Starting phenix.real_space_refine
on Wed Mar  4 02:54:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6iww_9743/03_2026/6iww_9743.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6iww_9743/03_2026/6iww_9743.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6iww_9743/03_2026/6iww_9743.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6iww_9743/03_2026/6iww_9743.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6iww_9743/03_2026/6iww_9743.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6iww_9743/03_2026/6iww_9743.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.022
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      69      5.16       5
     C    6741      2.51       5
     N    1653      2.21       5
     O    1764      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10227
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 3054
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 420, 3054
          Classifications: {'peptide': 420}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 397}
    Chain: "B"
      Number of atoms: 320
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 320
          Classifications: {'peptide': 42}
          Link IDs: {'TRANS': 41}
    Chain: "C"
      Number of atoms: 3054
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 420, 3054
          Classifications: {'peptide': 420}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 397}
    Chain: "D"
      Number of atoms: 320
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 320
          Classifications: {'peptide': 42}
          Link IDs: {'TRANS': 41}
    Chain: "E"
      Number of atoms: 3054
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 420, 3054
          Classifications: {'peptide': 420}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 397}
    Chain: "F"
      Number of atoms: 320
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 320
          Classifications: {'peptide': 42}
          Link IDs: {'TRANS': 41}
    Chain: "A"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'LMT': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'LMT': 1}
          Classifications: {'undetermined': 1}
    Chain: "E"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'LMT': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.40, per 1000 atoms: 0.23
  Number of scatterers: 10227
  At special positions: 0
  Unit cell: (104.304, 106.944, 85.8195, 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      69     16.00
     O    1764      8.00
     N    1653      7.00
     C    6741      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.91
  Conformation dependent library (CDL) restraints added in 603.5 milliseconds
  

