Starting phenix.real_space_refine
on Sun May  3 12:52:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/20yv_67420/05_2026/20yv_67420.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/20yv_67420/05_2026/20yv_67420.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.28
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/20yv_67420/05_2026/20yv_67420.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/20yv_67420/05_2026/20yv_67420.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/20yv_67420/05_2026/20yv_67420.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/20yv_67420/05_2026/20yv_67420.map"
  }
  resolution = 3.28
  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=   1.000
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      40      5.16       5
     C    8346      2.51       5
     N    2189      2.21       5
     O    2452      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13027
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3937
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 478, 3937
          Classifications: {'peptide': 478}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 463}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 3952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 480, 3952
          Classifications: {'peptide': 480}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 464}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 2566
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 312, 2566
          Classifications: {'peptide': 312}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 301}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2572
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2572
          Classifications: {'peptide': 313}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 302}
          Chain breaks: 1
  Time building chain proxies: 3.18, per 1000 atoms: 0.24
  Number of scatterers: 13027
  At special positions: 0
  Unit cell: (114.57, 118.845, 104.31, 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      40     16.00
     O    2452      8.00
     N    2189      7.00
     C    8346      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  82 " - pdb=" SG  CYS A 273 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  82 " - pdb=" SG  CYS B 273 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  82 " - pdb=" SG  CYS D 273 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.05
  Conformation dependent library (CDL) restraints added in 581.4 milliseconds
  

