Starting phenix.real_space_refine
on Fri Feb 14 14:33:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6iww_9743/02_2025/6iww_9743.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6iww_9743/02_2025/6iww_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6iww_9743/02_2025/6iww_9743.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6iww_9743/02_2025/6iww_9743.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6iww_9743/02_2025/6iww_9743.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6iww_9743/02_2025/6iww_9743.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.022
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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.22, per 1000 atoms: 0.61
  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: 2.75
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 1.26
  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: 3.08

  Time building geometry restraints manager: 3.18 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
}

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:             0.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     25.620
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.860
-------------------------------------------------------------------------------
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= 0.514
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.19 (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
 TRP   0.005   0.002   TRP A  32 
 HIS   0.009   0.002   HIS C  72 
 PHE   0.025   0.003   PHE A 141 
 TYR   0.015   0.003   TYR E 118 
 ARG   0.002   0.000   ARG C 242 

*********************** 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  : 1.032 
Fit side-chains
REVERT: A  149 ASP cc_start: 0.8613 (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: 0.8340 (tpp) cc_final: 0.7946 (tpp)
REVERT: A  429 TYR cc_start: 0.7884 (t80) cc_final: 0.7643 (t80)
REVERT: C  161 LEU cc_start: 0.8925 (tp) cc_final: 0.8686 (tp)
REVERT: C  175 LEU cc_start: 0.8979 (mp) cc_final: 0.8778 (mt)
REVERT: C  264 GLU cc_start: 0.7559 (tt0) cc_final: 0.6711 (tp30)
REVERT: C  338 GLN cc_start: 0.8762 (mp10) cc_final: 0.8414 (mp10)
REVERT: C  429 TYR cc_start: 0.7987 (t80) cc_final: 0.7565 (t80)
REVERT: D    7 LEU cc_start: 0.8545 (mt) cc_final: 0.8216 (mt)
REVERT: E  115 ASP cc_start: 0.8360 (m-30) cc_final: 0.8047 (m-30)
REVERT: E  175 LEU cc_start: 0.8791 (mp) cc_final: 0.8530 (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: 0.2227
  time to fit residues: 120.3836
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  : 1.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 116 optimal weight:    9.9990
   chunk 104 optimal weight:    0.7980
   chunk 58 optimal weight:    0.8980
   chunk 35 optimal weight:    7.9990
   chunk 70 optimal weight:    8.9990
   chunk 55 optimal weight:    1.9990
   chunk 108 optimal weight:    7.9990
   chunk 41 optimal weight:    4.9990
   chunk 65 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9980
   chunk 125 optimal weight:    2.9990
   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  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

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.118720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.102041 restraints weight = 16215.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.103651 restraints weight = 11015.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.104575 restraints weight = 8661.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.2646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10401  Z= 0.233
  Angle     :  0.696   6.545  14118  Z= 0.340
  Chirality :  0.043   0.161   1779
  Planarity :  0.006   0.052   1737
  Dihedral  :  8.588  59.741   1617
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 10.06 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.83 (0.21), residues: 1374
  helix: -0.93 (0.15), residues: 1050
  sheet:  None (None), residues: 0
  loop : -1.63 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.003   TRP E  32 
 HIS   0.003   0.001   HIS A  72 
 PHE   0.014   0.002   PHE A 268 
 TYR   0.021   0.002   TYR A 182 
 ARG   0.004   0.000   ARG E 158 

