Starting phenix.real_space_refine
on Wed Mar  4 11:52:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vyf_21458/03_2026/6vyf_21458.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vyf_21458/03_2026/6vyf_21458.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vyf_21458/03_2026/6vyf_21458.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vyf_21458/03_2026/6vyf_21458.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vyf_21458/03_2026/6vyf_21458.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vyf_21458/03_2026/6vyf_21458.map"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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      92      5.16       5
     C    8656      2.51       5
     N    2312      2.21       5
     O    2564      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 68 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13624
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3406
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 432, 3406
          Classifications: {'peptide': 432}
          Link IDs: {'PTRANS': 14, 'TRANS': 417}
          Chain breaks: 3
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 2.24, per 1000 atoms: 0.16
  Number of scatterers: 13624
  At special positions: 0
  Unit cell: (126.145, 100.248, 117.791, 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      92     16.00
     O    2564      8.00
     N    2312      7.00
     C    8656      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.75
  Conformation dependent library (CDL) restraints added in 432.2 milliseconds
  

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3248

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 12 sheets defined
      47.5% alpha, 8.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 38
      removed outlier: 3.563A  pdb=" N   ASN A  38 " --> pdb=" O   ASN A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 68
      removed outlier: 3.885A  pdb=" N   GLU A  49 " --> pdb=" O   SER A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 166
      removed outlier: 4.279A  pdb=" N   ALA A 157 " --> pdb=" O   PHE A 153 " (cutoff:3.500A)
      removed outlier: 4.863A  pdb=" N   GLU A 158 " --> pdb=" O   ASP A 154 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLU A 166 " --> pdb=" O   TYR A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 229
      removed outlier: 3.885A  pdb=" N   ALA A 225 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   PHE A 226 " --> pdb=" O   MET A 222 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL A 227 " --> pdb=" O   ASN A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 252
      removed outlier: 3.635A  pdb=" N   THR A 245 " --> pdb=" O   ASP A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 296
    Processing helix  chain 'A' and resid 303 through 312
      removed outlier: 3.723A  pdb=" N   TRP A 311 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   HIS A 312 " --> pdb=" O   VAL A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 326
      removed outlier: 3.769A  pdb=" N   ILE A 325 " --> pdb=" O   PHE A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 342
    Processing helix  chain 'A' and resid 348 through 352
      removed outlier: 3.617A  pdb=" N   TRP A 351 " --> pdb=" O   GLU A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 366
      removed outlier: 3.647A  pdb=" N   GLY A 361 " --> pdb=" O   ASN A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 383
      removed outlier: 3.788A  pdb=" N   LYS A 380 " --> pdb=" O   ARG A 376 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ASP A 381 " --> pdb=" O   LYS A 377 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ALA A 382 " --> pdb=" O   VAL A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 421
      removed outlier: 3.533A  pdb=" N   SER A 401 " --> pdb=" O   LYS A 397 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ILE A 414 " --> pdb=" O   ALA A 410 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ALA A 416 " --> pdb=" O   ALA A 412 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ILE A 417 " --> pdb=" O   ALA A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 426
      removed outlier: 4.035A  pdb=" N   GLU A 425 " --> pdb=" O   LYS A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 456
      removed outlier: 3.537A  pdb=" N   VAL A 454 " --> pdb=" O   GLU A 450 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU A 456 " --> pdb=" O   LEU A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 461
      No H-bonds generated for 'chain 'A' and resid 459 through 461'
    Processing helix  chain 'A' and resid 470 through 486
      removed outlier: 4.601A  pdb=" N   ALA A 476 " --> pdb=" O   SER A 472 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   SER A 484 " --> pdb=" O   ALA A 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 38
      removed outlier: 3.563A  pdb=" N   ASN B  38 " --> pdb=" O   ASN B  34 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 68
      removed outlier: 3.885A  pdb=" N   GLU B  49 " --> pdb=" O   SER B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 166
      removed outlier: 4.278A  pdb=" N   ALA B 157 " --> pdb=" O   PHE B 153 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   GLU B 158 " --> pdb=" O   ASP B 154 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLU B 166 " --> pdb=" O   TYR B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 229
      removed outlier: 3.885A  pdb=" N   ALA B 225 " --> pdb=" O   LEU B 221 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   PHE B 226 " --> pdb=" O   MET B 222 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL B 227 " --> pdb=" O   ASN B 223 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 240 through 252
      removed outlier: 3.635A  pdb=" N   THR B 245 " --> pdb=" O   ASP B 241 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 296
    Processing helix  chain 'B' and resid 303 through 312
      removed outlier: 3.722A  pdb=" N   TRP B 311 " --> pdb=" O   LEU B 307 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   HIS B 312 " --> pdb=" O   VAL B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 321 through 326
      removed outlier: 3.769A  pdb=" N   ILE B 325 " --> pdb=" O   PHE B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 342
    Processing helix  chain 'B' and resid 348 through 352
      removed outlier: 3.617A  pdb=" N   TRP B 351 " --> pdb=" O   GLU B 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 366
      removed outlier: 3.647A  pdb=" N   GLY B 361 " --> pdb=" O   ASN B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 383
      removed outlier: 3.788A  pdb=" N   LYS B 380 " --> pdb=" O   ARG B 376 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ASP B 381 " --> pdb=" O   LYS B 377 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ALA B 382 " --> pdb=" O   VAL B 378 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 421
      removed outlier: 3.533A  pdb=" N   SER B 401 " --> pdb=" O   LYS B 397 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ILE B 414 " --> pdb=" O   ALA B 410 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ALA B 416 " --> pdb=" O   ALA B 412 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ILE B 417 " --> pdb=" O   ALA B 413 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 426
      removed outlier: 4.035A  pdb=" N   GLU B 425 " --> pdb=" O   LYS B 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 456
      removed outlier: 3.538A  pdb=" N   VAL B 454 " --> pdb=" O   GLU B 450 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LEU B 456 " --> pdb=" O   LEU B 452 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 461
      No H-bonds generated for 'chain 'B' and resid 459 through 461'
    Processing helix  chain 'B' and resid 470 through 486
      removed outlier: 4.601A  pdb=" N   ALA B 476 " --> pdb=" O   SER B 472 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   SER B 484 " --> pdb=" O   ALA B 480 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 38
      removed outlier: 3.563A  pdb=" N   ASN C  38 " --> pdb=" O   ASN C  34 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 68
      removed outlier: 3.885A  pdb=" N   GLU C  49 " --> pdb=" O   SER C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 153 through 166
      removed outlier: 4.279A  pdb=" N   ALA C 157 " --> pdb=" O   PHE C 153 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   GLU C 158 " --> pdb=" O   ASP C 154 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLU C 166 " --> pdb=" O   TYR C 162 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 219 through 229
      removed outlier: 3.885A  pdb=" N   ALA C 225 " --> pdb=" O   LEU C 221 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   PHE C 226 " --> pdb=" O   MET C 222 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL C 227 " --> pdb=" O   ASN C 223 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 240 through 252
      removed outlier: 3.635A  pdb=" N   THR C 245 " --> pdb=" O   ASP C 241 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 292 through 296
    Processing helix  chain 'C' and resid 303 through 312