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3042

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 9 sheets defined
      60.8% alpha, 8.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 47 through 52
    Processing helix  chain 'A' and resid 70 through 91
      removed outlier: 3.999A  pdb=" N   ILE A  89 " --> pdb=" O   PHE A  85 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   SER A  90 " --> pdb=" O   THR A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 159
      removed outlier: 3.563A  pdb=" N   LEU A 134 " --> pdb=" O   GLY A 130 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LYS A 159 " --> pdb=" O   LYS A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 180
      removed outlier: 3.707A  pdb=" N   GLY A 177 " --> pdb=" O   MET A 173 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ARG A 178 " --> pdb=" O   LYS A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 194
    Processing helix  chain 'A' and resid 219 through 234
      removed outlier: 3.779A  pdb=" N   GLU A 234 " --> pdb=" O   LYS A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 271
      Proline residue:  A 257  - end of helix
      removed outlier: 3.632A  pdb=" N   LYS A 263 " --> pdb=" O   SER A 259 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ASN A 271 " --> pdb=" O   ALA A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 302
    Processing helix  chain 'A' and resid 302 through 311
      removed outlier: 3.919A  pdb=" N   GLN A 306 " --> pdb=" O   ASN A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 325
    Processing helix  chain 'A' and resid 327 through 346
      removed outlier: 4.145A  pdb=" N   GLU A 331 " --> pdb=" O   ASP A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 368
      removed outlier: 3.557A  pdb=" N   PHE A 364 " --> pdb=" O   ALA A 360 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   GLU A 365 " --> pdb=" O   PHE A 361 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   SER A 366 " --> pdb=" O   ASP A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 388
      removed outlier: 3.657A  pdb=" N   GLU A 388 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 395
    Processing helix  chain 'A' and resid 396 through 411
      removed outlier: 3.769A  pdb=" N   GLN A 400 " --> pdb=" O   SER A 396 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   TYR A 401 " --> pdb=" O   LYS A 397 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LEU A 409 " --> pdb=" O   ILE A 405 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   SER A 411 " --> pdb=" O   ASN A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 434
    Processing helix  chain 'A' and resid 441 through 455
      removed outlier: 3.619A  pdb=" N   LYS A 455 " --> pdb=" O   ASP A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 480
    Processing helix  chain 'A' and resid 514 through 529
      removed outlier: 3.784A  pdb=" N   GLY A 518 " --> pdb=" O   THR A 514 " (cutoff:3.500A)
      Proline residue:  A 519  - end of helix
      removed outlier: 4.437A  pdb=" N   ARG A 522 " --> pdb=" O   GLY A 518 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   PHE A 523 " --> pdb=" O   PRO A 519 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   TYR A 524 " --> pdb=" O   LEU A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 559
      removed outlier: 3.633A  pdb=" N   LYS A 547 " --> pdb=" O   ILE A 543 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   THR A 550 " --> pdb=" O   VAL A 546 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ALA A 551 " --> pdb=" O   LYS A 547 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   TRP A 556 " --> pdb=" O   PHE A 552 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   SER A 559 " --> pdb=" O   LEU A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 576
      removed outlier: 3.617A  pdb=" N   TYR A 570 " --> pdb=" O   ILE A 566 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 39
    Processing helix  chain 'B' and resid 47 through 52
    Processing helix  chain 'B' and resid 70 through 88
      removed outlier: 3.524A  pdb=" N   ILE B  81 " --> pdb=" O   LEU B  77 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU B  88 " --> pdb=" O   GLY B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 159
    Processing helix  chain 'B' and resid 162 through 180
    Processing helix  chain 'B' and resid 191 through 194
    Processing helix  chain 'B' and resid 219 through 234
      removed outlier: 3.527A  pdb=" N   GLU B 234 " --> pdb=" O   LYS B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 246 through 250
      removed outlier: 4.355A  pdb=" N   GLU B 250 " --> pdb=" O   SER B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 271
      removed outlier: 3.982A  pdb=" N   TYR B 255 " --> pdb=" O   ASN B 251 " (cutoff:3.500A)
      Proline residue:  B 257  - end of helix
      removed outlier: 3.887A  pdb=" N   ASN B 271 " --> pdb=" O   ALA B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 302
    Processing helix  chain 'B' and resid 302 through 310
      removed outlier: 3.917A  pdb=" N   GLN B 306 " --> pdb=" O   ASN B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 315 through 325
      removed outlier: 3.738A  pdb=" N   ASN B 325 " --> pdb=" O   LYS B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 346
      removed outlier: 4.118A  pdb=" N   GLU B 331 " --> pdb=" O   ASP B 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 368
      removed outlier: 4.015A  pdb=" N   GLU B 365 " --> pdb=" O   PHE B 361 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   SER B 366 " --> pdb=" O   ASP B 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 375 through 388
      removed outlier: 3.570A  pdb=" N   THR B 379 " --> pdb=" O   THR B 375 " (cutoff:3.500A)
      Proline residue:  B 382  - end of helix
      removed outlier: 4.216A  pdb=" N   GLU B 388 " --> pdb=" O   ILE B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 410
    Processing helix  chain 'B' and resid 417 through 431
      removed outlier: 3.666A  pdb=" N   ALA B 421 " --> pdb=" O   ASP B 417 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   SER B 423 " --> pdb=" O   GLN B 419 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 455
      removed outlier: 3.549A  pdb=" N   LYS B 455 " --> pdb=" O   ASP B 451 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 480
    Processing helix  chain 'B' and resid 513 through 515
      No H-bonds generated for 'chain 'B' and resid 513 through 515'
    Processing helix  chain 'B' and resid 516 through 529
      removed outlier: 3.670A  pdb=" N   LEU B 520 " --> pdb=" O   THR B 516 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ARG B 522 " --> pdb=" O   GLY B 518 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   GLU B 526 " --> pdb=" O   ARG B 522 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 539 through 559
      removed outlier: 3.628A  pdb=" N   ALA B 551 " --> pdb=" O   LYS B 547 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   SER B 559 " --> pdb=" O   LEU B 555 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 566 through 576
      removed outlier: 3.520A  pdb=" N   TYR B 570 " --> pdb=" O   ILE B 566 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   TYR B 576 " --> pdb=" O   ARG B 572 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 47 through 52
    Processing helix  chain 'C' and resid 70 through 88
      removed outlier: 3.505A  pdb=" N   ILE C  81 " --> pdb=" O   LEU C  77 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 130 through 157
      removed outlier: 3.757A  pdb=" N   LEU C 134 " --> pdb=" O   GLY C 130 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 162 through 183
      removed outlier: 3.629A  pdb=" N   LEU C 168 " --> pdb=" O   ALA C 164 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   MET C 173 " --> pdb=" O   VAL C 169 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   LYS C 174 " --> pdb=" O   GLU C 170 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   VAL C 175 " --> pdb=" O   GLU C 171 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ILE C 176 " --> pdb=" O   CYS C 172 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   GLY C 177 " --> pdb=" O   MET C 173 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ARG C 178 " --> pdb=" O   LYS C 174 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   PHE C 183 " --> pdb=" O   LEU C 179 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 191 through 194
    Processing helix  chain 'C' and resid 219 through 233
    Processing helix  chain 'C' and resid 251 through 267
      removed outlier: 4.173A  pdb=" N   TYR C 255 " --> pdb=" O   ASN C 251 " (cutoff:3.500A)
      Proline residue:  C 257  - end of helix
    Processing helix  chain 'C' and resid 296 through 302
    Processing helix  chain 'C' and resid 303 through 310
    Processing helix  chain 'C' and resid 315 through 325
    Processing helix  chain 'C' and resid 327 through 347
      removed outlier: 4.220A  pdb=" N   GLU C 331 " --> pdb=" O   ASP C 327 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   VAL C 347 " --> pdb=" O   VAL C 343 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 356 through 365
      removed outlier: 3.926A  pdb=" N   GLU C 365 " --> pdb=" O   PHE C 361 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 47 through 52
    Processing helix  chain 'D' and resid 70 through 91
      removed outlier: 3.585A  pdb=" N   ILE D  74 " --> pdb=" O   ASP D  70 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   LEU D  77 " --> pdb=" O   LYS D  73 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   ILE D  89 " --> pdb=" O   PHE D  85 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   SER D  90 " --> pdb=" O   THR D  86 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 130 through 159
      removed outlier: 3.539A  pdb=" N   ARG D 151 " --> pdb=" O   GLU D 147 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LYS D 159 " --> pdb=" O   LYS D 155 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 162 through 183
      removed outlier: 3.563A  pdb=" N   VAL D 175 " --> pdb=" O   GLU D 171 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   GLY D 177 " --> pdb=" O   MET D 173 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   ARG D 178 " --> pdb=" O   LYS D 174 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   THR D 182 " --> pdb=" O   ARG D 178 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   PHE D 183 " --> pdb=" O   LEU D 179 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 219 through 234
      removed outlier: 3.502A  pdb=" N   GLY D 229 " --> pdb=" O   LEU D 225 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 251 through 271
      Proline residue:  D 257  - end of helix
      removed outlier: 3.554A  pdb=" N   LYS D 270 " --> pdb=" O   TYR D 266 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   ASN D 271 " --> pdb=" O   ALA D 267 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 303 through 310
    Processing helix  chain 'D' and resid 315 through 325
      removed outlier: 3.676A  pdb=" N   ASN D 325 " --> pdb=" O   LYS D 321 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 327 through 346
      removed outlier: 4.380A  pdb=" N   GLU D 331 " --> pdb=" O   ASP D 327 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 356 through 364
    Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 46
      removed outlier: 7.220A  pdb=" N   THR A 350 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   THR A 100 " --> pdb=" O   THR A 350 " (cutoff:3.500A)
      removed outlier: 7.266A  pdb=" N   VAL A 352 " --> pdb=" O   THR A 100 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   ILE A 102 " --> pdb=" O   VAL A 352 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   ILE A 104 " --> pdb=" O   ILE A 127 " (cutoff:3.500A)
      removed outlier: 5.467A  pdb=" N   ILE A 127 " --> pdb=" O   ILE A 104 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 184 through 186
    Processing sheet with id=AA3, first strand: chain 'B' and resid 42 through 46
      removed outlier: 6.341A  pdb=" N   THR B  96 " --> pdb=" O   ALA B 348 " (cutoff:3.500A)
      removed outlier: 7.921A  pdb=" N   THR B 350 " --> pdb=" O   THR B  96 " (cutoff:3.500A)
      removed outlier: 8.175A  pdb=" N   LEU B  98 " --> pdb=" O   THR B 350 " (cutoff:3.500A)
      removed outlier: 12.331A  pdb=" N   VAL B 352 " --> pdb=" O   LEU B  98 " (cutoff:3.500A)
      removed outlier: 9.372A  pdb=" N   THR B 100 " --> pdb=" O   VAL B 352 " (cutoff:3.500A)
      removed outlier: 6.993A  pdb=" N   ILE B 104 " --> pdb=" O   ILE B 127 " (cutoff:3.500A)
      removed outlier: 5.426A  pdb=" N   ILE B 127 " --> pdb=" O   ILE B 104 " (cutoff:3.500A)
      removed outlier: 9.240A  pdb=" N   ILE B 201 " --> pdb=" O   GLN B  56 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   LEU B  58 " --> pdb=" O   ILE B 201 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 184 through 186
    Processing sheet with id=AA5, first strand: chain 'C' and resid 41 through 46
      removed outlier: 6.362A  pdb=" N   ALA C 348 " --> pdb=" O   PHE C  97 " (cutoff:3.500A)
      removed outlier: 4.889A  pdb=" N   GLY C  99 " --> pdb=" O   ALA C 348 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   THR C 350 " --> pdb=" O   GLY C  99 " (cutoff:3.500A)
      removed outlier: 4.816A  pdb=" N   HIS C 105 " --> pdb=" O   ALA C 354 " (cutoff:3.500A)
      removed outlier: 7.128A  pdb=" N   ILE C 102 " --> pdb=" O   ILE C 128 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   GLY C  57 " --> pdb=" O   MET C 125 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   ILE C 127 " --> pdb=" O   GLY C  57 " (cutoff:3.500A)
      removed outlier: 7.088A  pdb=" N   TYR C  59 " --> pdb=" O   ILE C 127 " (cutoff:3.500A)
      removed outlier: 8.386A  pdb=" N   ASP C 129 " --> pdb=" O   TYR C  59 " (cutoff:3.500A)
      removed outlier: 9.063A  pdb=" N   ILE C 201 " --> pdb=" O   GLN C  56 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   LEU C  58 " --> pdb=" O   ILE C 201 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 184 through 186
    Processing sheet with id=AA7, first strand: chain 'D' and resid 40 through 46
      removed outlier: 6.347A  pdb=" N   THR D  96 " --> pdb=" O   ALA D 348 " (cutoff:3.500A)
      removed outlier: 8.222A  pdb=" N   THR D 350 " --> pdb=" O   THR D  96 " (cutoff:3.500A)
      removed outlier: 8.904A  pdb=" N   LEU D  98 " --> pdb=" O   THR D 350 " (cutoff:3.500A)
      removed outlier: 12.828A  pdb=" N   VAL D 352 " --> pdb=" O   LEU D  98 " (cutoff:3.500A)
      removed outlier: 9.794A  pdb=" N   THR D 100 " --> pdb=" O   VAL D 352 " (cutoff:3.500A)
      removed outlier: 11.935A  pdb=" N   ALA D 354 " --> pdb=" O   THR D 100 " (cutoff:3.500A)
      removed outlier: 10.268A  pdb=" N   ILE D 102 " --> pdb=" O   ALA D 354 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   ILE D 104 " --> pdb=" O   ILE D 127 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   ILE D 127 " --> pdb=" O   ILE D 104 " (cutoff:3.500A)
      removed outlier: 8.975A  pdb=" N   ILE D 201 " --> pdb=" O   GLN D  56 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   LEU D  58 " --> pdb=" O   ILE D 201 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 184 through 186
    Processing sheet with id=AA9, first strand: chain 'D' and resid 206 through 207