  2748 Ramachandran restraints generated.
    1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2484

  Finding SS restraints...
    Secondary structure from input PDB file:
      93 helices and 0 sheets defined
      82.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 37
      removed outlier: 3.765A  pdb=" N   ILE A  22 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LEU A  24 " --> pdb=" O   GLN A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 55
      removed outlier: 3.682A  pdb=" N   ASN A  55 " --> pdb=" O   GLY A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 73
      removed outlier: 3.671A  pdb=" N   HIS A  73 " --> pdb=" O   LEU A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 86
    Processing helix  chain 'A' and resid 93 through 100
    Processing helix  chain 'A' and resid 102 through 116
    Processing helix  chain 'A' and resid 121 through 131
      removed outlier: 3.527A  pdb=" N   ILE A 131 " --> pdb=" O   TYR A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 147
      removed outlier: 3.682A  pdb=" N   PHE A 141 " --> pdb=" O   PRO A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 155
    Processing helix  chain 'A' and resid 156 through 160
    Processing helix  chain 'A' and resid 161 through 166
      removed outlier: 3.510A  pdb=" N   ALA A 165 " --> pdb=" O   LEU A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 183
      removed outlier: 3.963A  pdb=" N   PHE A 171 " --> pdb=" O   GLN A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 198
      removed outlier: 3.934A  pdb=" N   ALA A 195 " --> pdb=" O   PRO A 191 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ILE A 196 " --> pdb=" O   GLN A 192 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   GLY A 197 " --> pdb=" O   ALA A 193 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   ILE A 198 " --> pdb=" O   ALA A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 202
    Processing helix  chain 'A' and resid 203 through 214
      removed outlier: 4.217A  pdb=" N   TYR A 209 " --> pdb=" O   PRO A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 217
      No H-bonds generated for 'chain 'A' and resid 215 through 217'
    Processing helix  chain 'A' and resid 218 through 228
    Processing helix  chain 'A' and resid 229 through 231
      No H-bonds generated for 'chain 'A' and resid 229 through 231'
    Processing helix  chain 'A' and resid 232 through 245
      Proline residue:  A 238  - end of helix
      removed outlier: 3.524A  pdb=" N   THR A 245 " --> pdb=" O   MET A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 251
    Processing helix  chain 'A' and resid 261 through 279
      Proline residue:  A 269  - end of helix
    Processing helix  chain 'A' and resid 280 through 282
      No H-bonds generated for 'chain 'A' and resid 280 through 282'
    Processing helix  chain 'A' and resid 283 through 300
      removed outlier: 3.661A  pdb=" N   MET A 289 " --> pdb=" O   PRO A 285 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLY A 293 " --> pdb=" O   MET A 289 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   GLY A 300 " --> pdb=" O   MET A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 310
      removed outlier: 3.694A  pdb=" N   GLN A 310 " --> pdb=" O   SER A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 327
      removed outlier: 5.055A  pdb=" N   ILE A 319 " --> pdb=" O   ASN A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 335
    Processing helix  chain 'A' and resid 336 through 363
      removed outlier: 3.984A  pdb=" N   LEU A 340 " --> pdb=" O   GLN A 336 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   GLY A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   VAL A 347 " --> pdb=" O   LEU A 343 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   ILE A 348 " --> pdb=" O   LEU A 344 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   PHE A 350 " --> pdb=" O   GLY A 346 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ALA A 355 " --> pdb=" O   GLY A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 381
      removed outlier: 3.745A  pdb=" N   VAL A 381 " --> pdb=" O   SER A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 399
      removed outlier: 3.647A  pdb=" N   SER A 398 " --> pdb=" O   VAL A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 431
      removed outlier: 3.936A  pdb=" N   ASN A 412 " --> pdb=" O   ALA A 408 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   ALA A 420 " --> pdb=" O   VAL A 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 43
      removed outlier: 3.915A  pdb=" N   ALA B  38 " --> pdb=" O   ARG B  34 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 18 through 37
      removed outlier: 3.742A  pdb=" N   ILE C  22 " --> pdb=" O   ALA C  18 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ALA C  36 " --> pdb=" O   TRP C  32 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 40 through 55
      removed outlier: 3.570A  pdb=" N   LEU C  45 " --> pdb=" O   PRO C  41 " (cutoff:3.500A)
      Proline residue:  C  46  - end of helix
      removed outlier: 3.724A  pdb=" N   ASN C  55 " --> pdb=" O   GLY C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 64 through 73
      removed outlier: 3.684A  pdb=" N   HIS C  73 " --> pdb=" O   LEU C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 86
    Processing helix  chain 'C' and resid 93 through 100
      removed outlier: 3.536A  pdb=" N   LEU C 100 " --> pdb=" O   GLU C  96 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 116
    Processing helix  chain 'C' and resid 121 through 130
    Processing helix  chain 'C' and resid 135 through 147
      removed outlier: 3.700A  pdb=" N   PHE C 141 " --> pdb=" O   PRO C 137 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 150 through 155
    Processing helix  chain 'C' and resid 156 through 160
    Processing helix  chain 'C' and resid 161 through 166
    Processing helix  chain 'C' and resid 167 through 183
      removed outlier: 3.898A  pdb=" N   PHE C 171 " --> pdb=" O   GLN C 167 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 189 through 198
      removed outlier: 4.195A  pdb=" N   ALA C 195 " --> pdb=" O   PRO C 191 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   ILE C 196 " --> pdb=" O   GLN C 192 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   GLY C 197 " --> pdb=" O   ALA C 193 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   ILE C 198 " --> pdb=" O   ALA C 194 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 199 through 202
    Processing helix  chain 'C' and resid 203 through 214
      removed outlier: 4.228A  pdb=" N   TYR C 209 " --> pdb=" O   PRO C 205 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 215 through 217
      No H-bonds generated for 'chain 'C' and resid 215 through 217'
    Processing helix  chain 'C' and resid 218 through 228
    Processing helix  chain 'C' and resid 229 through 231
      No H-bonds generated for 'chain 'C' and resid 229 through 231'
    Processing helix  chain 'C' and resid 232 through 245
      Proline residue:  C 238  - end of helix
      removed outlier: 3.559A  pdb=" N   THR C 245 " --> pdb=" O   MET C 241 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 246 through 251
      removed outlier: 3.505A  pdb=" N   ARG C 250 " --> pdb=" O   SER C 246 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 261 through 279
      Proline residue:  C 269  - end of helix
    Processing helix  chain 'C' and resid 280 through 282
      No H-bonds generated for 'chain 'C' and resid 280 through 282'
    Processing helix  chain 'C' and resid 283 through 300
      removed outlier: 3.670A  pdb=" N   MET C 289 " --> pdb=" O   PRO C 285 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   GLY C 293 " --> pdb=" O   MET C 289 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   GLY C 300 " --> pdb=" O   MET C 296 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 305 through 310
      removed outlier: 3.717A  pdb=" N   GLN C 310 " --> pdb=" O   SER C 306 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 313 through 327
      removed outlier: 4.993A  pdb=" N   ILE C 319 " --> pdb=" O   ASN C 315 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 330 through 335
    Processing helix  chain 'C' and resid 336 through 364
      removed outlier: 4.015A  pdb=" N   LEU C 340 " --> pdb=" O   GLN C 336 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   GLY C 341 " --> pdb=" O   PRO C 337 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   VAL C 347 " --> pdb=" O   LEU C 343 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   ILE C 348 " --> pdb=" O   LEU C 344 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   PHE C 350 " --> pdb=" O   GLY C 346 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ALA C 355 " --> pdb=" O   GLY C 351 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 376 through 381
      removed outlier: 3.735A  pdb=" N   VAL C 381 " --> pdb=" O   SER C 378 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 385 through 399
      removed outlier: 3.580A  pdb=" N   SER C 398 " --> pdb=" O   VAL C 394 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 408 through 431
      removed outlier: 3.969A  pdb=" N   ASN C 412 " --> pdb=" O   ALA C 408 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ALA C 420 " --> pdb=" O   VAL C 416 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 43
      removed outlier: 3.915A  pdb=" N   ALA D  38 " --> pdb=" O   ARG D  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 18 through 37
      removed outlier: 3.689A  pdb=" N   ILE E  22 " --> pdb=" O   ALA E  18 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LEU E  24 " --> pdb=" O   GLN E  20 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 40 through 55
      removed outlier: 3.594A  pdb=" N   LEU E  45 " --> pdb=" O   PRO E  41 " (cutoff:3.500A)
      Proline residue:  E  46  - end of helix
      removed outlier: 3.725A  pdb=" N   ASN E  55 " --> pdb=" O   GLY E  51 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 64 through 73
      removed outlier: 3.700A  pdb=" N   HIS E  73 " --> pdb=" O   LEU E  69 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 74 through 86
    Processing helix  chain 'E' and resid 93 through 100
    Processing helix  chain 'E' and resid 102 through 116
    Processing helix  chain 'E' and resid 121 through 130
    Processing helix  chain 'E' and resid 135 through 147
      removed outlier: 3.667A  pdb=" N   PHE E 141 " --> pdb=" O   PRO E 137 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 150 through 155
    Processing helix  chain 'E' and resid 156 through 160
    Processing helix  chain 'E' and resid 161 through 166
      removed outlier: 3.697A  pdb=" N   ALA E 165 " --> pdb=" O   LEU E 161 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 167 through 183
      removed outlier: 3.857A  pdb=" N   PHE E 171 " --> pdb=" O   GLN E 167 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 189 through 198
      removed outlier: 3.547A  pdb=" N   ALA E 195 " --> pdb=" O   PRO E 191 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLY E 197 " --> pdb=" O   ALA E 193 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   ILE E 198 " --> pdb=" O   ALA E 194 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 199 through 202
    Processing helix  chain 'E' and resid 203 through 214
      removed outlier: 4.292A  pdb=" N   TYR E 209 " --> pdb=" O   PRO E 205 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 215 through 217
      No H-bonds generated for 'chain 'E' and resid 215 through 217'
    Processing helix  chain 'E' and resid 218 through 228
    Processing helix  chain 'E' and resid 229 through 231
      No H-bonds generated for 'chain 'E' and resid 229 through 231'
    Processing helix  chain 'E' and resid 232 through 245
      Proline residue:  E 238  - end of helix
      removed outlier: 3.546A  pdb=" N   THR E 245 " --> pdb=" O   MET E 241 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 246 through 251
    Processing helix  chain 'E' and resid 261 through 279
      Proline residue:  E 269  - end of helix
    Processing helix  chain 'E' and resid 280 through 282
      No H-bonds generated for 'chain 'E' and resid 280 through 282'
    Processing helix  chain 'E' and resid 283 through 299
      removed outlier: 3.649A  pdb=" N   MET E 289 " --> pdb=" O   PRO E 285 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLY E 293 " --> pdb=" O   MET E 289 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 305 through 311
    Processing helix  chain 'E' and resid 313 through 327
      removed outlier: 5.044A  pdb=" N   ILE E 319 " --> pdb=" O   ASN E 315 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 330 through 335
    Processing helix  chain 'E' and resid 336 through 364
      removed outlier: 3.965A  pdb=" N   LEU E 340 " --> pdb=" O   GLN E 336 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   GLY E 341 " --> pdb=" O   PRO E 337 " (cutoff:3.500A)
      removed outlier: 4.671A  pdb=" N   VAL E 347 " --> pdb=" O   LEU E 343 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   ILE E 348 " --> pdb=" O   LEU E 344 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   PHE E 350 " --> pdb=" O   GLY E 346 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ALA E 355 " --> pdb=" O   GLY E 351 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 376 through 381
      removed outlier: 3.538A  pdb=" N   GLY E 380 " --> pdb=" O   GLY E 377 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   VAL E 381 " --> pdb=" O   SER E 378 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 385 through 399
      removed outlier: 3.584A  pdb=" N   SER E 398 " --> pdb=" O   VAL E 394 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 408 through 431
      removed outlier: 3.855A  pdb=" N   ASN E 412 " --> pdb=" O   ALA E 408 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ALA E 420 " --> pdb=" O   VAL E 416 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 3 through 43
      removed outlier: 3.914A  pdb=" N   ALA F  38 " --> pdb=" O   ARG F  34 " (cutoff:3.500A)

    682 hydrogen bonds defined for protein.
    2004 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.75