      removed outlier: 3.723A  pdb=" N   TRP C 311 " --> pdb=" O   LEU C 307 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   HIS C 312 " --> pdb=" O   VAL C 308 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 321 through 326
      removed outlier: 3.768A  pdb=" N   ILE C 325 " --> pdb=" O   PHE C 321 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 329 through 342
    Processing helix  chain 'C' and resid 348 through 352
      removed outlier: 3.617A  pdb=" N   TRP C 351 " --> pdb=" O   GLU C 348 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 357 through 366
      removed outlier: 3.647A  pdb=" N   GLY C 361 " --> pdb=" O   ASN C 357 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 376 through 383
      removed outlier: 3.787A  pdb=" N   LYS C 380 " --> pdb=" O   ARG C 376 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ASP C 381 " --> pdb=" O   LYS C 377 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ALA C 382 " --> pdb=" O   VAL C 378 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 388 through 421
      removed outlier: 3.533A  pdb=" N   SER C 401 " --> pdb=" O   LYS C 397 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ILE C 414 " --> pdb=" O   ALA C 410 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA C 416 " --> pdb=" O   ALA C 412 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ILE C 417 " --> pdb=" O   ALA C 413 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 422 through 426
      removed outlier: 4.036A  pdb=" N   GLU C 425 " --> pdb=" O   LYS C 422 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 444 through 456
      removed outlier: 3.537A  pdb=" N   VAL C 454 " --> pdb=" O   GLU C 450 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU C 456 " --> pdb=" O   LEU C 452 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 459 through 461
      No H-bonds generated for 'chain 'C' and resid 459 through 461'
    Processing helix  chain 'C' and resid 470 through 486
      removed outlier: 4.601A  pdb=" N   ALA C 476 " --> pdb=" O   SER C 472 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   SER C 484 " --> pdb=" O   ALA C 480 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 26 through 38
      removed outlier: 3.562A  pdb=" N   ASN D  38 " --> pdb=" O   ASN D  34 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 68
      removed outlier: 3.885A  pdb=" N   GLU D  49 " --> pdb=" O   SER D  45 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 153 through 166
      removed outlier: 4.278A  pdb=" N   ALA D 157 " --> pdb=" O   PHE D 153 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   GLU D 158 " --> pdb=" O   ASP D 154 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLU D 166 " --> pdb=" O   TYR D 162 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 219 through 229
      removed outlier: 3.884A  pdb=" N   ALA D 225 " --> pdb=" O   LEU D 221 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   PHE D 226 " --> pdb=" O   MET D 222 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL D 227 " --> pdb=" O   ASN D 223 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 240 through 252
      removed outlier: 3.635A  pdb=" N   THR D 245 " --> pdb=" O   ASP D 241 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 292 through 296
    Processing helix  chain 'D' and resid 303 through 312
      removed outlier: 3.723A  pdb=" N   TRP D 311 " --> pdb=" O   LEU D 307 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   HIS D 312 " --> pdb=" O   VAL D 308 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 321 through 326
      removed outlier: 3.769A  pdb=" N   ILE D 325 " --> pdb=" O   PHE D 321 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 329 through 342
    Processing helix  chain 'D' and resid 348 through 352
      removed outlier: 3.617A  pdb=" N   TRP D 351 " --> pdb=" O   GLU D 348 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 357 through 366
      removed outlier: 3.647A  pdb=" N   GLY D 361 " --> pdb=" O   ASN D 357 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 376 through 383
      removed outlier: 3.787A  pdb=" N   LYS D 380 " --> pdb=" O   ARG D 376 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ASP D 381 " --> pdb=" O   LYS D 377 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ALA D 382 " --> pdb=" O   VAL D 378 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 388 through 421
      removed outlier: 3.533A  pdb=" N   SER D 401 " --> pdb=" O   LYS D 397 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ILE D 414 " --> pdb=" O   ALA D 410 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA D 416 " --> pdb=" O   ALA D 412 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ILE D 417 " --> pdb=" O   ALA D 413 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 422 through 426
      removed outlier: 4.036A  pdb=" N   GLU D 425 " --> pdb=" O   LYS D 422 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 444 through 456
      removed outlier: 3.538A  pdb=" N   VAL D 454 " --> pdb=" O   GLU D 450 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU D 456 " --> pdb=" O   LEU D 452 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 459 through 461
      No H-bonds generated for 'chain 'D' and resid 459 through 461'
    Processing helix  chain 'D' and resid 470 through 486
      removed outlier: 4.600A  pdb=" N   ALA D 476 " --> pdb=" O   SER D 472 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   SER D 484 " --> pdb=" O   ALA D 480 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 83
      removed outlier: 3.968A  pdb=" N   GLY A 272 " --> pdb=" O   ILE A 291 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   TYR A 261 " --> pdb=" O   TYR A 275 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   CYS A 260 " --> pdb=" O   SER A 430 " (cutoff:3.500A)
      removed outlier: 7.475A  pdb=" N   GLY A 432 " --> pdb=" O   CYS A 260 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   ILE A 262 " --> pdb=" O   GLY A 432 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   ASP A 434 " --> pdb=" O   ILE A 262 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   ILE A 264 " --> pdb=" O   ASP A 434 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   PHE A 429 " --> pdb=" O   ILE A 464 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 101
    Processing sheet with id=AA3, first strand: chain 'A' and resid 177 through 178
    Processing sheet with id=AA4, first strand: chain 'B' and resid 82 through 83
      removed outlier: 3.968A  pdb=" N   GLY B 272 " --> pdb=" O   ILE B 291 " (cutoff:3.500A)
      removed outlier: 7.282A  pdb=" N   TYR B 261 " --> pdb=" O   TYR B 275 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   CYS B 260 " --> pdb=" O   SER B 430 " (cutoff:3.500A)
      removed outlier: 7.475A  pdb=" N   GLY B 432 " --> pdb=" O   CYS B 260 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   ILE B 262 " --> pdb=" O   GLY B 432 " (cutoff:3.500A)
      removed outlier: 7.776A  pdb=" N   ASP B 434 " --> pdb=" O   ILE B 262 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   ILE B 264 " --> pdb=" O   ASP B 434 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   PHE B 429 " --> pdb=" O   ILE B 464 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 101
    Processing sheet with id=AA6, first strand: chain 'B' and resid 177 through 178
    Processing sheet with id=AA7, first strand: chain 'C' and resid 82 through 83
      removed outlier: 3.967A  pdb=" N   GLY C 272 " --> pdb=" O   ILE C 291 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   TYR C 261 " --> pdb=" O   TYR C 275 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   CYS C 260 " --> pdb=" O   SER C 430 " (cutoff:3.500A)
      removed outlier: 7.475A  pdb=" N   GLY C 432 " --> pdb=" O   CYS C 260 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   ILE C 262 " --> pdb=" O   GLY C 432 " (cutoff:3.500A)
      removed outlier: 7.776A  pdb=" N   ASP C 434 " --> pdb=" O   ILE C 262 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   ILE C 264 " --> pdb=" O   ASP C 434 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   PHE C 429 " --> pdb=" O   ILE C 464 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 101
    Processing sheet with id=AA9, first strand: chain 'C' and resid 177 through 178
    Processing sheet with id=AB1, first strand: chain 'D' and resid 82 through 83
      removed outlier: 3.968A  pdb=" N   GLY D 272 " --> pdb=" O   ILE D 291 " (cutoff:3.500A)
      removed outlier: 7.282A  pdb=" N   TYR D 261 " --> pdb=" O   TYR D 275 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   CYS D 260 " --> pdb=" O   SER D 430 " (cutoff:3.500A)
      removed outlier: 7.475A  pdb=" N   GLY D 432 " --> pdb=" O   CYS D 260 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   ILE D 262 " --> pdb=" O   GLY D 432 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   ASP D 434 " --> pdb=" O   ILE D 262 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   ILE D 264 " --> pdb=" O   ASP D 434 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   PHE D 429 " --> pdb=" O   ILE D 464 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 96 through 101
    Processing sheet with id=AB3, first strand: chain 'D' and resid 177 through 178

    536 hydrogen bonds defined for protein.