    664 hydrogen bonds defined for protein.
    1965 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: 2.00

  Time building geometry restraints manager: 1.34 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: 4178
        1.34 -     1.46: 2929
        1.46 -     1.58: 6115
        1.58 -     1.70: 0
        1.70 -     1.82: 64
  Bond restraints: 13286
  Sorted by residual:
  bond pdb=" CA  ASN A 271 "
       pdb=" CB  ASN A 271 "
    ideal  model  delta    sigma   weight residual
    1.527  1.569 -0.042 1.75e-02 3.27e+03 5.83e+00
  bond pdb=" CA  VAL B  60 "
       pdb=" C   VAL B  60 "
    ideal  model  delta    sigma   weight residual
    1.528  1.537 -0.009 8.10e-03 1.52e+04 1.33e+00
  bond pdb=" CA  VAL B 120 "
       pdb=" CB  VAL B 120 "
    ideal  model  delta    sigma   weight residual
    1.537  1.549 -0.012 1.29e-02 6.01e+03 8.63e-01
  bond pdb=" CB  ASN A 386 "
       pdb=" CG  ASN A 386 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 2.50e-02 1.60e+03 8.08e-01
  bond pdb=" CA  TYR D 204 "
       pdb=" CB  TYR D 204 "
    ideal  model  delta    sigma   weight residual
    1.530  1.545 -0.015 1.69e-02 3.50e+03 7.69e-01
  ... (remaining 13281 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.33: 17484
        1.33 -     2.67: 340
        2.67 -     4.00: 53
        4.00 -     5.34: 15
        5.34 -     6.67: 3
  Bond angle restraints: 17895
  Sorted by residual:
  angle pdb=" CA  GLU B 403 "
        pdb=" CB  GLU B 403 "
        pdb=" CG  GLU B 403 "
      ideal   model   delta    sigma   weight residual
     114.10  120.77   -6.67 2.00e+00 2.50e-01 1.11e+01
  angle pdb=" CA  TYR D 204 "
        pdb=" CB  TYR D 204 "
        pdb=" CG  TYR D 204 "
      ideal   model   delta    sigma   weight residual
     113.90  119.33   -5.43 1.80e+00 3.09e-01 9.09e+00
  angle pdb=" CA  CYS B  52 "
        pdb=" C   CYS B  52 "
        pdb=" N   GLU B  53 "
      ideal   model   delta    sigma   weight residual
     114.87  118.61   -3.74 1.55e+00 4.16e-01 5.81e+00
  angle pdb=" C   ALA D 203 "
        pdb=" N   TYR D 204 "
        pdb=" CA  TYR D 204 "
      ideal   model   delta    sigma   weight residual
     121.54  125.94   -4.40 1.91e+00 2.74e-01 5.30e+00
  angle pdb=" C   ASN A 271 "
        pdb=" CA  ASN A 271 "
        pdb=" CB  ASN A 271 "
      ideal   model   delta    sigma   weight residual
     111.23  114.92   -3.69 1.68e+00 3.54e-01 4.83e+00
  ... (remaining 17890 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 6800
       17.85 -    35.71: 1000
       35.71 -    53.56: 248
       53.56 -    71.41: 50
       71.41 -    89.27: 14
  Dihedral angle restraints: 8112
    sinusoidal: 3419
      harmonic: 4693
  Sorted by residual:
  dihedral pdb=" CB  CYS B  82 "
           pdb=" SG  CYS B  82 "
           pdb=" SG  CYS B 273 "
           pdb=" CB  CYS B 273 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -151.17   65.17     1      1.00e+01 1.00e-02 5.57e+01
  dihedral pdb=" CA  GLU B 394 "
           pdb=" C   GLU B 394 "
           pdb=" N   ARG B 395 "
           pdb=" CA  ARG B 395 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.62   18.38     0      5.00e+00 4.00e-02 1.35e+01
  dihedral pdb=" CA  LEU B 344 "
           pdb=" C   LEU B 344 "
           pdb=" N   ASP B 345 "
           pdb=" CA  ASP B 345 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.87  -17.13     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 8109 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1232
       0.031 -    0.062: 504
       0.062 -    0.094: 157
       0.094 -    0.125: 59
       0.125 -    0.156: 11
  Chirality restraints: 1963
  Sorted by residual:
  chirality pdb=" CA  VAL A 120 "
            pdb=" N   VAL A 120 "
            pdb=" C   VAL A 120 "
            pdb=" CB  VAL A 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.09e-01
  chirality pdb=" CA  VAL B 120 "
            pdb=" N   VAL B 120 "
            pdb=" C   VAL B 120 "
            pdb=" CB  VAL B 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.51e-01
  chirality pdb=" CA  ILE A 101 "
            pdb=" N   ILE A 101 "
            pdb=" C   ILE A 101 "
            pdb=" CB  ILE A 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.45e-01
  ... (remaining 1960 not shown)