  Time building geometry restraints manager: 1.18 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: 3146
        1.34 -     1.46: 1606
        1.46 -     1.57: 5520
        1.57 -     1.69: 0
        1.69 -     1.81: 129
  Bond restraints: 10401
  Sorted by residual:
  bond pdb=" C6' LMT E1000 "
       pdb=" O6' LMT E1000 "
    ideal  model  delta    sigma   weight residual
    1.407  1.364  0.043 2.00e-02 2.50e+03 4.52e+00
  bond pdb=" C8  LMT E1000 "
       pdb=" C9  LMT E1000 "
    ideal  model  delta    sigma   weight residual
    1.531  1.490  0.041 2.00e-02 2.50e+03 4.12e+00
  bond pdb=" C6' LMT C1000 "
       pdb=" O6' LMT C1000 "
    ideal  model  delta    sigma   weight residual
    1.407  1.367  0.040 2.00e-02 2.50e+03 4.09e+00
  bond pdb=" C8  LMT A1000 "
       pdb=" C9  LMT A1000 "
    ideal  model  delta    sigma   weight residual
    1.531  1.491  0.040 2.00e-02 2.50e+03 4.04e+00
  bond pdb=" C8  LMT C1000 "
       pdb=" C9  LMT C1000 "
    ideal  model  delta    sigma   weight residual
    1.531  1.491  0.040 2.00e-02 2.50e+03 4.02e+00
  ... (remaining 10396 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 13147
        1.88 -     3.77: 768
        3.77 -     5.65: 138
        5.65 -     7.53: 44
        7.53 -     9.42: 21
  Bond angle restraints: 14118
  Sorted by residual:
  angle pdb=" N   PRO E 238 "
        pdb=" CA  PRO E 238 "
        pdb=" C   PRO E 238 "
      ideal   model   delta    sigma   weight residual
     110.70  115.58   -4.88 1.22e+00 6.72e-01 1.60e+01
  angle pdb=" N   PRO A 238 "
        pdb=" CA  PRO A 238 "
        pdb=" C   PRO A 238 "
      ideal   model   delta    sigma   weight residual
     110.70  115.49   -4.79 1.22e+00 6.72e-01 1.54e+01
  angle pdb=" N   PRO C 238 "
        pdb=" CA  PRO C 238 "
        pdb=" C   PRO C 238 "
      ideal   model   delta    sigma   weight residual
     110.70  115.32   -4.62 1.22e+00 6.72e-01 1.43e+01
  angle pdb=" CA  PRO E 238 "
        pdb=" C   PRO E 238 "
        pdb=" N   PRO E 239 "
      ideal   model   delta    sigma   weight residual
     117.93  122.31   -4.38 1.20e+00 6.94e-01 1.33e+01
  angle pdb=" CA  PRO A 238 "
        pdb=" C   PRO A 238 "
        pdb=" N   PRO A 239 "
      ideal   model   delta    sigma   weight residual
     117.93  122.30   -4.37 1.20e+00 6.94e-01 1.33e+01
  ... (remaining 14113 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.11: 6138
       22.11 -    44.22: 147
       44.22 -    66.33: 24
       66.33 -    88.44: 1
       88.44 -   110.55: 23
  Dihedral angle restraints: 6333
    sinusoidal: 2448
      harmonic: 3885
  Sorted by residual:
  dihedral pdb=" CA  ALA A 130 "
           pdb=" C   ALA A 130 "
           pdb=" N   ILE A 131 "
           pdb=" CA  ILE A 131 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.15  -19.85     0      5.00e+00 4.00e-02 1.58e+01
  dihedral pdb=" CA  ALA C 130 "
           pdb=" C   ALA C 130 "
           pdb=" N   ILE C 131 "
           pdb=" CA  ILE C 131 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.47  -19.53     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  ALA A 231 "
           pdb=" C   ALA A 231 "
           pdb=" N   LEU A 232 "
           pdb=" CA  LEU A 232 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.75   19.25     0      5.00e+00 4.00e-02 1.48e+01
  ... (remaining 6330 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1202
       0.055 -    0.109: 451
       0.109 -    0.164: 99
       0.164 -    0.219: 16
       0.219 -    0.273: 11
  Chirality restraints: 1779
  Sorted by residual:
  chirality pdb=" CB  ILE C 131 "
            pdb=" CA  ILE C 131 "
            pdb=" CG1 ILE C 131 "
            pdb=" CG2 ILE C 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.27 2.00e-01 2.50e+01 1.87e+00
  chirality pdb=" CB  ILE A 131 "
            pdb=" CA  ILE A 131 "
            pdb=" CG1 ILE A 131 "
            pdb=" CG2 ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.27 2.00e-01 2.50e+01 1.87e+00
  chirality pdb=" CB  ILE E 131 "
            pdb=" CA  ILE E 131 "
            pdb=" CG1 ILE E 131 "
            pdb=" CG2 ILE E 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.71e+00
  ... (remaining 1776 not shown)

  Planarity restraints: 1737
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 151 "   -0.040 5.00e-02 4.00e+02   6.09e-02 5.94e+00
        pdb=" N   PRO A 152 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A 152 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 152 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY E 151 "   -0.040 5.00e-02 4.00e+02   6.01e-02 5.78e+00
        pdb=" N   PRO E 152 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO E 152 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO E 152 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY C 151 "   -0.039 5.00e-02 4.00e+02   5.90e-02 5.57e+00
        pdb=" N   PRO C 152 "    0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO C 152 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO C 152 "   -0.033 5.00e-02 4.00e+02
  ... (remaining 1734 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 3030
        2.82 -     3.34: 10086
        3.34 -     3.86: 17001
        3.86 -     4.38: 20139
        4.38 -     4.90: 33674
  Nonbonded interactions: 83930
  Sorted by model distance:
  nonbonded pdb=" O   GLY C 201 "
            pdb=" OG  SER C 382 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" O   VAL A 144 "
            pdb=" OG1 THR A 148 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" OH  TYR A 229 "
            pdb=" O   LEU A 343 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   GLY A 201 "
            pdb=" OG  SER A 382 "
     model   vdw
     2.320 3.040
  nonbonded pdb=" OH  TYR E 229 "
            pdb=" O   LEU E 343 "
     model   vdw
     2.321 3.040
  ... (remaining 83925 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.560
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.430
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
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      :  0.008   0.064  10401  Z= 0.333
  Angle     :  1.088   9.417  14118  Z= 0.547
  Chirality :  0.060   0.273   1779
  Planarity :  0.009   0.061   1737
  Dihedral  : 13.483 110.551   3849
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.19 (0.17), residues: 1374
  helix: -2.71 (0.12), residues: 1038
  sheet:  None (None), residues: 0
  loop : -2.14 (0.28), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 242 
 TYR   0.015   0.003   TYR E 118 
 PHE   0.025   0.003   PHE A 141 
 TRP   0.005   0.002   TRP A  32 
 HIS   0.009   0.002   HIS C  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00800 (10401)
  covalent geometry    : angle       1.08842 (14118)
  hydrogen bonds       : bond        0.16987 (  682)
  hydrogen bonds       : angle       7.19375 ( 2004)