    1536 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: 1.74

  Time building geometry restraints manager: 1.04 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4424
        1.34 -     1.46: 3140
        1.46 -     1.58: 6204
        1.58 -     1.70: 0
        1.70 -     1.82: 128
  Bond restraints: 13896
  Sorted by residual:
  bond pdb=" C   HIS A  68 "
       pdb=" N   PRO A  69 "
    ideal  model  delta    sigma   weight residual
    1.334  1.321  0.012 8.40e-03 1.42e+04 2.11e+00
  bond pdb=" C   HIS C  68 "
       pdb=" N   PRO C  69 "
    ideal  model  delta    sigma   weight residual
    1.334  1.322  0.012 8.40e-03 1.42e+04 1.93e+00
  bond pdb=" C   HIS B  68 "
       pdb=" N   PRO B  69 "
    ideal  model  delta    sigma   weight residual
    1.334  1.322  0.012 8.40e-03 1.42e+04 1.90e+00
  bond pdb=" C   HIS D  68 "
       pdb=" N   PRO D  69 "
    ideal  model  delta    sigma   weight residual
    1.334  1.322  0.011 8.40e-03 1.42e+04 1.86e+00
  bond pdb=" CA  GLN B 319 "
       pdb=" C   GLN B 319 "
    ideal  model  delta    sigma   weight residual
    1.530  1.517  0.013 1.17e-02 7.31e+03 1.29e+00
  ... (remaining 13891 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 18424
        2.10 -     4.20: 296
        4.20 -     6.30: 20
        6.30 -     8.40: 0
        8.40 -    10.50: 4
  Bond angle restraints: 18744
  Sorted by residual:
  angle pdb=" CB  MET B 222 "
        pdb=" CG  MET B 222 "
        pdb=" SD  MET B 222 "
      ideal   model   delta    sigma   weight residual
     112.70  123.20  -10.50 3.00e+00 1.11e-01 1.22e+01
  angle pdb=" CB  MET C 222 "
        pdb=" CG  MET C 222 "
        pdb=" SD  MET C 222 "
      ideal   model   delta    sigma   weight residual
     112.70  123.17  -10.47 3.00e+00 1.11e-01 1.22e+01
  angle pdb=" CB  MET A 222 "
        pdb=" CG  MET A 222 "
        pdb=" SD  MET A 222 "
      ideal   model   delta    sigma   weight residual
     112.70  123.16  -10.46 3.00e+00 1.11e-01 1.22e+01
  angle pdb=" CB  MET D 222 "
        pdb=" CG  MET D 222 "
        pdb=" SD  MET D 222 "
      ideal   model   delta    sigma   weight residual
     112.70  123.16  -10.46 3.00e+00 1.11e-01 1.22e+01
  angle pdb=" N   ASN C 315 "
        pdb=" CA  ASN C 315 "
        pdb=" C   ASN C 315 "
      ideal   model   delta    sigma   weight residual
     110.61  106.52    4.09 1.25e+00 6.40e-01 1.07e+01
  ... (remaining 18739 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.77: 7116
       13.77 -    27.53: 900
       27.53 -    41.30: 288
       41.30 -    55.06: 52
       55.06 -    68.83: 20
  Dihedral angle restraints: 8376
    sinusoidal: 3352
      harmonic: 5024
  Sorted by residual:
  dihedral pdb=" CA  PHE B 108 "
           pdb=" C   PHE B 108 "
           pdb=" N   ARG B 109 "
           pdb=" CA  ARG B 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -146.55  -33.45     0      5.00e+00 4.00e-02 4.47e+01
  dihedral pdb=" CA  PHE C 108 "
           pdb=" C   PHE C 108 "
           pdb=" N   ARG C 109 "
           pdb=" CA  ARG C 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -146.55  -33.45     0      5.00e+00 4.00e-02 4.47e+01
  dihedral pdb=" CA  PHE A 108 "
           pdb=" C   PHE A 108 "
           pdb=" N   ARG A 109 "
           pdb=" CA  ARG A 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -146.58  -33.42     0      5.00e+00 4.00e-02 4.47e+01
  ... (remaining 8373 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1282
       0.035 -    0.070: 563
       0.070 -    0.105: 144
       0.105 -    0.141: 67
       0.141 -    0.176: 4
  Chirality restraints: 2060
  Sorted by residual:
  chirality pdb=" CA  ILE B 291 "
            pdb=" N   ILE B 291 "
            pdb=" C   ILE B 291 "
            pdb=" CB  ILE B 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.73e-01
  chirality pdb=" CA  ILE C 291 "
            pdb=" N   ILE C 291 "
            pdb=" C   ILE C 291 "
            pdb=" CB  ILE C 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.38e-01
  chirality pdb=" CA  ILE D 291 "
            pdb=" N   ILE D 291 "
            pdb=" C   ILE D 291 "
            pdb=" CB  ILE D 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.37e-01
  ... (remaining 2057 not shown)

  Planarity restraints: 2396
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 184 "   -0.026 5.00e-02 4.00e+02   3.95e-02 2.50e+00
        pdb=" N   PRO C 185 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO C 185 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO C 185 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 184 "   -0.026 5.00e-02 4.00e+02   3.93e-02 2.48e+00
        pdb=" N   PRO A 185 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 185 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 185 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE D 184 "    0.026 5.00e-02 4.00e+02   3.91e-02 2.45e+00
        pdb=" N   PRO D 185 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO D 185 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D 185 "    0.022 5.00e-02 4.00e+02
  ... (remaining 2393 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 2386
        2.76 -     3.29: 12880
        3.29 -     3.83: 20541
        3.83 -     4.36: 25628
        4.36 -     4.90: 43787
  Nonbonded interactions: 105222
  Sorted by model distance:
  nonbonded pdb=" O   GLU A 322 "
            pdb=" OG  SER A 326 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" O   GLU C 322 "
            pdb=" OG  SER C 326 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" O   GLU D 322 "
            pdb=" OG  SER D 326 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" O   GLU B 322 "
            pdb=" OG  SER B 326 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" O   PRO B  74 "
            pdb=" ND1 HIS B  75 "
     model   vdw
     2.226 3.120
  ... (remaining 105217 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.010
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.460
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
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      :  0.005   0.033  13896  Z= 0.243
  Angle     :  0.678  10.495  18744  Z= 0.404
  Chirality :  0.044   0.176   2060
  Planarity :  0.004   0.040   2396
  Dihedral  : 13.956  68.828   5128
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  7.46 %
    Favored  : 92.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.53 (0.18), residues: 1696
  helix: -2.08 (0.16), residues: 728
  sheet: -0.89 (0.33), residues: 228
  loop : -3.04 (0.19), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 123 
 TYR   0.016   0.002   TYR D 162 
 PHE   0.016   0.001   PHE B 108 
 TRP   0.008   0.001   TRP B 311 
 HIS   0.006   0.002   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00549 (13896)
  covalent geometry    : angle       0.67764 (18744)
  hydrogen bonds       : bond        0.20910 (  536)
  hydrogen bonds       : angle       7.63680 ( 1536)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 193
  time to evaluate  : 0.578 
Fit side-chains
REVERT: A  124 ASP cc_start: 0.7549 (p0) cc_final: 0.7334 (p0)
REVERT: A  180 PHE cc_start: 0.8068 (t80) cc_final: 0.7790 (t80)
REVERT: A  222 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.7177 (tpp)
REVERT: A  318 ARG cc_start: 0.8046 (mmm-85) cc_final: 0.7821 (mtp85)
REVERT: B   25 ILE cc_start: 0.7691 (mm) cc_final: 0.7469 (mm)