  Planarity restraints: 2265
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR D 204 "    0.010 2.00e-02 2.50e+03   1.94e-02 3.78e+00
        pdb=" C   TYR D 204 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   TYR D 204 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ASP D 205 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 448 "    0.015 2.00e-02 2.50e+03   1.41e-02 3.47e+00
        pdb=" CG  PHE B 448 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 448 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 448 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 448 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 448 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 448 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 120 "    0.029 5.00e-02 4.00e+02   4.35e-02 3.03e+00
        pdb=" N   PRO C 121 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO C 121 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO C 121 "    0.024 5.00e-02 4.00e+02
  ... (remaining 2262 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 976
        2.74 -     3.28: 12687
        3.28 -     3.82: 20834
        3.82 -     4.36: 24431
        4.36 -     4.90: 42820
  Nonbonded interactions: 101748
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 359 "
            pdb=" O   ASP D  93 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OG  SER B 553 "
            pdb=" OH  TYR B 570 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" OH  TYR B  63 "
            pdb=" OE2 GLU B 357 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OE2 GLU A 295 "
            pdb=" OG  SER A 298 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" OG  SER C 160 "
            pdb=" OD2 ASP C 165 "
     model   vdw
     2.258 3.040
  ... (remaining 101743 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 34 through 480 or resid 513 through 576))
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'D' and resid 34 through 365)
}

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:             4.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     12.640
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  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:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
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      :  0.003   0.042  13289  Z= 0.120
  Angle     :  0.485   6.675  17901  Z= 0.273
  Chirality :  0.040   0.156   1963
  Planarity :  0.004   0.043   2265
  Dihedral  : 17.678  89.266   5061
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  : 26.44 %
    Favored  : 73.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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:  0.53 (0.22), residues: 1555
  helix:  1.56 (0.18), residues: 865
  sheet: -0.74 (0.46), residues: 128
  loop : -1.31 (0.26), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  76 
 TYR   0.017   0.001   TYR C 228 
 PHE   0.032   0.001   PHE B 448 
 TRP   0.006   0.001   TRP A 167 
 HIS   0.004   0.001   HIS B 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (13286)
  covalent geometry    : angle       0.48333 (17895)
  SS BOND              : bond        0.00192 (    3)
  SS BOND              : angle       2.40564 (    6)
  hydrogen bonds       : bond        0.14391 (  664)
  hydrogen bonds       : angle       5.63841 ( 1965)

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 112
  time to evaluate  : 0.446 
Fit side-chains
REVERT: B  262 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8238 (ttt90)
  outliers start: 2
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1591
  time to fit residues: 24.2555
Evaluate side-chains
  110 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 109
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  262 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9990
   chunk 149 optimal weight:    0.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
C  54 ASN
D  83 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.142108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.111670 restraints weight = 20425.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 2.26
r_work: 0.3123 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.0721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  13289  Z= 0.201
  Angle     :  0.547   5.135  17901  Z= 0.300
  Chirality :  0.043   0.146   1963
  Planarity :  0.005   0.045   2265
  Dihedral  :  4.353  46.294   1741
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 24.43 %
    Favored  : 71.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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:  0.54 (0.21), residues: 1555
  helix:  1.54 (0.17), residues: 876
  sheet: -0.70 (0.46), residues: 128
  loop : -1.33 (0.26), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  76 
 TYR   0.025   0.002   TYR C 228 
 PHE   0.031   0.002   PHE B 448 
 TRP   0.010   0.001   TRP C  48 
 HIS   0.009   0.002   HIS B 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 (13286)
  covalent geometry    : angle       0.54589 (17895)
  SS BOND              : bond        0.00276 (    3)
  SS BOND              : angle       1.59976 (    6)
  hydrogen bonds       : bond        0.05806 (  664)
  hydrogen bonds       : angle       4.46799 ( 1965)

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 115
  time to evaluate  : 0.522 
Fit side-chains
REVERT: A  364 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7112 (m-80)
REVERT: B  119 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7802 (t70)
REVERT: B  358 ASP cc_start: 0.7335 (p0) cc_final: 0.7105 (p0)
REVERT: B  394 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6196 (pp20)
REVERT: B  451 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7326 (p0)
REVERT: C   65 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7783 (ptt90)
REVERT: D  248 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6475 (tt0)
  outliers start: 52
  outliers final: 23
  residues processed: 159
  average time/residue: 0.1370
  time to fit residues: 30.2432
Evaluate side-chains
  130 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 101
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  131 GLN
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  307 ASN
Chi-restraints excluded: chain A residue  364 PHE
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  119 ASP
Chi-restraints excluded: chain B residue  157 ASN
Chi-restraints excluded: chain B residue  207 SER
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  274 LYS
Chi-restraints excluded: chain B residue  394 GLU
Chi-restraints excluded: chain B residue  431 LEU
Chi-restraints excluded: chain B residue  451 ASP
Chi-restraints excluded: chain B residue  546 VAL
Chi-restraints excluded: chain C residue   65 ARG
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue   78 ILE
Chi-restraints excluded: chain C residue  111 THR
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  309 LEU
Chi-restraints excluded: chain C residue  317 TYR
Chi-restraints excluded: chain D residue  115 ILE
Chi-restraints excluded: chain D residue  248 GLU
Chi-restraints excluded: chain D residue  366 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 127 optimal weight:    2.9990
   chunk 121 optimal weight:    0.9980
   chunk 137 optimal weight:    0.7980
   chunk 94 optimal weight:    5.9990
   chunk 89 optimal weight:    1.9990
   chunk 129 optimal weight:    4.9990
   chunk 149 optimal weight:    4.9990
   chunk 148 optimal weight:    1.9990
   chunk 117 optimal weight:    0.0570
   chunk 81 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9990
   overall best weight:    0.7700