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

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

  2748 Ramachandran restraints generated.
    1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2748 Ramachandran restraints generated.
    1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  389 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 389
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A  149 ASP cc_start: 0.8614 (t0) cc_final: 0.8349 (t0)
REVERT: A  264 GLU cc_start: 0.7728 (tt0) cc_final: 0.6947 (tp30)
REVERT: A  289 MET cc_start: 0.8341 (tpp) cc_final: 0.7949 (tpp)
REVERT: A  429 TYR cc_start: 0.7884 (t80) cc_final: 0.7640 (t80)
REVERT: C  161 LEU cc_start: 0.8925 (tp) cc_final: 0.8684 (tp)
REVERT: C  264 GLU cc_start: 0.7558 (tt0) cc_final: 0.6712 (tp30)
REVERT: C  338 GLN cc_start: 0.8762 (mp10) cc_final: 0.8413 (mp10)
REVERT: C  429 TYR cc_start: 0.7987 (t80) cc_final: 0.7563 (t80)
REVERT: D    7 LEU cc_start: 0.8545 (mt) cc_final: 0.8217 (mt)
REVERT: E  115 ASP cc_start: 0.8360 (m-30) cc_final: 0.8048 (m-30)
REVERT: E  175 LEU cc_start: 0.8791 (mp) cc_final: 0.8527 (mt)
REVERT: E  253 ARG cc_start: 0.7682 (mmt-90) cc_final: 0.7197 (mmt-90)
REVERT: E  264 GLU cc_start: 0.7925 (tt0) cc_final: 0.7056 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 389
  average time/residue: 0.0959
  time to fit residues: 52.7914
Evaluate side-chains
  235 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    0.4980
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    6.9990
   chunk 55 optimal weight:    8.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  20 GLN
A  72 HIS
A  77 GLN
A 106 GLN
C  72 HIS
C 106 GLN
C 192 GLN
E  20 GLN
E  72 HIS
** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.119951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.103286 restraints weight = 16222.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.104913 restraints weight = 10940.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.106077 restraints weight = 8575.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.106613 restraints weight = 7426.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.106690 restraints weight = 6743.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10401  Z= 0.151
  Angle     :  0.687   6.385  14118  Z= 0.337
  Chirality :  0.043   0.161   1779
  Planarity :  0.006   0.051   1737
  Dihedral  :  8.575  59.630   1617
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  :  9.87 %
    Favored  : 87.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.83 (0.21), residues: 1374
  helix: -0.96 (0.15), residues: 1056
  sheet:  None (None), residues: 0
  loop : -1.48 (0.33), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 158 
 TYR   0.020   0.002   TYR A 182 
 PHE   0.015   0.002   PHE A 268 
 TRP   0.014   0.002   TRP E  32 
 HIS   0.003   0.001   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (10401)
  covalent geometry    : angle       0.68674 (14118)
  hydrogen bonds       : bond        0.03915 (  682)
  hydrogen bonds       : angle       4.77050 ( 2004)

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

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

  2748 Ramachandran restraints generated.
    1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2748 Ramachandran restraints generated.
    1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 296
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ILE cc_start: 0.9222 (mm) cc_final: 0.8989 (mm)
REVERT: A  111 ASN cc_start: 0.8160 (t0) cc_final: 0.7755 (t0)
REVERT: A  159 THR cc_start: 0.8503 (p) cc_final: 0.8214 (p)
REVERT: A  173 THR cc_start: 0.9158 (m) cc_final: 0.8696 (p)
REVERT: A  245 THR cc_start: 0.8025 (m) cc_final: 0.7696 (t)
REVERT: A  248 LYS cc_start: 0.8189 (tppt) cc_final: 0.7945 (pptt)
REVERT: A  365 ASN cc_start: 0.6681 (OUTLIER) cc_final: 0.6463 (m-40)
REVERT: B   42 ARG cc_start: 0.4769 (tmt-80) cc_final: 0.4193 (mtm180)
REVERT: C  109 MET cc_start: 0.7674 (mmm) cc_final: 0.7453 (mmp)
REVERT: C  149 ASP cc_start: 0.8255 (t0) cc_final: 0.8027 (t70)
REVERT: C  159 THR cc_start: 0.8800 (p) cc_final: 0.8446 (p)
REVERT: C  248 LYS cc_start: 0.8263 (tppt) cc_final: 0.8019 (tmmt)
REVERT: C  429 TYR cc_start: 0.7990 (t80) cc_final: 0.7595 (t80)
REVERT: D   10 GLU cc_start: 0.6428 (mt-10) cc_final: 0.6109 (mt-10)
REVERT: E   23 MET cc_start: 0.8584 (tpp) cc_final: 0.8275 (tpp)
REVERT: E  110 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7066 (tm-30)
REVERT: E  111 ASN cc_start: 0.8177 (t0) cc_final: 0.7813 (t0)
REVERT: E  248 LYS cc_start: 0.8066 (tppt) cc_final: 0.7766 (tmmt)
REVERT: E  264 GLU cc_start: 0.8018 (tt0) cc_final: 0.7028 (tp30)
REVERT: E  412 ASN cc_start: 0.8569 (t0) cc_final: 0.8335 (t0)
REVERT: F   10 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6614 (mt-10)
  outliers start: 24
  outliers final: 15
  residues processed: 308
  average time/residue: 0.0910
  time to fit residues: 40.0921
Evaluate side-chains
  264 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 248
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue   87 CYS
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  365 ASN
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain C residue   87 CYS
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  282 ASP
Chi-restraints excluded: chain C residue  306 SER
Chi-restraints excluded: chain C residue  347 VAL
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  161 LEU
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  384 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 106 optimal weight:    6.9990
   chunk 75 optimal weight:    0.8980
   chunk 114 optimal weight:    0.3980
   chunk 123 optimal weight:    0.9980
   chunk 98 optimal weight:    3.9990
   chunk 84 optimal weight:    6.9990
   chunk 89 optimal weight:    2.9990
   chunk 32 optimal weight:   10.0000
   chunk 88 optimal weight:    7.9990
   chunk 78 optimal weight:    4.9990
   overall best weight:    1.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 106 GLN
A 167 GLN
A 237 GLN
E  77 GLN
E 106 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.115557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.098546 restraints weight = 16603.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.100124 restraints weight = 11307.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.101227 restraints weight = 8883.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.101600 restraints weight = 7653.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.101601 restraints weight = 7154.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.3238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10401  Z= 0.178
  Angle     :  0.678   6.678  14118  Z= 0.332
  Chirality :  0.044   0.177   1779
  Planarity :  0.006   0.048   1737
  Dihedral  :  7.310  51.740   1617
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 13.98 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -0.97 (0.22), residues: 1374
  helix: -0.21 (0.16), residues: 1092
  sheet:  None (None), residues: 0
  loop : -1.88 (0.33), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 389 
 TYR   0.017   0.003   TYR C 227 
 PHE   0.015   0.002   PHE A  39 
 TRP   0.008   0.002   TRP E  32 
 HIS   0.008   0.002   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 (10401)
  covalent geometry    : angle       0.67783 (14118)
  hydrogen bonds       : bond        0.03850 (  682)
  hydrogen bonds       : angle       4.64973 ( 2004)