REVERT: B  180 PHE cc_start: 0.8103 (t80) cc_final: 0.7757 (t80)
REVERT: B  222 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.6976 (tpp)
REVERT: B  310 ASP cc_start: 0.8513 (t70) cc_final: 0.8177 (t0)
REVERT: C  180 PHE cc_start: 0.8109 (t80) cc_final: 0.7861 (t80)
REVERT: C  222 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.7189 (tpp)
REVERT: D  180 PHE cc_start: 0.8111 (t80) cc_final: 0.7777 (t80)
REVERT: D  222 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7182 (tpp)
REVERT: D  318 ARG cc_start: 0.8008 (mmm-85) cc_final: 0.7780 (mtp85)
  outliers start: 4
  outliers final: 0
  residues processed: 193
  average time/residue: 0.1434
  time to fit residues: 38.1697
Evaluate side-chains
  143 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 139
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 MET
Chi-restraints excluded: chain B residue  222 MET
Chi-restraints excluded: chain C residue  222 MET
Chi-restraints excluded: chain D residue  222 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:   20.0000
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    3.9990
   chunk 149 optimal weight:    3.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 366 ASN
A 449 GLN
A 485 GLN
B 340 ASN
B 366 ASN
B 485 GLN
C 366 ASN
C 449 GLN
C 485 GLN
D 340 ASN
D 366 ASN
D 449 GLN
D 485 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.149564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.109235 restraints weight = 19098.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 2.01
r_work: 0.3088 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2954 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.1171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021  13896  Z= 0.154
  Angle     :  0.542   6.015  18744  Z= 0.296
  Chirality :  0.043   0.152   2060
  Planarity :  0.004   0.037   2396
  Dihedral  :  5.707  46.847   1864
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 12.10 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.17 (0.20), residues: 1696
  helix: -0.53 (0.19), residues: 748
  sheet: -0.49 (0.34), residues: 228
  loop : -2.77 (0.20), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 216 
 TYR   0.013   0.002   TYR B 162 
 PHE   0.015   0.001   PHE B 108 
 TRP   0.009   0.001   TRP B 311 
 HIS   0.007   0.002   HIS C  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (13896)
  covalent geometry    : angle       0.54188 (18744)
  hydrogen bonds       : bond        0.05744 (  536)
  hydrogen bonds       : angle       4.62991 ( 1536)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 158
  time to evaluate  : 0.518 
Fit side-chains
REVERT: A  180 PHE cc_start: 0.8227 (t80) cc_final: 0.7876 (t80)
REVERT: B   25 ILE cc_start: 0.7900 (mm) cc_final: 0.7632 (mm)
REVERT: B  180 PHE cc_start: 0.8328 (t80) cc_final: 0.7924 (t80)
REVERT: B  221 LEU cc_start: 0.7187 (mt) cc_final: 0.6951 (mt)
REVERT: C  180 PHE cc_start: 0.8261 (t80) cc_final: 0.7965 (t80)
REVERT: D  124 ASP cc_start: 0.7749 (p0) cc_final: 0.7544 (p0)
REVERT: D  180 PHE cc_start: 0.8243 (t80) cc_final: 0.7908 (t80)
  outliers start: 23
  outliers final: 18
  residues processed: 168
  average time/residue: 0.1390
  time to fit residues: 32.9237
Evaluate side-chains
  152 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  309 MET
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  309 MET
Chi-restraints excluded: chain B residue  434 ASP
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  160 ILE
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  309 MET
Chi-restraints excluded: chain C residue  434 ASP
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue  127 THR
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  309 MET
Chi-restraints excluded: chain D residue  434 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 119 optimal weight:    6.9990
   chunk 29 optimal weight:    8.9990
   chunk 171 optimal weight:    8.9990
   chunk 137 optimal weight:    8.9990
   chunk 78 optimal weight:    0.9990
   chunk 117 optimal weight:    9.9990
   chunk 91 optimal weight:    0.9980
   chunk 37 optimal weight:    6.9990
   chunk 46 optimal weight:    4.9990
   chunk 42 optimal weight:    9.9990
   chunk 64 optimal weight:    7.9990
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 449 GLN
B 252 GLN
C 449 GLN
D 449 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.147073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.112396 restraints weight = 19555.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 2.14
r_work: 0.2989 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2857 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8699
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.032  13896  Z= 0.233
  Angle     :  0.601   6.125  18744  Z= 0.323
  Chirality :  0.046   0.162   2060
  Planarity :  0.004   0.033   2396
  Dihedral  :  5.462  33.802   1852
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 13.10 %
    Favored  : 83.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.85 (0.20), residues: 1696
  helix: -0.16 (0.20), residues: 744
  sheet: -0.39 (0.35), residues: 228
  loop : -2.70 (0.20), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 159 
 TYR   0.015   0.002   TYR C 162 
 PHE   0.016   0.002   PHE B 108 
 TRP   0.008   0.001   TRP B 311 
 HIS   0.010   0.002   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00567 (13896)
  covalent geometry    : angle       0.60098 (18744)
  hydrogen bonds       : bond        0.06476 (  536)
  hydrogen bonds       : angle       4.59341 ( 1536)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 139
  time to evaluate  : 0.651 
Fit side-chains
REVERT: A   75 HIS cc_start: 0.8202 (OUTLIER) cc_final: 0.7341 (p-80)
REVERT: A  180 PHE cc_start: 0.8259 (t80) cc_final: 0.7852 (t80)
REVERT: B   25 ILE cc_start: 0.7819 (mm) cc_final: 0.7513 (mm)
REVERT: B   75 HIS cc_start: 0.8230 (OUTLIER) cc_final: 0.7288 (p-80)
REVERT: B  180 PHE cc_start: 0.8322 (t80) cc_final: 0.7982 (t80)
REVERT: B  318 ARG cc_start: 0.8582 (mmm-85) cc_final: 0.8282 (mtp85)
REVERT: C   75 HIS cc_start: 0.8204 (OUTLIER) cc_final: 0.7344 (p-80)
REVERT: C  180 PHE cc_start: 0.8283 (t80) cc_final: 0.7869 (t80)
REVERT: D   75 HIS cc_start: 0.8209 (OUTLIER) cc_final: 0.7348 (p-80)
REVERT: D  180 PHE cc_start: 0.8258 (t80) cc_final: 0.7842 (t80)
REVERT: D  318 ARG cc_start: 0.8563 (mmm-85) cc_final: 0.8297 (mtp85)
  outliers start: 47
  outliers final: 37
  residues processed: 173
  average time/residue: 0.1287
  time to fit residues: 32.1677
Evaluate side-chains
  176 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 135
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue   75 HIS
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  309 MET
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   75 HIS
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  309 MET
Chi-restraints excluded: chain B residue  434 ASP
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   75 HIS
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  160 ILE
Chi-restraints excluded: chain C residue  162 TYR
Chi-restraints excluded: chain C residue  190 SER
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  265 ILE
Chi-restraints excluded: chain C residue  309 MET
Chi-restraints excluded: chain C residue  434 ASP
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue   75 HIS