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.145105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.113234 restraints weight = 20365.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 2.45
r_work: 0.3145 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.0780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13289  Z= 0.112
  Angle     :  0.452   5.511  17901  Z= 0.250
  Chirality :  0.040   0.144   1963
  Planarity :  0.004   0.047   2265
  Dihedral  :  3.857  17.327   1737
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 24.01 %
    Favored  : 72.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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:  0.87 (0.22), residues: 1555
  helix:  1.86 (0.18), residues: 877
  sheet: -0.72 (0.45), residues: 130
  loop : -1.25 (0.26), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  76 
 TYR   0.016   0.001   TYR C 228 
 PHE   0.022   0.001   PHE B 448 
 TRP   0.009   0.001   TRP D  48 
 HIS   0.005   0.001   HIS B 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (13286)
  covalent geometry    : angle       0.45172 (17895)
  SS BOND              : bond        0.00380 (    3)
  SS BOND              : angle       1.38012 (    6)
  hydrogen bonds       : bond        0.04471 (  664)
  hydrogen bonds       : angle       4.14901 ( 1965)

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 117
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
REVERT: A  132 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7282 (mm110)
REVERT: A  364 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.7051 (m-80)
REVERT: B  119 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7707 (t70)
REVERT: B  262 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8407 (ttt-90)
REVERT: B  358 ASP cc_start: 0.7480 (p0) cc_final: 0.7279 (p0)
REVERT: B  441 ARG cc_start: 0.7698 (mtt90) cc_final: 0.7421 (mtp85)
REVERT: B  451 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7317 (p0)
REVERT: C  106 ASP cc_start: 0.8933 (OUTLIER) cc_final: 0.8372 (m-30)
REVERT: D  363 MET cc_start: 0.8458 (mtm) cc_final: 0.8174 (mtm)
  outliers start: 50
  outliers final: 25
  residues processed: 162
  average time/residue: 0.1348
  time to fit residues: 30.6106
Evaluate side-chains
  138 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 107
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TRP
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   93 ASP
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  132 GLN
Chi-restraints excluded: chain A residue  307 ASN
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  364 PHE
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  119 ASP
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  262 ARG
Chi-restraints excluded: chain B residue  274 LYS
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  431 LEU
Chi-restraints excluded: chain B residue  451 ASP
Chi-restraints excluded: chain C residue  106 ASP
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  314 PHE
Chi-restraints excluded: chain C residue  317 TYR
Chi-restraints excluded: chain D residue  104 ILE
Chi-restraints excluded: chain D residue  115 ILE
Chi-restraints excluded: chain D residue  176 ILE
Chi-restraints excluded: chain D residue  323 ILE
Chi-restraints excluded: chain D residue  366 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 103 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 38 optimal weight:    7.9990
   chunk 21 optimal weight:    7.9990
   chunk 134 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 120 optimal weight:    3.9990
   chunk 156 optimal weight:    2.9990
   chunk 153 optimal weight:    9.9990
   chunk 57 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
C 307 ASN
D  83 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.141904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.109875 restraints weight = 20358.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 2.42
r_work: 0.3083 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.0988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  13289  Z= 0.216
  Angle     :  0.556   5.650  17901  Z= 0.303
  Chirality :  0.043   0.145   1963
  Planarity :  0.005   0.045   2265
  Dihedral  :  4.168  19.343   1737
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 23.52 %
    Favored  : 71.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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:  0.52 (0.21), residues: 1555
  helix:  1.57 (0.17), residues: 871
  sheet: -0.80 (0.45), residues: 128
  loop : -1.37 (0.26), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 346 
 TYR   0.026   0.002   TYR C 228 
 PHE   0.026   0.002   PHE B 448 
 TRP   0.009   0.001   TRP A 208 
 HIS   0.009   0.002   HIS B 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 (13286)
  covalent geometry    : angle       0.55447 (17895)
  SS BOND              : bond        0.00524 (    3)
  SS BOND              : angle       2.26977 (    6)
  hydrogen bonds       : bond        0.05782 (  664)
  hydrogen bonds       : angle       4.32333 ( 1965)

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 112
  time to evaluate  : 0.516 
Fit side-chains
REVERT: A  132 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7542 (mm110)
REVERT: A  364 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7125 (m-80)
REVERT: B  119 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7848 (t70)
REVERT: B  262 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8306 (ttt90)
REVERT: B  451 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7426 (p0)
REVERT: C   65 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.8013 (ptt90)
REVERT: C   76 ARG cc_start: 0.7812 (ttp-110) cc_final: 0.7596 (ttp-110)
REVERT: D  363 MET cc_start: 0.8570 (mtm) cc_final: 0.8190 (mtm)
  outliers start: 70
  outliers final: 48
  residues processed: 176
  average time/residue: 0.1352
  time to fit residues: 33.6643
Evaluate side-chains
  152 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 98
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   93 ASP
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  131 GLN
Chi-restraints excluded: chain A residue  132 GLN
Chi-restraints excluded: chain A residue  158 LYS
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  307 ASN
Chi-restraints excluded: chain A residue  364 PHE
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue   90 SER
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  107 THR
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  119 ASP
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  157 ASN
Chi-restraints excluded: chain B residue  207 SER
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  262 ARG
Chi-restraints excluded: chain B residue  274 LYS
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  431 LEU
Chi-restraints excluded: chain B residue  451 ASP
Chi-restraints excluded: chain B residue  546 VAL
Chi-restraints excluded: chain B residue  554 VAL
Chi-restraints excluded: chain C residue   56 GLN
Chi-restraints excluded: chain C residue   65 ARG
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue  111 THR
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  296 ILE
Chi-restraints excluded: chain C residue  309 LEU
Chi-restraints excluded: chain C residue  314 PHE
Chi-restraints excluded: chain C residue  317 TYR
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue  104 ILE
Chi-restraints excluded: chain D residue  115 ILE
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  176 ILE
Chi-restraints excluded: chain D residue  323 ILE
Chi-restraints excluded: chain D residue  366 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 130 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 87 optimal weight:    4.9990
   chunk 111 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 150 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9990
   chunk 98 optimal weight:    4.9990
   chunk 100 optimal weight:    5.9990
   chunk 125 optimal weight:    1.9990
   overall best weight:    1.1386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.143954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.112562 restraints weight = 20407.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 2.52
r_work: 0.3121 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.0955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13289  Z= 0.134
  Angle     :  0.479   5.309  17901  Z= 0.264
  Chirality :  0.041   0.156   1963
  Planarity :  0.004   0.048   2265
  Dihedral  :  3.981  18.006   1737
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 24.01 %
    Favored  : 71.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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:  0.74 (0.22), residues: 1555
  helix:  1.79 (0.18), residues: 869
  sheet: -0.80 (0.45), residues: 130
  loop : -1.31 (0.26), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 346 
 TYR   0.020   0.001   TYR C 228 
 PHE   0.018   0.002   PHE B 448 
 TRP   0.009   0.001   TRP C  48 
 HIS   0.006   0.001   HIS B 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (13286)
  covalent geometry    : angle       0.47744 (17895)
  SS BOND              : bond        0.00263 (    3)
  SS BOND              : angle       2.00548 (    6)
  hydrogen bonds       : bond        0.04765 (  664)
  hydrogen bonds       : angle       4.13594 ( 1965)