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

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

  2748 Ramachandran restraints generated.
    1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2748 Ramachandran restraints generated.
    1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 272
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A  111 ASN cc_start: 0.8257 (t0) cc_final: 0.7867 (t0)
REVERT: A  173 THR cc_start: 0.9144 (m) cc_final: 0.8634 (p)
REVERT: A  360 MET cc_start: 0.8904 (tpp) cc_final: 0.8578 (tpp)
REVERT: A  378 SER cc_start: 0.8904 (p) cc_final: 0.8548 (p)
REVERT: A  426 MET cc_start: 0.8349 (ttm) cc_final: 0.7854 (mtp)
REVERT: B   15 MET cc_start: 0.7289 (ttp) cc_final: 0.6514 (ttp)
REVERT: B   42 ARG cc_start: 0.4820 (tmt-80) cc_final: 0.4204 (mtm180)
REVERT: C  110 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7064 (tm-30)
REVERT: C  149 ASP cc_start: 0.8206 (t0) cc_final: 0.7964 (t70)
REVERT: C  429 TYR cc_start: 0.8059 (t80) cc_final: 0.7606 (t80)
REVERT: D   10 GLU cc_start: 0.6481 (mt-10) cc_final: 0.6233 (mt-10)
REVERT: E  110 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7131 (tm-30)
REVERT: E  111 ASN cc_start: 0.8389 (t0) cc_final: 0.7874 (t0)
REVERT: E  264 GLU cc_start: 0.7942 (tt0) cc_final: 0.7053 (tp30)
REVERT: E  412 ASN cc_start: 0.8634 (t0) cc_final: 0.8399 (t0)
REVERT: E  429 TYR cc_start: 0.8371 (t80) cc_final: 0.8149 (t80)
REVERT: F   10 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6629 (mt-10)
  outliers start: 29
  outliers final: 22
  residues processed: 286
  average time/residue: 0.0872
  time to fit residues: 36.3501
Evaluate side-chains
  255 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 233
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue   87 CYS
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   87 CYS
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  306 SER
Chi-restraints excluded: chain C residue  347 VAL
Chi-restraints excluded: chain E residue   64 THR
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  161 LEU
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  282 ASP
Chi-restraints excluded: chain E residue  296 MET
Chi-restraints excluded: chain E residue  384 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 85 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 136 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 81 optimal weight:    7.9990
   chunk 48 optimal weight:    2.9990
   chunk 127 optimal weight:    0.0570
   chunk 77 optimal weight:    0.5980
   chunk 103 optimal weight:    0.8980
   chunk 96 optimal weight:    0.0870
   chunk 114 optimal weight:    1.9990
   overall best weight:    0.5278

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

Flipped N/Q/H residues before XYZ refinement:
A  77 GLN
A 365 ASN
A 407 HIS
C  77 GLN
** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.118404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.102245 restraints weight = 16548.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.103584 restraints weight = 11159.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.104778 restraints weight = 8823.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.105140 restraints weight = 7544.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.105657 restraints weight = 7043.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.3588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10401  Z= 0.122
  Angle     :  0.622  12.093  14118  Z= 0.303
  Chirality :  0.042   0.183   1779
  Planarity :  0.006   0.047   1737
  Dihedral  :  6.603  54.486   1617
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 16.95 %
    Favored  : 79.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -0.29 (0.23), residues: 1374
  helix:  0.28 (0.16), residues: 1077
  sheet:  None (None), residues: 0
  loop : -1.61 (0.33), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 389 
 TYR   0.013   0.002   TYR A 429 
 PHE   0.013   0.001   PHE A 268 
 TRP   0.006   0.001   TRP E  32 
 HIS   0.007   0.001   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (10401)
  covalent geometry    : angle       0.62243 (14118)
  hydrogen bonds       : bond        0.03413 (  682)
  hydrogen bonds       : angle       4.42507 ( 2004)

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

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

  2748 Ramachandran restraints generated.
    1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2748 Ramachandran restraints generated.
    1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 268
  time to evaluate  : 0.378 
Fit side-chains
REVERT: A  426 MET cc_start: 0.8262 (ttm) cc_final: 0.7925 (mtp)
REVERT: B   15 MET cc_start: 0.7164 (ttp) cc_final: 0.6441 (ttp)
REVERT: B   42 ARG cc_start: 0.4961 (tmt-80) cc_final: 0.4178 (mtm180)
REVERT: C  149 ASP cc_start: 0.8329 (t0) cc_final: 0.8018 (t70)
REVERT: C  173 THR cc_start: 0.9326 (m) cc_final: 0.9113 (p)
REVERT: C  208 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9045 (mt)
REVERT: C  406 MET cc_start: 0.7523 (tpp) cc_final: 0.7300 (tpp)
REVERT: C  429 TYR cc_start: 0.7933 (t80) cc_final: 0.7453 (t80)
REVERT: E  110 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7133 (tm-30)
REVERT: E  111 ASN cc_start: 0.8115 (t0) cc_final: 0.7759 (t0)
REVERT: E  248 LYS cc_start: 0.8319 (tppt) cc_final: 0.7799 (pttp)
REVERT: E  264 GLU cc_start: 0.7859 (tt0) cc_final: 0.6994 (tp30)
REVERT: F   10 GLU cc_start: 0.6755 (mt-10) cc_final: 0.6389 (mt-10)
  outliers start: 38
  outliers final: 20
  residues processed: 287
  average time/residue: 0.0841
  time to fit residues: 35.3451
Evaluate side-chains
  251 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 230
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  318 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain C residue  318 THR
Chi-restraints excluded: chain C residue  347 VAL
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue   64 THR
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  161 LEU
Chi-restraints excluded: chain E residue  219 LEU
Chi-restraints excluded: chain E residue  287 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 110 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 125 optimal weight:    1.9990
   chunk 105 optimal weight:    6.9990
   chunk 15 optimal weight:    0.0470
   chunk 38 optimal weight:    4.9990
   chunk 82 optimal weight:    7.9990
   chunk 128 optimal weight:    0.7980
   chunk 31 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.9682

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

Flipped N/Q/H residues before XYZ refinement:
A  77 GLN
A 407 HIS
C  77 GLN
C 370 ASN
** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.118593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.101816 restraints weight = 16375.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.103412 restraints weight = 11160.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.104352 restraints weight = 8777.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.105170 restraints weight = 7577.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.105170 restraints weight = 6854.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.3848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10401  Z= 0.132
  Angle     :  0.622  10.057  14118  Z= 0.301
  Chirality :  0.042   0.177   1779
  Planarity :  0.005   0.048   1737
  Dihedral  :  6.404  51.485   1617
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 18.77 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  0.01 (0.23), residues: 1374
  helix:  0.53 (0.17), residues: 1059
  sheet:  None (None), residues: 0
  loop : -1.53 (0.33), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 389 
 TYR   0.019   0.002   TYR C 127 
 PHE   0.012   0.001   PHE A  39 
 TRP   0.006   0.001   TRP C  32 
 HIS   0.003   0.001   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (10401)
  covalent geometry    : angle       0.62150 (14118)
  hydrogen bonds       : bond        0.03390 (  682)
  hydrogen bonds       : angle       4.38150 ( 2004)