*********************** 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
  312 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 290
  time to evaluate  : 0.993 
Fit side-chains
REVERT: A  111 ASN cc_start: 0.8198 (t0) cc_final: 0.7800 (t0)
REVERT: A  159 THR cc_start: 0.8546 (p) cc_final: 0.8255 (p)
REVERT: A  173 THR cc_start: 0.9171 (m) cc_final: 0.8712 (p)
REVERT: A  245 THR cc_start: 0.8074 (m) cc_final: 0.7816 (t)
REVERT: A  248 LYS cc_start: 0.8233 (tppt) cc_final: 0.7979 (pptt)
REVERT: A  292 PHE cc_start: 0.8994 (t80) cc_final: 0.8729 (t80)
REVERT: A  365 ASN cc_start: 0.6748 (OUTLIER) cc_final: 0.6533 (m-40)
REVERT: B   15 MET cc_start: 0.6966 (ttp) cc_final: 0.6628 (ttp)
REVERT: B   42 ARG cc_start: 0.4844 (tmt-80) cc_final: 0.4228 (mtm180)
REVERT: C  109 MET cc_start: 0.7707 (mmm) cc_final: 0.7489 (mmp)
REVERT: C  149 ASP cc_start: 0.8261 (t0) cc_final: 0.8043 (t70)
REVERT: C  159 THR cc_start: 0.8771 (p) cc_final: 0.8391 (p)
REVERT: C  248 LYS cc_start: 0.8283 (tppt) cc_final: 0.8038 (tmmt)
REVERT: C  429 TYR cc_start: 0.7999 (t80) cc_final: 0.7602 (t80)
REVERT: E  110 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7090 (tm-30)
REVERT: E  111 ASN cc_start: 0.8229 (t0) cc_final: 0.7769 (t0)
REVERT: E  248 LYS cc_start: 0.8075 (tppt) cc_final: 0.7764 (tmmt)
REVERT: E  264 GLU cc_start: 0.8074 (tt0) cc_final: 0.7062 (tp30)
REVERT: E  412 ASN cc_start: 0.8589 (t0) cc_final: 0.8382 (t0)
REVERT: F   10 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6685 (mt-10)
  outliers start: 22
  outliers final: 15
  residues processed: 301
  average time/residue: 0.2183
  time to fit residues: 92.7085
Evaluate side-chains
  256 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 240
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
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 103 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0050
   chunk 115 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   chunk 108 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 122 optimal weight:    0.3980
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
A 106 GLN
A 237 GLN
A 407 HIS
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 = 0.3300 r_free = 0.3300 target = 0.119328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.103301 restraints weight = 16454.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.104720 restraints weight = 11071.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.105824 restraints weight = 8719.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.3253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10401  Z= 0.188
  Angle     :  0.631   7.707  14118  Z= 0.307
  Chirality :  0.042   0.152   1779
  Planarity :  0.006   0.048   1737
  Dihedral  :  7.042  55.360   1617
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 13.70 %
    Favored  : 84.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.22), residues: 1374
  helix: -0.03 (0.16), residues: 1035
  sheet:  None (None), residues: 0
  loop : -1.51 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP C  32 
 HIS   0.009   0.001   HIS A 407 
 PHE   0.017   0.001   PHE A 292 
 TYR   0.018   0.002   TYR E 127 
 ARG   0.005   0.001   ARG E 389 