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 113
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
REVERT: A  132 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7401 (mm110)
REVERT: A  158 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7757 (mmtt)
REVERT: A  272 ILE cc_start: 0.6288 (OUTLIER) cc_final: 0.5900 (mt)
REVERT: A  364 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7082 (m-80)
REVERT: B  119 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7731 (t70)
REVERT: B  262 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8416 (ttt-90)
REVERT: B  451 ASP cc_start: 0.7582 (OUTLIER) cc_final: 0.7368 (p0)
REVERT: C   76 ARG cc_start: 0.7806 (ttp-110) cc_final: 0.7586 (ttp-110)
REVERT: D  363 MET cc_start: 0.8499 (mtm) cc_final: 0.8158 (mtm)
  outliers start: 64
  outliers final: 44
  residues processed: 172
  average time/residue: 0.1264
  time to fit residues: 30.6529
Evaluate side-chains
  155 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 104
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   93 ASP
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  132 GLN
Chi-restraints excluded: chain A residue  158 LYS
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  238 LYS
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  364 PHE
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   90 SER
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  119 ASP
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  207 SER
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  262 ARG
Chi-restraints excluded: chain B residue  274 LYS
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  431 LEU
Chi-restraints excluded: chain B residue  451 ASP
Chi-restraints excluded: chain B residue  540 ASN
Chi-restraints excluded: chain C residue   56 GLN
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  272 ILE
Chi-restraints excluded: chain C residue  296 ILE
Chi-restraints excluded: chain C residue  314 PHE
Chi-restraints excluded: chain C residue  317 TYR
Chi-restraints excluded: chain C residue  349 ILE
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   54 ASN
Chi-restraints excluded: chain D residue  104 ILE
Chi-restraints excluded: chain D residue  115 ILE
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  176 ILE
Chi-restraints excluded: chain D residue  323 ILE
Chi-restraints excluded: chain D residue  349 ILE
Chi-restraints excluded: chain D residue  366 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 148 optimal weight:    0.0970
   chunk 156 optimal weight:    1.9990
   chunk 121 optimal weight:   10.0000
   chunk 154 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 75 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    0.6980
   chunk 136 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
D  83 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.146186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.114327 restraints weight = 20164.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 2.38
r_work: 0.3156 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.1117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  13289  Z= 0.105
  Angle     :  0.443   5.428  17901  Z= 0.244
  Chirality :  0.039   0.141   1963
  Planarity :  0.004   0.050   2265
  Dihedral  :  3.745  17.172   1737
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 24.22 %
    Favored  : 71.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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:  0.96 (0.22), residues: 1555
  helix:  1.97 (0.18), residues: 877
  sheet: -0.79 (0.44), residues: 134
  loop : -1.26 (0.26), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  76 
 TYR   0.017   0.001   TYR A 228 
 PHE   0.018   0.001   PHE B 448 
 TRP   0.008   0.001   TRP D  48 
 HIS   0.005   0.001   HIS D  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 (13286)
  covalent geometry    : angle       0.44220 (17895)
  SS BOND              : bond        0.00122 (    3)
  SS BOND              : angle       1.65287 (    6)
  hydrogen bonds       : bond        0.04052 (  664)
  hydrogen bonds       : angle       3.96613 ( 1965)

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 120
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7291 (mm110)
REVERT: A  272 ILE cc_start: 0.6184 (OUTLIER) cc_final: 0.5824 (mt)
REVERT: A  571 ARG cc_start: 0.8294 (mtm110) cc_final: 0.7904 (ttm170)
REVERT: B  119 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7676 (t70)
REVERT: B  262 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8426 (ttt-90)
REVERT: B  358 ASP cc_start: 0.7464 (p0) cc_final: 0.7191 (p0)
REVERT: B  441 ARG cc_start: 0.7657 (mtt90) cc_final: 0.7413 (mtp85)
REVERT: B  451 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7324 (p0)
REVERT: B  513 HIS cc_start: 0.7341 (OUTLIER) cc_final: 0.6980 (t70)
REVERT: C   76 ARG cc_start: 0.7761 (ttp-110) cc_final: 0.7554 (ttp-110)
REVERT: C  254 LYS cc_start: 0.7890 (ttmt) cc_final: 0.7562 (tttt)
REVERT: D  363 MET cc_start: 0.8435 (mtm) cc_final: 0.8154 (mtm)
  outliers start: 59
  outliers final: 38
  residues processed: 172
  average time/residue: 0.1343
  time to fit residues: 31.9552
Evaluate side-chains
  155 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 111
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TRP
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   93 ASP
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  132 GLN
Chi-restraints excluded: chain A residue  158 LYS
Chi-restraints excluded: chain A residue  238 LYS
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   90 SER
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  119 ASP
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  207 SER
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  262 ARG
Chi-restraints excluded: chain B residue  274 LYS
Chi-restraints excluded: chain B residue  431 LEU
Chi-restraints excluded: chain B residue  451 ASP
Chi-restraints excluded: chain B residue  513 HIS
Chi-restraints excluded: chain B residue  540 ASN
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  272 ILE
Chi-restraints excluded: chain C residue  296 ILE
Chi-restraints excluded: chain C residue  314 PHE
Chi-restraints excluded: chain C residue  317 TYR
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue  104 ILE
Chi-restraints excluded: chain D residue  115 ILE
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  176 ILE
Chi-restraints excluded: chain D residue  349 ILE
Chi-restraints excluded: chain D residue  366 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 15 optimal weight:    0.1980
   chunk 1 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 131 optimal weight:    0.9980
   chunk 103 optimal weight:    0.0970
   chunk 90 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0970
   chunk 156 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9990
   chunk 93 optimal weight:    0.4980
   overall best weight:    0.3376

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.147772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.116341 restraints weight = 20175.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 2.39
r_work: 0.3192 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.1343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  13289  Z= 0.092
  Angle     :  0.439   5.664  17901  Z= 0.239
  Chirality :  0.039   0.137   1963
  Planarity :  0.004   0.052   2265
  Dihedral  :  3.580  16.619   1737
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 24.84 %
    Favored  : 71.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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:  1.22 (0.22), residues: 1555
  helix:  2.17 (0.18), residues: 883
  sheet: -0.65 (0.45), residues: 134
  loop : -1.14 (0.27), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 477 
 TYR   0.015   0.001   TYR A 228 
 PHE   0.022   0.001   PHE B 448 
 TRP   0.008   0.001   TRP D 208 
 HIS   0.004   0.001   HIS B 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00202 (13286)
  covalent geometry    : angle       0.43749 (17895)
  SS BOND              : bond        0.00051 (    3)
  SS BOND              : angle       1.99425 (    6)
  hydrogen bonds       : bond        0.03542 (  664)
  hydrogen bonds       : angle       3.83289 ( 1965)