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

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

  2748 Ramachandran restraints generated.
    1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2748 Ramachandran restraints generated.
    1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 261
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A   96 GLU cc_start: 0.7739 (mp0) cc_final: 0.7476 (mp0)
REVERT: A  241 MET cc_start: 0.6575 (mpp) cc_final: 0.6070 (mtm)
REVERT: A  264 GLU cc_start: 0.7593 (tt0) cc_final: 0.6704 (tp30)
REVERT: B   15 MET cc_start: 0.7137 (ttp) cc_final: 0.6561 (ttp)
REVERT: B   42 ARG cc_start: 0.4908 (tmt-80) cc_final: 0.4140 (mtm180)
REVERT: C  149 ASP cc_start: 0.8391 (t0) cc_final: 0.8057 (t70)
REVERT: C  173 THR cc_start: 0.9343 (m) cc_final: 0.9126 (p)
REVERT: C  264 GLU cc_start: 0.7318 (tt0) cc_final: 0.6791 (tp30)
REVERT: C  298 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7162 (mm-30)
REVERT: C  375 LEU cc_start: 0.8791 (mm) cc_final: 0.8526 (mt)
REVERT: C  406 MET cc_start: 0.7506 (tpp) cc_final: 0.7279 (tpp)
REVERT: C  429 TYR cc_start: 0.7963 (t80) cc_final: 0.7459 (t80)
REVERT: D   10 GLU cc_start: 0.6416 (mt-10) cc_final: 0.6166 (mt-10)
REVERT: E  110 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7216 (tm-30)
REVERT: E  111 ASN cc_start: 0.8168 (t0) cc_final: 0.7767 (t0)
REVERT: E  167 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8229 (mm110)
REVERT: E  264 GLU cc_start: 0.7892 (tt0) cc_final: 0.6991 (tp30)
REVERT: F   10 GLU cc_start: 0.6748 (mt-10) cc_final: 0.6495 (mt-10)
  outliers start: 37
  outliers final: 27
  residues processed: 280
  average time/residue: 0.0854
  time to fit residues: 35.1742
Evaluate side-chains
  259 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 232
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  318 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue  282 ASP
Chi-restraints excluded: chain C residue  306 SER
Chi-restraints excluded: chain C residue  318 THR
Chi-restraints excluded: chain C residue  347 VAL
Chi-restraints excluded: chain C residue  370 ASN
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue   64 THR
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  161 LEU
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  219 LEU
Chi-restraints excluded: chain E residue  282 ASP
Chi-restraints excluded: chain E residue  296 MET
Chi-restraints excluded: chain E residue  378 SER
Chi-restraints excluded: chain E residue  384 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 111 optimal weight:    0.9980
   chunk 47 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 101 optimal weight:    3.9990
   chunk 105 optimal weight:   10.0000
   chunk 35 optimal weight:    2.9990
   chunk 110 optimal weight:    0.9980
   chunk 88 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A 407 HIS
C 370 ASN
C 407 HIS
** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.117624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.100788 restraints weight = 16587.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.102390 restraints weight = 11142.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.103564 restraints weight = 8693.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.104163 restraints weight = 7451.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.104683 restraints weight = 6789.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.4025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10401  Z= 0.138
  Angle     :  0.640  10.677  14118  Z= 0.308
  Chirality :  0.042   0.189   1779
  Planarity :  0.005   0.046   1737
  Dihedral  :  6.321  50.442   1617
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 19.73 %
    Favored  : 76.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  0.20 (0.23), residues: 1374
  helix:  0.65 (0.17), residues: 1059
  sheet:  None (None), residues: 0
  loop : -1.42 (0.34), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 389 
 TYR   0.015   0.002   TYR C 127 
 PHE   0.015   0.001   PHE E 168 
 TRP   0.005   0.001   TRP C  32 
 HIS   0.008   0.001   HIS C 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (10401)
  covalent geometry    : angle       0.63978 (14118)
  hydrogen bonds       : bond        0.03388 (  682)
  hydrogen bonds       : angle       4.42250 ( 2004)

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

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

  2748 Ramachandran restraints generated.
    1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2748 Ramachandran restraints generated.
    1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 251
  time to evaluate  : 0.376 
Fit side-chains
REVERT: A   56 ILE cc_start: 0.9118 (mm) cc_final: 0.8862 (mm)
REVERT: A  173 THR cc_start: 0.8874 (m) cc_final: 0.8479 (p)
REVERT: A  241 MET cc_start: 0.6655 (mpp) cc_final: 0.6133 (mtm)
REVERT: B   15 MET cc_start: 0.7041 (ttp) cc_final: 0.6551 (ttp)
REVERT: B   42 ARG cc_start: 0.4877 (tmt-80) cc_final: 0.4066 (mtm180)
REVERT: C  110 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7609 (mm-30)
REVERT: C  149 ASP cc_start: 0.8348 (t0) cc_final: 0.7936 (t70)
REVERT: C  219 LEU cc_start: 0.9462 (tp) cc_final: 0.9247 (tp)
REVERT: C  264 GLU cc_start: 0.7428 (tt0) cc_final: 0.6664 (tp30)
REVERT: C  375 LEU cc_start: 0.8843 (mm) cc_final: 0.8513 (mt)
REVERT: C  429 TYR cc_start: 0.7964 (t80) cc_final: 0.7435 (t80)
REVERT: E  110 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7263 (tm-30)
REVERT: E  111 ASN cc_start: 0.8189 (t0) cc_final: 0.7747 (t0)
REVERT: E  167 GLN cc_start: 0.8481 (mm-40) cc_final: 0.8264 (mm110)
REVERT: E  248 LYS cc_start: 0.8376 (tppt) cc_final: 0.7894 (pttp)
REVERT: E  264 GLU cc_start: 0.7912 (tt0) cc_final: 0.6999 (tp30)
REVERT: E  389 ARG cc_start: 0.7995 (mtp-110) cc_final: 0.7794 (mtp180)
REVERT: F   10 GLU cc_start: 0.6728 (mt-10) cc_final: 0.6426 (mt-10)
  outliers start: 38
  outliers final: 26
  residues processed: 272
  average time/residue: 0.0855
  time to fit residues: 34.5641
Evaluate side-chains
  251 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 225
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 CYS
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  318 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  282 ASP
Chi-restraints excluded: chain C residue  306 SER
Chi-restraints excluded: chain C residue  318 THR
Chi-restraints excluded: chain C residue  347 VAL
Chi-restraints excluded: chain C residue  370 ASN
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue   64 THR
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  161 LEU
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  219 LEU
Chi-restraints excluded: chain E residue  282 ASP
Chi-restraints excluded: chain E residue  287 LEU
Chi-restraints excluded: chain E residue  296 MET
Chi-restraints excluded: chain E residue  378 SER
Chi-restraints excluded: chain E residue  416 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 137 optimal weight:    5.9990
   chunk 35 optimal weight:    0.4980
   chunk 6 optimal weight:    3.9990
   chunk 106 optimal weight:    0.8980
   chunk 111 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 48 optimal weight:    0.2980
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 237 GLN
A 407 HIS
C 370 ASN
C 407 HIS
** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.119202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.102417 restraints weight = 16280.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.103905 restraints weight = 11375.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.104976 restraints weight = 9032.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.105695 restraints weight = 7753.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.105984 restraints weight = 7074.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.4238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10401  Z= 0.127
  Angle     :  0.641  11.511  14118  Z= 0.309
  Chirality :  0.042   0.172   1779
  Planarity :  0.005   0.045   1737
  Dihedral  :  6.184  50.098   1617
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 21.07 %
    Favored  : 75.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  0.37 (0.23), residues: 1374
  helix:  0.74 (0.17), residues: 1056
  sheet:  None (None), residues: 0
  loop : -1.23 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 389 
 TYR   0.022   0.002   TYR E 429 
 PHE   0.013   0.001   PHE C 292 
 TRP   0.005   0.001   TRP C  32 
 HIS   0.005   0.001   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (10401)
  covalent geometry    : angle       0.64106 (14118)
  hydrogen bonds       : bond        0.03342 (  682)
  hydrogen bonds       : angle       4.40088 ( 2004)