*********************** 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
  315 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 292
  time to evaluate  : 1.018 
Fit side-chains
REVERT: A  111 ASN cc_start: 0.8148 (t0) cc_final: 0.7778 (t0)
REVERT: A  360 MET cc_start: 0.8875 (tpp) cc_final: 0.8524 (tpp)
REVERT: B   15 MET cc_start: 0.6815 (ttp) cc_final: 0.6508 (ttp)
REVERT: B   42 ARG cc_start: 0.4881 (tmt-80) cc_final: 0.4244 (mtm180)
REVERT: C  110 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7087 (tm-30)
REVERT: C  149 ASP cc_start: 0.8157 (t0) cc_final: 0.7929 (t70)
REVERT: C  228 SER cc_start: 0.9102 (m) cc_final: 0.8853 (p)
REVERT: C  264 GLU cc_start: 0.7390 (tt0) cc_final: 0.6802 (tp30)
REVERT: C  350 PHE cc_start: 0.8137 (m-10) cc_final: 0.7812 (m-10)
REVERT: C  406 MET cc_start: 0.7650 (tpp) cc_final: 0.7365 (tpp)
REVERT: C  429 TYR cc_start: 0.8007 (t80) cc_final: 0.7571 (t80)
REVERT: E  110 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7101 (tm-30)
REVERT: E  111 ASN cc_start: 0.8247 (t0) cc_final: 0.7843 (t0)
REVERT: E  254 MET cc_start: 0.6217 (mmm) cc_final: 0.5973 (mmm)
REVERT: E  264 GLU cc_start: 0.8066 (tt0) cc_final: 0.7091 (tp30)
REVERT: E  375 LEU cc_start: 0.8756 (mp) cc_final: 0.8542 (mt)
REVERT: F   10 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6643 (mt-10)
  outliers start: 23
  outliers final: 17
  residues processed: 303
  average time/residue: 0.2039
  time to fit residues: 88.6532
Evaluate side-chains
  252 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 235
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
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  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 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  282 ASP
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  384 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 17 optimal weight:    0.2980
   chunk 66 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9980
   chunk 104 optimal weight:    0.5980
   chunk 109 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 121 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 407 HIS
** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  55 ASN
E 106 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.119410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.102799 restraints weight = 16264.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.104472 restraints weight = 11002.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.105585 restraints weight = 8567.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.3614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10401  Z= 0.190
  Angle     :  0.615  11.678  14118  Z= 0.300
  Chirality :  0.041   0.154   1779
  Planarity :  0.005   0.047   1737
  Dihedral  :  6.466  51.544   1617
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 16.76 %
    Favored  : 80.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.23), residues: 1374
  helix:  0.44 (0.17), residues: 1032
  sheet:  None (None), residues: 0
  loop : -1.39 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  32 
 HIS   0.008   0.001   HIS A 407 
 PHE   0.015   0.001   PHE A 292 
 TYR   0.016   0.002   TYR E 182 
 ARG   0.007   0.000   ARG E 389 

*********************** 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
  304 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 273
  time to evaluate  : 1.151 
Fit side-chains
REVERT: A  426 MET cc_start: 0.8240 (ttm) cc_final: 0.7959 (mtp)
REVERT: B   15 MET cc_start: 0.6823 (ttp) cc_final: 0.6549 (ttp)
REVERT: B   42 ARG cc_start: 0.4953 (tmt-80) cc_final: 0.4180 (mtm180)
REVERT: C  110 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7501 (tm-30)
REVERT: C  149 ASP cc_start: 0.8319 (t0) cc_final: 0.8017 (t70)
REVERT: C  228 SER cc_start: 0.9227 (m) cc_final: 0.8993 (p)
REVERT: C  264 GLU cc_start: 0.7299 (tt0) cc_final: 0.6711 (tp30)
REVERT: C  375 LEU cc_start: 0.8805 (mm) cc_final: 0.8481 (mp)
REVERT: C  406 MET cc_start: 0.7576 (tpp) cc_final: 0.7363 (tpp)
REVERT: E   23 MET cc_start: 0.8664 (mmm) cc_final: 0.8270 (tpt)
REVERT: E  110 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7156 (tm-30)
REVERT: E  111 ASN cc_start: 0.8150 (t0) cc_final: 0.7793 (t0)
REVERT: E  248 LYS cc_start: 0.8405 (tppt) cc_final: 0.7867 (pttp)
REVERT: E  264 GLU cc_start: 0.8013 (tt0) cc_final: 0.7059 (tp30)
  outliers start: 31
  outliers final: 22
  residues processed: 292
  average time/residue: 0.1969
  time to fit residues: 83.2905
Evaluate side-chains
  260 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 238
  time to evaluate  : 1.183 
-------------------------------------------------------------------------------
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  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 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  282 ASP
Chi-restraints excluded: chain C residue  306 SER
Chi-restraints excluded: chain C residue  347 VAL
Chi-restraints excluded: chain E residue   42 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  296 MET
Chi-restraints excluded: chain E residue  384 VAL
Chi-restraints excluded: chain E residue  416 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 128 optimal weight:    0.9990
   chunk 61 optimal weight:    5.9990
   chunk 97 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 103 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 89 optimal weight:    1.9990
   chunk 13 optimal weight:    8.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.1584