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 130
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7125 (mm110)
REVERT: A  272 ILE cc_start: 0.6238 (OUTLIER) cc_final: 0.5869 (mt)
REVERT: A  571 ARG cc_start: 0.8249 (mtm110) cc_final: 0.7878 (ttm170)
REVERT: B  119 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7477 (t70)
REVERT: B  262 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8408 (ttt-90)
REVERT: B  358 ASP cc_start: 0.7436 (p0) cc_final: 0.7159 (p0)
REVERT: B  513 HIS cc_start: 0.7327 (OUTLIER) cc_final: 0.7044 (t70)
REVERT: C  254 LYS cc_start: 0.7744 (ttmt) cc_final: 0.7416 (tttm)
REVERT: D  363 MET cc_start: 0.8369 (mtm) cc_final: 0.8087 (mtm)
  outliers start: 51
  outliers final: 36
  residues processed: 176
  average time/residue: 0.1449
  time to fit residues: 35.1119
Evaluate side-chains
  156 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 115
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TRP
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   93 ASP
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  132 GLN
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  238 LYS
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  403 GLU
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   90 SER
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  119 ASP
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  262 ARG
Chi-restraints excluded: chain B residue  274 LYS
Chi-restraints excluded: chain B residue  431 LEU
Chi-restraints excluded: chain B residue  513 HIS
Chi-restraints excluded: chain B residue  540 ASN
Chi-restraints excluded: chain B residue  544 ASP
Chi-restraints excluded: chain C residue  111 THR
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  272 ILE
Chi-restraints excluded: chain C residue  296 ILE
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  317 TYR
Chi-restraints excluded: chain D residue  115 ILE
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  176 ILE
Chi-restraints excluded: chain D residue  323 ILE
Chi-restraints excluded: chain D residue  366 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 106 optimal weight:    0.9990
   chunk 83 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 151 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 59 optimal weight:    0.8980
   chunk 56 optimal weight:    0.6980
   chunk 136 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 110 optimal weight:    4.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
D  83 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.145305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.113615 restraints weight = 20051.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3375 rms_B_bonded: 2.39
r_work: 0.3147 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.1302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13289  Z= 0.128
  Angle     :  0.474   6.584  17901  Z= 0.259
  Chirality :  0.040   0.139   1963
  Planarity :  0.004   0.050   2265
  Dihedral  :  3.684  18.060   1737
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 24.84 %
    Favored  : 71.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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 (0.22), residues: 1555
  helix:  2.05 (0.18), residues: 885
  sheet: -0.56 (0.46), residues: 132
  loop : -1.25 (0.27), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  76 
 TYR   0.020   0.001   TYR C 228 
 PHE   0.024   0.002   PHE B 448 
 TRP   0.006   0.001   TRP A 208 
 HIS   0.006   0.001   HIS B 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (13286)
  covalent geometry    : angle       0.47198 (17895)
  SS BOND              : bond        0.00063 (    3)
  SS BOND              : angle       2.22427 (    6)
  hydrogen bonds       : bond        0.04264 (  664)
  hydrogen bonds       : angle       3.91325 ( 1965)

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 115
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
REVERT: A  132 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7313 (mm110)
REVERT: A  272 ILE cc_start: 0.6321 (OUTLIER) cc_final: 0.5966 (mt)
REVERT: A  571 ARG cc_start: 0.8232 (mtm110) cc_final: 0.7877 (ttm170)
REVERT: B  119 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7591 (t70)
REVERT: B  262 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8458 (ttt-90)
REVERT: B  304 LYS cc_start: 0.8277 (mmmt) cc_final: 0.8049 (mmmt)
REVERT: C  106 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8409 (m-30)
REVERT: C  254 LYS cc_start: 0.7790 (ttmt) cc_final: 0.7467 (tttm)
REVERT: D  363 MET cc_start: 0.8465 (mtm) cc_final: 0.8172 (mtm)
  outliers start: 56
  outliers final: 43
  residues processed: 166
  average time/residue: 0.1385
  time to fit residues: 32.0055
Evaluate side-chains
  157 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 109
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TRP
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   93 ASP
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  132 GLN
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  238 LYS
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   90 SER
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  119 ASP
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  207 SER
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  262 ARG
Chi-restraints excluded: chain B residue  274 LYS
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  431 LEU
Chi-restraints excluded: chain B residue  540 ASN
Chi-restraints excluded: chain B residue  544 ASP
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue  106 ASP
Chi-restraints excluded: chain C residue  111 THR
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  272 ILE
Chi-restraints excluded: chain C residue  296 ILE
Chi-restraints excluded: chain C residue  314 PHE
Chi-restraints excluded: chain C residue  317 TYR
Chi-restraints excluded: chain C residue  349 ILE
Chi-restraints excluded: chain D residue   54 ASN
Chi-restraints excluded: chain D residue  115 ILE
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  176 ILE
Chi-restraints excluded: chain D residue  323 ILE
Chi-restraints excluded: chain D residue  349 ILE
Chi-restraints excluded: chain D residue  366 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 116 optimal weight:    7.9990
   chunk 151 optimal weight:    1.9990
   chunk 146 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 27 optimal weight:    0.4980
   chunk 153 optimal weight:    4.9990
   chunk 4 optimal weight:    0.8980
   chunk 45 optimal weight:    9.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 513 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.144812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.112956 restraints weight = 20315.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3364 rms_B_bonded: 2.44
r_work: 0.3133 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.1237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13289  Z= 0.140
  Angle     :  0.488   6.084  17901  Z= 0.267
  Chirality :  0.040   0.142   1963
  Planarity :  0.004   0.049   2265
  Dihedral  :  3.786  18.152   1737
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 25.05 %
    Favored  : 71.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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:  1.00 (0.22), residues: 1555
  helix:  1.99 (0.18), residues: 878
  sheet: -0.61 (0.45), residues: 132
  loop : -1.26 (0.26), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C  76 
 TYR   0.023   0.001   TYR C 228 
 PHE   0.027   0.002   PHE B 448 
 TRP   0.007   0.001   TRP C  48 
 HIS   0.006   0.001   HIS B 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (13286)
  covalent geometry    : angle       0.48568 (17895)
  SS BOND              : bond        0.00121 (    3)
  SS BOND              : angle       2.41560 (    6)
  hydrogen bonds       : bond        0.04555 (  664)
  hydrogen bonds       : angle       3.97470 ( 1965)