Chi-restraints excluded: chain D residue  127 THR
Chi-restraints excluded: chain D residue  162 TYR
Chi-restraints excluded: chain D residue  190 SER
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  265 ILE
Chi-restraints excluded: chain D residue  309 MET
Chi-restraints excluded: chain D residue  434 ASP
Chi-restraints excluded: chain D residue  439 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 157 optimal weight:    0.9980
   chunk 100 optimal weight:    8.9990
   chunk 23 optimal weight:    0.7980
   chunk 41 optimal weight:    8.9990
   chunk 96 optimal weight:   20.0000
   chunk 120 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 67 optimal weight:    6.9990
   chunk 25 optimal weight:    0.8980
   chunk 161 optimal weight:    2.9990
   chunk 136 optimal weight:    0.9980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A 340 ASN
C 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.152652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.113112 restraints weight = 19426.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 1.95
r_work: 0.3093 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start:          0.1779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  13896  Z= 0.106
  Angle     :  0.479   5.510  18744  Z= 0.262
  Chirality :  0.042   0.154   2060
  Planarity :  0.003   0.030   2396
  Dihedral  :  4.725  27.968   1852
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 15.73 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.37 (0.20), residues: 1696
  helix:  0.57 (0.20), residues: 728
  sheet: -0.26 (0.37), residues: 192
  loop : -2.64 (0.19), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 159 
 TYR   0.011   0.001   TYR B 162 
 PHE   0.015   0.001   PHE B 108 
 TRP   0.007   0.001   TRP C 311 
 HIS   0.007   0.002   HIS C  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (13896)
  covalent geometry    : angle       0.47867 (18744)
  hydrogen bonds       : bond        0.04333 (  536)
  hydrogen bonds       : angle       4.03362 ( 1536)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 158
  time to evaluate  : 0.475 
Fit side-chains
REVERT: A  180 PHE cc_start: 0.8208 (t80) cc_final: 0.7842 (t80)
REVERT: B   25 ILE cc_start: 0.7892 (mm) cc_final: 0.7585 (mm)
REVERT: B   75 HIS cc_start: 0.7911 (OUTLIER) cc_final: 0.7318 (p-80)
REVERT: B  180 PHE cc_start: 0.8274 (t80) cc_final: 0.7785 (t80)
REVERT: B  434 ASP cc_start: 0.8850 (OUTLIER) cc_final: 0.7962 (t0)
REVERT: C  180 PHE cc_start: 0.8254 (t80) cc_final: 0.7881 (t80)
REVERT: C  434 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.7976 (t0)
REVERT: D  180 PHE cc_start: 0.8220 (t80) cc_final: 0.7841 (t80)
  outliers start: 39
  outliers final: 18
  residues processed: 177
  average time/residue: 0.1224
  time to fit residues: 31.1173
Evaluate side-chains
  159 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 138
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain B residue   75 HIS
Chi-restraints excluded: chain B residue  162 TYR
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  324 MET
Chi-restraints excluded: chain B residue  434 ASP
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  265 ILE
Chi-restraints excluded: chain C residue  299 ASP
Chi-restraints excluded: chain C residue  324 MET
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  434 ASP
Chi-restraints excluded: chain C residue  439 VAL
Chi-restraints excluded: chain D residue  162 TYR
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  299 ASP
Chi-restraints excluded: chain D residue  324 MET
Chi-restraints excluded: chain D residue  433 VAL
Chi-restraints excluded: chain D residue  434 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 119 optimal weight:    5.9990
   chunk 123 optimal weight:    9.9990
   chunk 143 optimal weight:    0.0050
   chunk 12 optimal weight:    1.9990
   chunk 95 optimal weight:    9.9990
   chunk 1 optimal weight:    2.9990
   chunk 56 optimal weight:    9.9990
   chunk 103 optimal weight:    6.9990
   chunk 60 optimal weight:    7.9990
   chunk 51 optimal weight:    8.9990
   overall best weight:    3.6002

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

Flipped N/Q/H residues before XYZ refinement:
** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 449 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.148118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.107831 restraints weight = 19464.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 2.00
r_work: 0.3012 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2879 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8709
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028  13896  Z= 0.200
  Angle     :  0.556   5.954  18744  Z= 0.300
  Chirality :  0.045   0.185   2060
  Planarity :  0.004   0.030   2396
  Dihedral  :  5.088  30.307   1852
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.25 %
    Favored  : 91.75 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 15.05 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.38 (0.20), residues: 1696
  helix:  0.39 (0.20), residues: 748
  sheet: -0.32 (0.35), residues: 228
  loop : -2.60 (0.20), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 159 
 TYR   0.013   0.002   TYR D 162 
 PHE   0.015   0.001   PHE B 108 
 TRP   0.008   0.001   TRP C 311 
 HIS   0.014   0.002   HIS C  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 (13896)
  covalent geometry    : angle       0.55608 (18744)
  hydrogen bonds       : bond        0.05746 (  536)
  hydrogen bonds       : angle       4.26960 ( 1536)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 140
  time to evaluate  : 0.525 
Fit side-chains
REVERT: A  180 PHE cc_start: 0.8248 (t80) cc_final: 0.7878 (t80)
REVERT: B   25 ILE cc_start: 0.7857 (mm) cc_final: 0.7511 (mm)
REVERT: B   75 HIS cc_start: 0.8132 (OUTLIER) cc_final: 0.7340 (p-80)
REVERT: B  180 PHE cc_start: 0.8310 (t80) cc_final: 0.7900 (t80)
REVERT: B  318 ARG cc_start: 0.8627 (mmm-85) cc_final: 0.8335 (mtp85)
REVERT: B  338 MET cc_start: 0.9268 (mmm) cc_final: 0.8845 (mmt)
REVERT: B  434 ASP cc_start: 0.8957 (OUTLIER) cc_final: 0.8045 (t70)
REVERT: C  180 PHE cc_start: 0.8261 (t80) cc_final: 0.7885 (t80)
REVERT: C  338 MET cc_start: 0.9264 (mmm) cc_final: 0.8792 (mmp)
REVERT: C  434 ASP cc_start: 0.8898 (OUTLIER) cc_final: 0.7958 (t0)
REVERT: D  180 PHE cc_start: 0.8259 (t80) cc_final: 0.7884 (t80)
REVERT: D  338 MET cc_start: 0.9290 (mmm) cc_final: 0.8832 (mmp)
REVERT: D  434 ASP cc_start: 0.8894 (OUTLIER) cc_final: 0.7967 (t0)
  outliers start: 50
  outliers final: 38
  residues processed: 177
  average time/residue: 0.1209
  time to fit residues: 31.0885
Evaluate side-chains
  176 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 134
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  309 MET
Chi-restraints excluded: chain A residue  340 ASN
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  434 ASP
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   75 HIS
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  162 TYR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  309 MET
Chi-restraints excluded: chain B residue  385 MET
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  434 ASP
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  162 TYR
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  265 ILE