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

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

  2748 Ramachandran restraints generated.
    1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2748 Ramachandran restraints generated.
    1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 257
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A   56 ILE cc_start: 0.9066 (mm) cc_final: 0.8760 (mm)
REVERT: A  173 THR cc_start: 0.8895 (m) cc_final: 0.8547 (p)
REVERT: A  241 MET cc_start: 0.6794 (mpp) cc_final: 0.6336 (mtm)
REVERT: B   15 MET cc_start: 0.7073 (ttp) cc_final: 0.6590 (ttp)
REVERT: C  149 ASP cc_start: 0.8403 (t0) cc_final: 0.7963 (t70)
REVERT: C  264 GLU cc_start: 0.7558 (tt0) cc_final: 0.6642 (tp30)
REVERT: C  375 LEU cc_start: 0.8871 (mm) cc_final: 0.8531 (mt)
REVERT: E  110 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7296 (tm-30)
REVERT: E  111 ASN cc_start: 0.8175 (t0) cc_final: 0.7822 (t0)
REVERT: E  167 GLN cc_start: 0.8427 (mm-40) cc_final: 0.8152 (mm110)
REVERT: E  264 GLU cc_start: 0.7933 (tt0) cc_final: 0.7000 (tp30)
REVERT: F   10 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6568 (mt-10)
  outliers start: 32
  outliers final: 26
  residues processed: 274
  average time/residue: 0.0832
  time to fit residues: 33.8843
Evaluate side-chains
  263 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 237
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue   87 CYS
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  318 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue  161 LEU
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  282 ASP
Chi-restraints excluded: chain C residue  306 SER
Chi-restraints excluded: chain C residue  347 VAL
Chi-restraints excluded: chain C residue  370 ASN
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue   64 THR
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  161 LEU
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  282 ASP
Chi-restraints excluded: chain E residue  287 LEU
Chi-restraints excluded: chain E residue  296 MET
Chi-restraints excluded: chain E residue  416 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 135 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 90 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 94 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 113 optimal weight:    1.9990
   chunk 105 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A  77 GLN
A 167 GLN
A 407 HIS
C 370 ASN
C 407 HIS
** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 370 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.118969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.102299 restraints weight = 16240.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.103726 restraints weight = 11350.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.104832 restraints weight = 9040.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.105335 restraints weight = 7813.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.105818 restraints weight = 7183.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.4358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10401  Z= 0.134
  Angle     :  0.670  11.551  14118  Z= 0.319
  Chirality :  0.042   0.174   1779
  Planarity :  0.005   0.045   1737
  Dihedral  :  6.137  48.428   1617
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 22.13 %
    Favored  : 74.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  0.49 (0.23), residues: 1374
  helix:  0.84 (0.17), residues: 1056
  sheet:  None (None), residues: 0
  loop : -1.23 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 258 
 TYR   0.023   0.002   TYR E 429 
 PHE   0.011   0.001   PHE A  49 
 TRP   0.005   0.001   TRP C  32 
 HIS   0.005   0.001   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (10401)
  covalent geometry    : angle       0.66978 (14118)
  hydrogen bonds       : bond        0.03391 (  682)
  hydrogen bonds       : angle       4.41292 ( 2004)

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

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

  2748 Ramachandran restraints generated.
    1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2748 Ramachandran restraints generated.
    1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 248
  time to evaluate  : 0.400 
Fit side-chains
REVERT: A   56 ILE cc_start: 0.9050 (mm) cc_final: 0.8738 (mm)
REVERT: A  241 MET cc_start: 0.6737 (mpp) cc_final: 0.6292 (mtm)
REVERT: B    7 LEU cc_start: 0.8520 (mm) cc_final: 0.8312 (mt)
REVERT: C  149 ASP cc_start: 0.8392 (t0) cc_final: 0.7988 (t70)
REVERT: C  173 THR cc_start: 0.9352 (m) cc_final: 0.9097 (p)
REVERT: C  375 LEU cc_start: 0.8907 (mm) cc_final: 0.8567 (mt)
REVERT: E  111 ASN cc_start: 0.8140 (t0) cc_final: 0.7670 (t0)
REVERT: E  167 GLN cc_start: 0.8414 (mm-40) cc_final: 0.8153 (mm110)
REVERT: E  248 LYS cc_start: 0.8619 (tppt) cc_final: 0.7968 (pttp)
REVERT: E  264 GLU cc_start: 0.7949 (tt0) cc_final: 0.7010 (tp30)
REVERT: F   10 GLU cc_start: 0.6705 (mt-10) cc_final: 0.6357 (mt-10)
  outliers start: 31
  outliers final: 25
  residues processed: 262
  average time/residue: 0.0792
  time to fit residues: 31.5009
Evaluate side-chains
  253 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 228
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 CYS
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  318 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue  282 ASP
Chi-restraints excluded: chain C residue  306 SER
Chi-restraints excluded: chain C residue  318 THR
Chi-restraints excluded: chain C residue  347 VAL
Chi-restraints excluded: chain C residue  370 ASN
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue   64 THR
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  161 LEU
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  282 ASP
Chi-restraints excluded: chain E residue  287 LEU
Chi-restraints excluded: chain E residue  296 MET
Chi-restraints excluded: chain E residue  340 LEU
Chi-restraints excluded: chain E residue  416 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 90 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 130 optimal weight:    0.9990
   chunk 41 optimal weight:    4.9990
   chunk 129 optimal weight:    2.9990
   chunk 69 optimal weight:    6.9990
   chunk 74 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 86 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 407 HIS
C 370 ASN
C 407 HIS
** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.116521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.100056 restraints weight = 16366.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.101357 restraints weight = 11395.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.102422 restraints weight = 9182.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.102898 restraints weight = 7951.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.103394 restraints weight = 7337.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.4397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10401  Z= 0.163
  Angle     :  0.705  14.131  14118  Z= 0.332
  Chirality :  0.044   0.178   1779
  Planarity :  0.005   0.046   1737
  Dihedral  :  6.255  47.353   1617
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 22.80 %
    Favored  : 74.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  0.40 (0.23), residues: 1374
  helix:  0.79 (0.17), residues: 1059
  sheet:  None (None), residues: 0
  loop : -1.36 (0.34), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 258 
 TYR   0.025   0.003   TYR E 429 
 PHE   0.014   0.001   PHE A 292 
 TRP   0.005   0.001   TRP C  32 
 HIS   0.005   0.001   HIS A 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (10401)
  covalent geometry    : angle       0.70470 (14118)
  hydrogen bonds       : bond        0.03505 (  682)
  hydrogen bonds       : angle       4.54505 ( 2004)

