residues processed: 116
  average time/residue: 0.2075
  time to fit residues: 30.2595
Evaluate side-chains
  116 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain A residue  375 LYS
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  288 GLN
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain C residue  277 ILE
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 E residue  375 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  277 ILE
Chi-restraints excluded: chain G residue  314 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 11 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   overall best weight:    1.0382

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4897 r_free = 0.4897 target = 0.166942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4574 r_free = 0.4574 target = 0.136061 restraints weight = 12991.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4594 r_free = 0.4594 target = 0.137347 restraints weight = 9814.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4599 r_free = 0.4599 target = 0.138029 restraints weight = 8146.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.4586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6903
moved from start:          0.6758

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= 0.235
  Angle     :  0.770  10.828   6606  Z= 0.374
  Chirality :  0.053   0.204    744
  Planarity :  0.004   0.039    846
  Dihedral  :  5.982  21.587    654
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 26.42 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.48 (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
 HIS   0.002   0.001   HIS E 329 
 PHE   0.018   0.002   PHE F 378 
 TYR   0.016   0.002   TYR E 310 
 ARG   0.004   0.001   ARG G 349 

********************** 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
  119 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.554 
Fit side-chains
REVERT: A  310 TYR cc_start: 0.8042 (t80) cc_final: 0.7628 (t80)
REVERT: A  315 LEU cc_start: 0.8027 (mp) cc_final: 0.7800 (tt)
REVERT: A  349 ARG cc_start: 0.6915 (mtt-85) cc_final: 0.5488 (ptt-90)
REVERT: A  372 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8042 (mp0)
REVERT: B  315 LEU cc_start: 0.7859 (mp) cc_final: 0.7594 (tp)
REVERT: B  372 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7402 (mm-30)
REVERT: E  349 ARG cc_start: 0.6911 (mtt-85) cc_final: 0.5478 (ptt-90)
REVERT: F  315 LEU cc_start: 0.7707 (mp) cc_final: 0.7287 (tp)
REVERT: F  317 LYS cc_start: 0.7916 (mttm) cc_final: 0.7615 (mttm)
REVERT: G  370 LYS cc_start: 0.6722 (mttt) cc_final: 0.6346 (pptt)
  outliers start: 17
  outliers final: 13
  residues processed: 113
  average time/residue: 0.1733
  time to fit residues: 24.7827
Evaluate side-chains
  114 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain C residue  277 ILE
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 E residue  375 LYS
Chi-restraints excluded: chain F residue  285 SER
Chi-restraints excluded: chain F residue  344 LEU
Chi-restraints excluded: chain G residue  277 ILE
Chi-restraints excluded: chain G residue  314 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 8 optimal weight:    7.9990
   chunk 47 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 55 optimal weight:    0.0170
   chunk 43 optimal weight:    0.0370
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.5698

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

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 = 0.171325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4658 r_free = 0.4658 target = 0.141538 restraints weight = 11659.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4684 r_free = 0.4684 target = 0.143200 restraints weight = 7752.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4695 r_free = 0.4695 target = 0.144111 restraints weight = 6101.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.4641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6786
moved from start:          0.6898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4944  Z= 0.195
  Angle     :  0.759  10.080   6606  Z= 0.365
  Chirality :  0.052   0.171    744
  Planarity :  0.004   0.043    846
  Dihedral  :  5.669  20.360    654
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.37 %
    Favored  : 90.63 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 27.13 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.35 (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
 HIS   0.003   0.001   HIS F 362 
 PHE   0.019   0.002   PHE G 378 
 TYR   0.018   0.002   TYR E 310 
 ARG   0.002   0.000   ARG C 349 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1880.01 seconds
wall clock time: 35 minutes 12.44 seconds (2112.44 seconds total)