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  434 ASP
Chi-restraints excluded: chain C residue  439 VAL
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue  127 THR
Chi-restraints excluded: chain D residue  162 TYR
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  265 ILE
Chi-restraints excluded: chain D residue  309 MET
Chi-restraints excluded: chain D residue  433 VAL
Chi-restraints excluded: chain D residue  434 ASP
Chi-restraints excluded: chain D residue  439 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 147 optimal weight:    0.1980
   chunk 104 optimal weight:    6.9990
   chunk 150 optimal weight:   10.0000
   chunk 166 optimal weight:    7.9990
   chunk 7 optimal weight:    7.9990
   chunk 75 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9990
   chunk 105 optimal weight:    5.9990
   chunk 146 optimal weight:    3.9990
   chunk 96 optimal weight:   20.0000
   chunk 136 optimal weight:    7.9990
   overall best weight:    2.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 252 GLN
** D 252 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 = 0.3775 r_free = 0.3775 target = 0.150317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.110049 restraints weight = 19255.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 2.01
r_work: 0.3097 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2964 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8703
moved from start:          0.1837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  13896  Z= 0.145
  Angle     :  0.511   5.299  18744  Z= 0.278
  Chirality :  0.043   0.186   2060
  Planarity :  0.003   0.030   2396
  Dihedral  :  4.909  29.278   1852
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 15.59 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.28 (0.20), residues: 1696
  helix:  0.54 (0.20), residues: 748
  sheet: -0.24 (0.38), residues: 192
  loop : -2.54 (0.19), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 159 
 TYR   0.012   0.001   TYR B 162 
 PHE   0.014   0.001   PHE B 108 
 TRP   0.007   0.001   TRP C 311 
 HIS   0.012   0.002   HIS C  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (13896)
  covalent geometry    : angle       0.51069 (18744)
  hydrogen bonds       : bond        0.05086 (  536)
  hydrogen bonds       : angle       4.11708 ( 1536)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 137
  time to evaluate  : 0.401 
Fit side-chains
REVERT: A  180 PHE cc_start: 0.8236 (t80) cc_final: 0.7948 (t80)
REVERT: B   25 ILE cc_start: 0.7880 (mm) cc_final: 0.7591 (mm)
REVERT: B   75 HIS cc_start: 0.8056 (OUTLIER) cc_final: 0.7379 (p-80)
REVERT: B  180 PHE cc_start: 0.8312 (t80) cc_final: 0.7897 (t80)
REVERT: B  338 MET cc_start: 0.9183 (mmm) cc_final: 0.8773 (mmt)
REVERT: B  434 ASP cc_start: 0.8858 (OUTLIER) cc_final: 0.7965 (t70)
REVERT: C  180 PHE cc_start: 0.8240 (t80) cc_final: 0.7884 (t80)
REVERT: C  434 ASP cc_start: 0.8852 (OUTLIER) cc_final: 0.7967 (t70)
REVERT: D  180 PHE cc_start: 0.8241 (t80) cc_final: 0.7888 (t80)
REVERT: D  434 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.7989 (t70)
  outliers start: 56
  outliers final: 42
  residues processed: 181
  average time/residue: 0.1159
  time to fit residues: 30.6604
Evaluate side-chains
  179 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 133
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  324 MET
Chi-restraints excluded: chain A residue  340 ASN
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  434 ASP
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   75 HIS
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  162 TYR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  324 MET
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  434 ASP
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain C residue   18 THR
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  162 TYR
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  265 ILE
Chi-restraints excluded: chain C residue  324 MET
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  434 ASP
Chi-restraints excluded: chain C residue  439 VAL
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue  127 THR
Chi-restraints excluded: chain D residue  162 TYR
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  265 ILE
Chi-restraints excluded: chain D residue  324 MET
Chi-restraints excluded: chain D residue  433 VAL
Chi-restraints excluded: chain D residue  434 ASP
Chi-restraints excluded: chain D residue  439 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 20 optimal weight:    0.0270
   chunk 93 optimal weight:    6.9990
   chunk 162 optimal weight:    0.9980
   chunk 140 optimal weight:    5.9990
   chunk 149 optimal weight:    0.5980
   chunk 148 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 122 optimal weight:    5.9990
   chunk 155 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 139 optimal weight:   10.0000
   overall best weight:    1.7242

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

Flipped N/Q/H residues before XYZ refinement:
** A 252 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 = 0.3794 r_free = 0.3794 target = 0.151914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.111891 restraints weight = 19090.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 1.98
r_work: 0.3051 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2919 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.2002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  13896  Z= 0.118
  Angle     :  0.482   5.228  18744  Z= 0.263
  Chirality :  0.042   0.185   2060
  Planarity :  0.003   0.029   2396
  Dihedral  :  4.665  27.013   1852
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 15.46 %
    Favored  : 80.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.09 (0.20), residues: 1696
  helix:  0.89 (0.20), residues: 728
  sheet: -0.16 (0.38), residues: 192
  loop : -2.57 (0.19), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 159 
 TYR   0.011   0.001   TYR B 162 
 PHE   0.014   0.001   PHE D 108 
 TRP   0.007   0.001   TRP C 311 
 HIS   0.011   0.002   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (13896)
  covalent geometry    : angle       0.48156 (18744)
  hydrogen bonds       : bond        0.04542 (  536)
  hydrogen bonds       : angle       3.94761 ( 1536)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 141
  time to evaluate  : 0.539 
Fit side-chains
REVERT: A  180 PHE cc_start: 0.8194 (t80) cc_final: 0.7867 (t80)
REVERT: B   25 ILE cc_start: 0.7808 (mm) cc_final: 0.7511 (mm)
REVERT: B  180 PHE cc_start: 0.8306 (t80) cc_final: 0.7831 (t80)
REVERT: B  338 MET cc_start: 0.9154 (mmm) cc_final: 0.8770 (mmt)
REVERT: B  434 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.7721 (t70)
REVERT: C  180 PHE cc_start: 0.8244 (t80) cc_final: 0.7874 (t80)
REVERT: C  222 MET cc_start: 0.7234 (tpp) cc_final: 0.7008 (tmm)
REVERT: C  434 ASP cc_start: 0.8729 (OUTLIER) cc_final: 0.7705 (t70)
REVERT: D  180 PHE cc_start: 0.8188 (t80) cc_final: 0.7817 (t80)
REVERT: D  222 MET cc_start: 0.7244 (tpp) cc_final: 0.7015 (tmm)
REVERT: D  434 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.7736 (t70)
  outliers start: 61
  outliers final: 47
  residues processed: 184
  average time/residue: 0.1208
  time to fit residues: 32.9165
Evaluate side-chains
  184 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 134