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.117628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.100275 restraints weight = 16395.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.102157 restraints weight = 10392.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.103371 restraints weight = 7823.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.3804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10401  Z= 0.213
  Angle     :  0.621   9.685  14118  Z= 0.303
  Chirality :  0.042   0.164   1779
  Planarity :  0.005   0.051   1737
  Dihedral  :  6.343  49.317   1617
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 17.91 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.23), residues: 1374
  helix:  0.66 (0.17), residues: 1032
  sheet:  None (None), residues: 0
  loop : -1.07 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  32 
 HIS   0.002   0.001   HIS A  73 
 PHE   0.020   0.001   PHE A 292 
 TYR   0.018   0.002   TYR C 127 
 ARG   0.003   0.000   ARG C 253 

*********************** 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
  287 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 250
  time to evaluate  : 1.186 
Fit side-chains
REVERT: B   42 ARG cc_start: 0.4963 (tmt-80) cc_final: 0.4137 (mtm180)
REVERT: C  110 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7379 (tm-30)
REVERT: C  149 ASP cc_start: 0.8412 (t0) cc_final: 0.8083 (t70)
REVERT: C  173 THR cc_start: 0.9362 (m) cc_final: 0.9106 (p)
REVERT: C  208 ILE cc_start: 0.9444 (OUTLIER) cc_final: 0.8966 (mt)
REVERT: C  219 LEU cc_start: 0.9439 (tp) cc_final: 0.9190 (tp)
REVERT: C  264 GLU cc_start: 0.7437 (tt0) cc_final: 0.6868 (tp30)
REVERT: C  298 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7228 (mm-30)
REVERT: C  375 LEU cc_start: 0.8868 (mm) cc_final: 0.8577 (mt)
REVERT: C  406 MET cc_start: 0.7555 (tpp) cc_final: 0.7319 (tpp)
REVERT: E   23 MET cc_start: 0.8696 (mmm) cc_final: 0.8162 (tpt)
REVERT: E   43 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8583 (tt)
REVERT: E  110 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7253 (tm-30)
REVERT: E  111 ASN cc_start: 0.8264 (t0) cc_final: 0.7865 (t0)
  outliers start: 37
  outliers final: 24
  residues processed: 273
  average time/residue: 0.2039
  time to fit residues: 80.8353
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  : 1.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   87 CYS
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  375 LEU
Chi-restraints excluded: chain A residue  384 VAL
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  208 ILE
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 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  384 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 75 optimal weight:    0.7980
   chunk 80 optimal weight:    7.9990
   chunk 57 optimal weight:    0.8980
   chunk 86 optimal weight:    1.9990
   chunk 109 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9980
   chunk 136 optimal weight:    0.8980
   chunk 131 optimal weight:    0.8980
   chunk 125 optimal weight:    0.8980
   chunk 99 optimal weight:    8.9990
   chunk 130 optimal weight:    2.9990
   overall best weight:    0.8180

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.119137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.102763 restraints weight = 16391.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.104331 restraints weight = 11107.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.105445 restraints weight = 8663.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.4013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10401  Z= 0.193
  Angle     :  0.621  11.174  14118  Z= 0.301
  Chirality :  0.041   0.175   1779
  Planarity :  0.005   0.050   1737
  Dihedral  :  6.205  49.603   1617
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 19.54 %
    Favored  : 77.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.23), residues: 1374
  helix:  0.84 (0.17), residues: 1029
  sheet:  None (None), residues: 0
  loop : -0.92 (0.33), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  32 
 HIS   0.004   0.001   HIS C 407 
 PHE   0.012   0.001   PHE A 292 
 TYR   0.019   0.002   TYR E 429 
 ARG   0.005   0.000   ARG E 389 