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 110
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
REVERT: A  132 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7354 (mm-40)
REVERT: A  272 ILE cc_start: 0.6235 (OUTLIER) cc_final: 0.5824 (mt)
REVERT: A  364 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.7090 (m-80)
REVERT: A  571 ARG cc_start: 0.8208 (mtm110) cc_final: 0.7848 (ttm170)
REVERT: B  119 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7687 (t70)
REVERT: B  262 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8419 (ttt-90)
REVERT: C  106 ASP cc_start: 0.8937 (OUTLIER) cc_final: 0.8420 (m-30)
REVERT: C  254 LYS cc_start: 0.7825 (ttmt) cc_final: 0.7522 (tttt)
REVERT: D  363 MET cc_start: 0.8463 (mtm) cc_final: 0.8149 (mtm)
  outliers start: 55
  outliers final: 48
  residues processed: 161
  average time/residue: 0.1457
  time to fit residues: 32.2323
Evaluate side-chains
  160 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 106
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TRP
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   93 ASP
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  132 GLN
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  238 LYS
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  364 PHE
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  513 HIS
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   90 SER
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  119 ASP
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  207 SER
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  262 ARG
Chi-restraints excluded: chain B residue  274 LYS
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  431 LEU
Chi-restraints excluded: chain B residue  540 ASN
Chi-restraints excluded: chain B residue  544 ASP
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue  106 ASP
Chi-restraints excluded: chain C residue  111 THR
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  200 MET
Chi-restraints excluded: chain C residue  272 ILE
Chi-restraints excluded: chain C residue  296 ILE
Chi-restraints excluded: chain C residue  317 TYR
Chi-restraints excluded: chain C residue  349 ILE
Chi-restraints excluded: chain D residue   54 ASN
Chi-restraints excluded: chain D residue  104 ILE
Chi-restraints excluded: chain D residue  115 ILE
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  176 ILE
Chi-restraints excluded: chain D residue  323 ILE
Chi-restraints excluded: chain D residue  349 ILE
Chi-restraints excluded: chain D residue  366 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 131 optimal weight:    0.5980
   chunk 156 optimal weight:    3.9990
   chunk 94 optimal weight:    4.9990
   chunk 78 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 121 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 83 optimal weight:    4.9990
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
A 513 HIS
D  83 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.143945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.112880 restraints weight = 20321.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 2.37
r_work: 0.3133 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.1237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13289  Z= 0.156
  Angle     :  0.510   8.499  17901  Z= 0.279
  Chirality :  0.041   0.143   1963
  Planarity :  0.004   0.054   2265
  Dihedral  :  3.873  18.402   1737
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 25.33 %
    Favored  : 70.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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:  0.89 (0.22), residues: 1555
  helix:  1.88 (0.18), residues: 883
  sheet: -0.63 (0.45), residues: 132
  loop : -1.29 (0.26), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D  76 
 TYR   0.025   0.002   TYR C 228 
 PHE   0.030   0.002   PHE B 448 
 TRP   0.007   0.001   TRP C  48 
 HIS   0.007   0.001   HIS B 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (13286)
  covalent geometry    : angle       0.50812 (17895)
  SS BOND              : bond        0.00131 (    3)
  SS BOND              : angle       2.35656 (    6)
  hydrogen bonds       : bond        0.04783 (  664)
  hydrogen bonds       : angle       4.02268 ( 1965)

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 109
  time to evaluate  : 0.392 
Fit side-chains
REVERT: A  132 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7380 (mm-40)
REVERT: A  364 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7083 (m-80)
REVERT: A  571 ARG cc_start: 0.8200 (mtm110) cc_final: 0.7848 (ttm170)
REVERT: B  119 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7671 (t70)
REVERT: B  262 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8410 (ttt-90)
REVERT: C  106 ASP cc_start: 0.8941 (OUTLIER) cc_final: 0.8420 (m-30)
REVERT: C  254 LYS cc_start: 0.7815 (ttmt) cc_final: 0.7514 (tttt)
REVERT: D  363 MET cc_start: 0.8442 (mtm) cc_final: 0.8109 (mtm)
  outliers start: 55
  outliers final: 47
  residues processed: 159
  average time/residue: 0.1372
  time to fit residues: 30.3846
Evaluate side-chains
  158 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 106
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   93 ASP
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  132 GLN
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  238 LYS
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  364 PHE
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   90 SER
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  119 ASP
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  207 SER
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  262 ARG
Chi-restraints excluded: chain B residue  274 LYS
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  431 LEU
Chi-restraints excluded: chain B residue  540 ASN
Chi-restraints excluded: chain B residue  544 ASP
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue  106 ASP
Chi-restraints excluded: chain C residue  111 THR
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  200 MET
Chi-restraints excluded: chain C residue  272 ILE
Chi-restraints excluded: chain C residue  296 ILE
Chi-restraints excluded: chain C residue  314 PHE
Chi-restraints excluded: chain C residue  317 TYR
Chi-restraints excluded: chain C residue  349 ILE
Chi-restraints excluded: chain D residue   54 ASN
Chi-restraints excluded: chain D residue  104 ILE
Chi-restraints excluded: chain D residue  115 ILE
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain D residue  176 ILE
Chi-restraints excluded: chain D residue  323 ILE
Chi-restraints excluded: chain D residue  349 ILE
Chi-restraints excluded: chain D residue  366 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 146 optimal weight:    0.0020
   chunk 106 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 99 optimal weight:    5.9990
   chunk 113 optimal weight:    2.9990
   chunk 102 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 68 optimal weight:    0.0870
   chunk 85 optimal weight:    4.9990
   chunk 100 optimal weight:    3.9990
   overall best weight:    0.9168

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.145090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.113493 restraints weight = 20151.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 2.42
r_work: 0.3144 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.1273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13289  Z= 0.121
  Angle     :  0.481   7.230  17901  Z= 0.263
  Chirality :  0.040   0.142   1963
  Planarity :  0.004   0.051   2265
  Dihedral  :  3.768  17.659   1737
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 25.40 %
    Favored  : 70.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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:  1.03 (0.22), residues: 1555
  helix:  2.00 (0.18), residues: 883
  sheet: -0.61 (0.45), residues: 132
  loop : -1.23 (0.27), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  76 
 TYR   0.022   0.001   TYR A 228 
 PHE   0.028   0.001   PHE B 448 
 TRP   0.007   0.001   TRP C  48 
 HIS   0.005   0.001   HIS B 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (13286)
  covalent geometry    : angle       0.47930 (17895)
  SS BOND              : bond        0.00091 (    3)
  SS BOND              : angle       2.20186 (    6)
  hydrogen bonds       : bond        0.04284 (  664)
  hydrogen bonds       : angle       3.94308 ( 1965)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2769.84 seconds
wall clock time: 48 minutes 27.25 seconds (2907.25 seconds total)