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  324 MET
Chi-restraints excluded: chain A residue  340 ASN
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  162 TYR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  324 MET
Chi-restraints excluded: chain B residue  367 ASP
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  434 ASP
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain C residue   18 THR
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  162 TYR
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  265 ILE
Chi-restraints excluded: chain C residue  291 ILE
Chi-restraints excluded: chain C residue  324 MET
Chi-restraints excluded: chain C residue  367 ASP
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  434 ASP
Chi-restraints excluded: chain C residue  439 VAL
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue  127 THR
Chi-restraints excluded: chain D residue  162 TYR
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  265 ILE
Chi-restraints excluded: chain D residue  291 ILE
Chi-restraints excluded: chain D residue  324 MET
Chi-restraints excluded: chain D residue  367 ASP
Chi-restraints excluded: chain D residue  433 VAL
Chi-restraints excluded: chain D residue  434 ASP
Chi-restraints excluded: chain D residue  439 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 89 optimal weight:    0.9990
   chunk 54 optimal weight:   20.0000
   chunk 32 optimal weight:    0.5980
   chunk 14 optimal weight:    0.2980
   chunk 31 optimal weight:   10.0000
   chunk 110 optimal weight:    0.9990
   chunk 119 optimal weight:    0.7980
   chunk 88 optimal weight:    2.9990
   chunk 105 optimal weight:    5.9990
   chunk 40 optimal weight:    0.2980
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
A 290 ASN
B 252 GLN
B 290 ASN
C 290 ASN
D 290 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.156128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.120207 restraints weight = 19021.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 2.13
r_work: 0.3118 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  13896  Z= 0.090
  Angle     :  0.447   5.157  18744  Z= 0.246
  Chirality :  0.041   0.166   2060
  Planarity :  0.003   0.029   2396
  Dihedral  :  4.229  23.625   1852
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 16.26 %
    Favored  : 80.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.20), residues: 1696
  helix:  1.28 (0.20), residues: 728
  sheet:  0.05 (0.38), residues: 192
  loop : -2.50 (0.19), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 159 
 TYR   0.012   0.001   TYR A 251 
 PHE   0.010   0.001   PHE C 108 
 TRP   0.006   0.001   TRP B  72 
 HIS   0.010   0.002   HIS D  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00180 (13896)
  covalent geometry    : angle       0.44744 (18744)
  hydrogen bonds       : bond        0.03434 (  536)
  hydrogen bonds       : angle       3.63351 ( 1536)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 147
  time to evaluate  : 0.552 
Fit side-chains
REVERT: A  180 PHE cc_start: 0.8096 (t80) cc_final: 0.7744 (t80)
REVERT: A  222 MET cc_start: 0.7271 (tpp) cc_final: 0.7021 (tmm)
REVERT: B   25 ILE cc_start: 0.7701 (mm) cc_final: 0.7495 (mm)
REVERT: B  109 ARG cc_start: 0.6984 (ptt90) cc_final: 0.6609 (ptt90)
REVERT: B  180 PHE cc_start: 0.8124 (t80) cc_final: 0.7744 (t80)
REVERT: B  228 ARG cc_start: 0.3618 (mtp180) cc_final: 0.3408 (mtm180)
REVERT: B  434 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7648 (t70)
REVERT: C  109 ARG cc_start: 0.6968 (ptt90) cc_final: 0.6585 (ptt90)
REVERT: C  180 PHE cc_start: 0.8137 (t80) cc_final: 0.7778 (t80)
REVERT: C  222 MET cc_start: 0.7193 (tpp) cc_final: 0.6850 (tmm)
REVERT: D  180 PHE cc_start: 0.8110 (t80) cc_final: 0.7765 (t80)
REVERT: D  222 MET cc_start: 0.7215 (tpp) cc_final: 0.6977 (tmm)
  outliers start: 55
  outliers final: 32
  residues processed: 189
  average time/residue: 0.1231
  time to fit residues: 33.6259
Evaluate side-chains
  161 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 128
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  324 MET
Chi-restraints excluded: chain A residue  340 ASN
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  434 ASP
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain C residue   18 THR
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  162 TYR
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  291 ILE
Chi-restraints excluded: chain C residue  434 ASP
Chi-restraints excluded: chain C residue  439 VAL
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue  127 THR
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  265 ILE
Chi-restraints excluded: chain D residue  291 ILE
Chi-restraints excluded: chain D residue  367 ASP
Chi-restraints excluded: chain D residue  434 ASP
Chi-restraints excluded: chain D residue  439 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 12 optimal weight:    9.9990
   chunk 140 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9990
   chunk 54 optimal weight:   20.0000
   chunk 154 optimal weight:    4.9990
   chunk 79 optimal weight:    0.0870
   chunk 106 optimal weight:    2.9990
   chunk 126 optimal weight:    0.9990
   chunk 83 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.6166

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

Flipped N/Q/H residues before XYZ refinement:
A 177 ASN
A 290 ASN
B 290 ASN
C 290 ASN
C 449 GLN
D 290 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.153583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.113449 restraints weight = 19248.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 2.01
r_work: 0.3075 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.2298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  13896  Z= 0.113
  Angle     :  0.473   6.390  18744  Z= 0.256
  Chirality :  0.042   0.173   2060
  Planarity :  0.003   0.027   2396
  Dihedral  :  4.354  24.426   1852
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.66 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 16.94 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.66 (0.20), residues: 1696
  helix:  1.35 (0.20), residues: 728
  sheet:  0.03 (0.39), residues: 192
  loop : -2.45 (0.19), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  67 
 TYR   0.011   0.001   TYR D 251 
 PHE   0.011   0.001   PHE B 226 
 TRP   0.006   0.001   TRP B 199 
 HIS   0.011   0.002   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (13896)
  covalent geometry    : angle       0.47267 (18744)
  hydrogen bonds       : bond        0.04201 (  536)
  hydrogen bonds       : angle       3.73039 ( 1536)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 131
  time to evaluate  : 0.548 
Fit side-chains
REVERT: A  180 PHE cc_start: 0.8170 (t80) cc_final: 0.7891 (t80)
REVERT: A  222 MET cc_start: 0.7298 (tpp) cc_final: 0.7056 (tmm)
REVERT: B   25 ILE cc_start: 0.7768 (mm) cc_final: 0.7533 (mm)
REVERT: B  109 ARG cc_start: 0.7091 (ptt90) cc_final: 0.6751 (ptt90)
REVERT: B  112 ARG cc_start: 0.8320 (ttt-90) cc_final: 0.7707 (ptm160)
REVERT: B  180 PHE cc_start: 0.8239 (t80) cc_final: 0.7811 (t80)
REVERT: B  222 MET cc_start: 0.7470 (mmm) cc_final: 0.7172 (tpt)
REVERT: C  180 PHE cc_start: 0.8142 (t80) cc_final: 0.7831 (t80)
REVERT: C  222 MET cc_start: 0.7249 (tpp) cc_final: 0.7021 (tmm)