*********************** 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
  301 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 266
  time to evaluate  : 1.280 
Fit side-chains
REVERT: A  173 THR cc_start: 0.8916 (m) cc_final: 0.8495 (p)
REVERT: B   42 ARG cc_start: 0.4802 (tmt-80) cc_final: 0.4024 (mtm180)
REVERT: C  149 ASP cc_start: 0.8266 (t0) cc_final: 0.7885 (t70)
REVERT: C  208 ILE cc_start: 0.9471 (OUTLIER) cc_final: 0.8986 (mt)
REVERT: C  219 LEU cc_start: 0.9411 (tp) cc_final: 0.9202 (tp)
REVERT: C  264 GLU cc_start: 0.7375 (tt0) cc_final: 0.6663 (tp30)
REVERT: C  375 LEU cc_start: 0.8866 (mm) cc_final: 0.8517 (mt)
REVERT: D   36 MET cc_start: 0.7442 (mmp) cc_final: 0.7033 (mmp)
REVERT: E   23 MET cc_start: 0.8586 (mmm) cc_final: 0.8063 (tpt)
REVERT: E   43 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8568 (tt)
REVERT: E  111 ASN cc_start: 0.8096 (t0) cc_final: 0.7728 (t0)
REVERT: E  115 ASP cc_start: 0.8003 (m-30) cc_final: 0.7801 (m-30)
REVERT: E  248 LYS cc_start: 0.8514 (tppt) cc_final: 0.7949 (pttp)
REVERT: E  264 GLU cc_start: 0.7905 (tt0) cc_final: 0.6987 (tp30)
  outliers start: 35
  outliers final: 27
  residues processed: 287
  average time/residue: 0.1945
  time to fit residues: 82.1061
Evaluate side-chains
  264 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 235
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
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  102 LEU
Chi-restraints excluded: chain A residue  219 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  375 LEU
Chi-restraints excluded: chain C residue   14 MET
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  208 ILE
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 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  384 VAL
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 55 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 56 optimal weight:    7.9990
   chunk 98 optimal weight:    2.9990
   chunk 81 optimal weight:    9.9990
   chunk 104 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 6 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 129 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 407 HIS
E 106 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.115368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.097818 restraints weight = 16662.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.099612 restraints weight = 10653.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.100820 restraints weight = 8072.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.4055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10401  Z= 0.278
  Angle     :  0.688  11.082  14118  Z= 0.330
  Chirality :  0.044   0.195   1779
  Planarity :  0.005   0.050   1737
  Dihedral  :  6.368  48.729   1617
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 20.50 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.23), residues: 1374
  helix:  0.79 (0.17), residues: 1032
  sheet:  None (None), residues: 0
  loop : -1.06 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  32 
 HIS   0.004   0.001   HIS C 407 
 PHE   0.013   0.001   PHE E  39 
 TYR   0.021   0.003   TYR E 429 
 ARG   0.007   0.001   ARG A 389 

*********************** 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
  273 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 237
  time to evaluate  : 0.876 
Fit side-chains
REVERT: A  173 THR cc_start: 0.8970 (m) cc_final: 0.8586 (p)
REVERT: C  149 ASP cc_start: 0.8427 (t0) cc_final: 0.8010 (t70)
REVERT: C  173 THR cc_start: 0.9373 (m) cc_final: 0.9127 (p)
REVERT: C  208 ILE cc_start: 0.9463 (OUTLIER) cc_final: 0.9030 (mt)
REVERT: C  264 GLU cc_start: 0.7669 (tt0) cc_final: 0.6667 (tp30)
REVERT: C  375 LEU cc_start: 0.9048 (mm) cc_final: 0.8736 (mt)
REVERT: D   19 MET cc_start: 0.6607 (mmt) cc_final: 0.6364 (mmt)
REVERT: E   23 MET cc_start: 0.8684 (mmm) cc_final: 0.8172 (tpt)
REVERT: E   43 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8668 (tt)
REVERT: E  111 ASN cc_start: 0.8166 (t0) cc_final: 0.7658 (t0)
REVERT: E  218 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8796 (tp)
REVERT: E  248 LYS cc_start: 0.8538 (tppt) cc_final: 0.7926 (pttt)
REVERT: E  412 ASN cc_start: 0.8640 (t0) cc_final: 0.8371 (t0)
  outliers start: 36
  outliers final: 29
  residues processed: 257
  average time/residue: 0.1953
  time to fit residues: 73.0818
Evaluate side-chains
  251 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 219
  time to evaluate  : 1.040 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   87 CYS
Chi-restraints excluded: chain A residue  219 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  375 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain C residue   14 MET
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  147 MET
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  208 ILE
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  386 MET
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  147 MET
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  218 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  416 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 90 optimal weight:   10.0000
   chunk 128 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 98 optimal weight:    5.9990
   chunk 93 optimal weight:    0.9990
   chunk 17 optimal weight:    0.2980
   chunk 61 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 25 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 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 = 0.3303 r_free = 0.3303 target = 0.118773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.101916 restraints weight = 16447.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.103438 restraints weight = 11219.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.104516 restraints weight = 8854.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
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   0.039  10401  Z= 0.194
  Angle     :  0.646  10.554  14118  Z= 0.310
  Chirality :  0.042   0.185   1779
  Planarity :  0.005   0.049   1737
  Dihedral  :  6.230  51.448   1617
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 12.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 21.74 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.23), residues: 1374
  helix:  0.92 (0.16), residues: 1029
  sheet:  None (None), residues: 0
  loop : -0.96 (0.33), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  32 
 HIS   0.003   0.001   HIS A 407 
 PHE   0.011   0.001   PHE A  49 
 TYR   0.023   0.002   TYR A 429 
 ARG   0.006   0.000   ARG A 389 