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

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

  2748 Ramachandran restraints generated.
    1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2748 Ramachandran restraints generated.
    1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 229
  time to evaluate  : 0.271 
Fit side-chains
REVERT: A   56 ILE cc_start: 0.9175 (mm) cc_final: 0.8949 (mm)
REVERT: C  149 ASP cc_start: 0.8343 (t0) cc_final: 0.7950 (t70)
REVERT: C  375 LEU cc_start: 0.8986 (mm) cc_final: 0.8679 (mt)
REVERT: E  111 ASN cc_start: 0.8077 (t0) cc_final: 0.7592 (t0)
REVERT: E  167 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8182 (mm110)
REVERT: E  248 LYS cc_start: 0.8572 (tppt) cc_final: 0.7942 (pttt)
REVERT: E  412 ASN cc_start: 0.8548 (t0) cc_final: 0.8348 (t0)
REVERT: F   19 MET cc_start: 0.6174 (OUTLIER) cc_final: 0.5818 (mmm)
  outliers start: 31
  outliers final: 28
  residues processed: 241
  average time/residue: 0.0752
  time to fit residues: 27.3658
Evaluate side-chains
  256 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 227
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 CYS
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue  161 LEU
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  282 ASP
Chi-restraints excluded: chain C residue  306 SER
Chi-restraints excluded: chain C residue  318 THR
Chi-restraints excluded: chain C residue  347 VAL
Chi-restraints excluded: chain C residue  370 ASN
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue   64 THR
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  161 LEU
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  219 LEU
Chi-restraints excluded: chain E residue  282 ASP
Chi-restraints excluded: chain E residue  287 LEU
Chi-restraints excluded: chain E residue  296 MET
Chi-restraints excluded: chain E residue  340 LEU
Chi-restraints excluded: chain E residue  416 VAL
Chi-restraints excluded: chain F residue   19 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 90 optimal weight:    0.0020
   chunk 131 optimal weight:    0.9990
   chunk 104 optimal weight:    0.2980
   chunk 91 optimal weight:    0.8980
   chunk 101 optimal weight:    8.9990
   chunk 83 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 118 optimal weight:    0.8980
   chunk 79 optimal weight:    0.4980
   chunk 100 optimal weight:    2.9990
   chunk 94 optimal weight:    0.0570
   overall best weight:    0.3506

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

Flipped N/Q/H residues before XYZ refinement:
A 370 ASN
A 407 HIS
C 156 ASN
C 370 ASN
C 407 HIS
** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.122555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.106021 restraints weight = 16014.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.107294 restraints weight = 11209.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.108537 restraints weight = 8970.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.109071 restraints weight = 7708.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.109071 restraints weight = 7059.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.4653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10401  Z= 0.124
  Angle     :  0.681  15.011  14118  Z= 0.322
  Chirality :  0.042   0.258   1779
  Planarity :  0.005   0.044   1737
  Dihedral  :  6.049  52.365   1617
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 24.23 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  0.58 (0.23), residues: 1374
  helix:  0.89 (0.16), residues: 1059
  sheet:  None (None), residues: 0
  loop : -1.16 (0.35), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 389 
 TYR   0.028   0.002   TYR E 429 
 PHE   0.015   0.001   PHE C 350 
 TRP   0.006   0.001   TRP C  32 
 HIS   0.005   0.001   HIS A 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (10401)
  covalent geometry    : angle       0.68110 (14118)
  hydrogen bonds       : bond        0.03295 (  682)
  hydrogen bonds       : angle       4.44042 ( 2004)

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

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

  2748 Ramachandran restraints generated.
    1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2748 Ramachandran restraints generated.
    1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 261
  time to evaluate  : 0.312 
Fit side-chains
REVERT: C  149 ASP cc_start: 0.8269 (t0) cc_final: 0.7983 (t70)
REVERT: D   36 MET cc_start: 0.7365 (mmp) cc_final: 0.6909 (mmp)
REVERT: E  111 ASN cc_start: 0.7943 (t0) cc_final: 0.7521 (t0)
REVERT: E  248 LYS cc_start: 0.8449 (tppt) cc_final: 0.7919 (pttt)
REVERT: E  254 MET cc_start: 0.6174 (mmt) cc_final: 0.5686 (mmt)
  outliers start: 26
  outliers final: 21
  residues processed: 270
  average time/residue: 0.0841
  time to fit residues: 33.6972
Evaluate side-chains
  262 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 241
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 CYS
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  318 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  370 ASN
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  282 ASP
Chi-restraints excluded: chain C residue  318 THR
Chi-restraints excluded: chain C residue  347 VAL
Chi-restraints excluded: chain C residue  370 ASN
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue   64 THR
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  161 LEU
Chi-restraints excluded: chain E residue  219 LEU
Chi-restraints excluded: chain E residue  287 LEU
Chi-restraints excluded: chain E residue  340 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 91 optimal weight:    6.9990
   chunk 35 optimal weight:    7.9990
   chunk 28 optimal weight:    4.9990
   chunk 96 optimal weight:    4.9990
   chunk 57 optimal weight:    4.9990
   chunk 127 optimal weight:    0.8980
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 370 ASN
C 370 ASN
C 407 HIS
** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 370 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.116289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.099149 restraints weight = 16568.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.100474 restraints weight = 11585.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.101605 restraints weight = 9265.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.101895 restraints weight = 8006.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.102406 restraints weight = 7538.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.4532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  10401  Z= 0.203
  Angle     :  0.760  14.368  14118  Z= 0.357
  Chirality :  0.046   0.198   1779
  Planarity :  0.005   0.046   1737
  Dihedral  :  6.246  46.448   1617
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 24.43 %
    Favored  : 72.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  0.42 (0.23), residues: 1374
  helix:  0.78 (0.16), residues: 1065
  sheet:  None (None), residues: 0
  loop : -1.27 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 258 
 TYR   0.023   0.002   TYR E 229 
 PHE   0.018   0.002   PHE C 168 
 TRP   0.005   0.001   TRP C  32 
 HIS   0.004   0.001   HIS A 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 (10401)
  covalent geometry    : angle       0.76026 (14118)
  hydrogen bonds       : bond        0.03668 (  682)
  hydrogen bonds       : angle       4.65156 ( 2004)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1477.26 seconds
wall clock time: 26 minutes 16.13 seconds (1576.13 seconds total)