REVERT: C  434 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.7803 (t70)
REVERT: D  180 PHE cc_start: 0.8152 (t80) cc_final: 0.7816 (t80)
REVERT: D  222 MET cc_start: 0.7272 (tpp) cc_final: 0.6886 (tmm)
REVERT: D  434 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.7828 (t70)
  outliers start: 46
  outliers final: 42
  residues processed: 169
  average time/residue: 0.1220
  time to fit residues: 30.4728
Evaluate side-chains
  174 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 130
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  290 ASN
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  324 MET
Chi-restraints excluded: chain A residue  340 ASN
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  290 ASN
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain B residue  367 ASP
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain C residue   18 THR
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  162 TYR
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  290 ASN
Chi-restraints excluded: chain C residue  291 ILE
Chi-restraints excluded: chain C residue  324 MET
Chi-restraints excluded: chain C residue  367 ASP
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  434 ASP
Chi-restraints excluded: chain C residue  439 VAL
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue  127 THR
Chi-restraints excluded: chain D residue  162 TYR
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  265 ILE
Chi-restraints excluded: chain D residue  290 ASN
Chi-restraints excluded: chain D residue  291 ILE
Chi-restraints excluded: chain D residue  433 VAL
Chi-restraints excluded: chain D residue  434 ASP
Chi-restraints excluded: chain D residue  439 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 166 optimal weight:    9.9990
   chunk 44 optimal weight:    2.9990
   chunk 64 optimal weight:   10.0000
   chunk 115 optimal weight:    6.9990
   chunk 111 optimal weight:    7.9990
   chunk 8 optimal weight:    8.9990
   chunk 45 optimal weight:    5.9990
   chunk 86 optimal weight:   10.0000
   chunk 36 optimal weight:    4.9990
   chunk 54 optimal weight:   20.0000
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 290 ASN
D 290 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.146362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.106408 restraints weight = 19383.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 1.94
r_work: 0.2993 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2862 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8738
moved from start:          0.2019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.042  13896  Z= 0.288
  Angle     :  0.657   5.669  18744  Z= 0.352
  Chirality :  0.049   0.204   2060
  Planarity :  0.004   0.030   2396
  Dihedral  :  5.350  30.036   1852
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.02 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 17.47 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.20), residues: 1696
  helix:  0.45 (0.19), residues: 744
  sheet: -0.24 (0.38), residues: 192
  loop : -2.45 (0.19), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 159 
 TYR   0.014   0.002   TYR D 282 
 PHE   0.020   0.002   PHE B 108 
 TRP   0.020   0.002   TRP D 351 
 HIS   0.018   0.003   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00699 (13896)
  covalent geometry    : angle       0.65726 (18744)
  hydrogen bonds       : bond        0.06773 (  536)
  hydrogen bonds       : angle       4.39421 ( 1536)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 145
  time to evaluate  : 0.517 
Fit side-chains
REVERT: A  180 PHE cc_start: 0.8227 (t80) cc_final: 0.7900 (t80)
REVERT: A  222 MET cc_start: 0.7318 (tpp) cc_final: 0.7057 (tmm)
REVERT: B   25 ILE cc_start: 0.7811 (mm) cc_final: 0.7496 (mm)
REVERT: B  180 PHE cc_start: 0.8256 (t80) cc_final: 0.7829 (t80)
REVERT: C  180 PHE cc_start: 0.8258 (t80) cc_final: 0.7864 (t80)
REVERT: C  222 MET cc_start: 0.7307 (tpp) cc_final: 0.7075 (tmm)
REVERT: C  434 ASP cc_start: 0.8796 (OUTLIER) cc_final: 0.8080 (t70)
REVERT: D  124 ASP cc_start: 0.7755 (p0) cc_final: 0.7537 (p0)
REVERT: D  180 PHE cc_start: 0.8262 (t80) cc_final: 0.7909 (t80)
REVERT: D  222 MET cc_start: 0.7303 (tpp) cc_final: 0.7069 (tmm)
REVERT: D  434 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8058 (t70)
  outliers start: 42
  outliers final: 34
  residues processed: 180
  average time/residue: 0.1129
  time to fit residues: 30.2004
Evaluate side-chains
  175 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 139
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  290 ASN
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  367 ASP
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain C residue   18 THR
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  162 TYR
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  291 ILE
Chi-restraints excluded: chain C residue  367 ASP
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  434 ASP
Chi-restraints excluded: chain C residue  439 VAL
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue  127 THR
Chi-restraints excluded: chain D residue  162 TYR
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  265 ILE
Chi-restraints excluded: chain D residue  290 ASN
Chi-restraints excluded: chain D residue  291 ILE
Chi-restraints excluded: chain D residue  309 MET
Chi-restraints excluded: chain D residue  433 VAL
Chi-restraints excluded: chain D residue  434 ASP
Chi-restraints excluded: chain D residue  439 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0570
   chunk 48 optimal weight:   10.0000
   chunk 3 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 113 optimal weight:    0.8980
   chunk 104 optimal weight:    4.9990
   chunk 92 optimal weight:    0.9980
   chunk 127 optimal weight:    0.0470
   chunk 167 optimal weight:    2.9990
   overall best weight:    0.5796

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

Flipped N/Q/H residues before XYZ refinement:
A 290 ASN
B 271 ASN
C 290 ASN
D 271 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.152821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.112888 restraints weight = 19307.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 1.99
r_work: 0.3072 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2938 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
moved from start:          0.2236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  13896  Z= 0.101
  Angle     :  0.489   5.326  18744  Z= 0.267
  Chirality :  0.042   0.177   2060
  Planarity :  0.003   0.027   2396
  Dihedral  :  4.642  27.255   1852
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 18.28 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.76 (0.20), residues: 1696
  helix:  1.13 (0.20), residues: 728
  sheet:  0.28 (0.38), residues: 184
  loop : -2.41 (0.20), residues: 784

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  67 
 TYR   0.012   0.001   TYR A 162 
 PHE   0.013   0.001   PHE A 108 
 TRP   0.006   0.001   TRP D 443 
 HIS   0.009   0.002   HIS D  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 (13896)
  covalent geometry    : angle       0.48935 (18744)
  hydrogen bonds       : bond        0.04284 (  536)
  hydrogen bonds       : angle       3.87337 ( 1536)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3397.14 seconds
wall clock time: 58 minutes 57.80 seconds (3537.80 seconds total)