*********************** 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
  283 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 249
  time to evaluate  : 1.090 
Fit side-chains
REVERT: A  173 THR cc_start: 0.8932 (m) cc_final: 0.8521 (p)
REVERT: C  110 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7758 (mt-10)
REVERT: C  149 ASP cc_start: 0.8260 (t0) cc_final: 0.7863 (t70)
REVERT: C  208 ILE cc_start: 0.9462 (OUTLIER) cc_final: 0.9001 (mt)
REVERT: C  264 GLU cc_start: 0.7615 (tt0) cc_final: 0.6704 (tp30)
REVERT: E   23 MET cc_start: 0.8418 (mmm) cc_final: 0.7920 (tpt)
REVERT: E   92 HIS cc_start: 0.6627 (m170) cc_final: 0.6338 (m-70)
REVERT: E  111 ASN cc_start: 0.7991 (t0) cc_final: 0.7550 (t0)
REVERT: E  115 ASP cc_start: 0.7974 (m-30) cc_final: 0.7755 (m-30)
REVERT: E  218 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8488 (tp)
REVERT: E  248 LYS cc_start: 0.8413 (tppt) cc_final: 0.8086 (pttt)
REVERT: F   10 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6289 (mt-10)
  outliers start: 34
  outliers final: 25
  residues processed: 269
  average time/residue: 0.1905
  time to fit residues: 75.1009
Evaluate side-chains
  251 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 224
  time to evaluate  : 1.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 THR
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  306 SER
Chi-restraints excluded: chain A residue  318 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain C residue   14 MET
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   87 CYS
Chi-restraints excluded: chain C residue  154 LEU
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  208 ILE
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   64 THR
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  147 MET
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  218 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  416 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 100 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 116 optimal weight:    6.9990
   chunk 67 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 84 optimal weight:    0.7980
   chunk 37 optimal weight:    4.9990
   chunk 42 optimal weight:    9.9990
   chunk 10 optimal weight:    3.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 407 HIS
C 156 ASN
C 370 ASN
C 407 HIS
** E  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 370 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.114287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.097488 restraints weight = 16707.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.098712 restraints weight = 11469.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.099854 restraints weight = 9198.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.4258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  10401  Z= 0.298
  Angle     :  0.716  13.172  14118  Z= 0.339
  Chirality :  0.045   0.187   1779
  Planarity :  0.005   0.045   1737
  Dihedral  :  6.444  48.937   1617
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 13.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 22.51 %
    Favored  : 74.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.23), residues: 1374
  helix:  0.83 (0.16), residues: 1035
  sheet:  None (None), residues: 0
  loop : -1.16 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  32 
 HIS   0.013   0.002   HIS C 407 
 PHE   0.014   0.001   PHE E  39 
 TYR   0.027   0.003   TYR C 429 
 ARG   0.009   0.001   ARG A 389 

*********************** 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
  261 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 225
  time to evaluate  : 1.140 
Fit side-chains
REVERT: A  173 THR cc_start: 0.8988 (m) cc_final: 0.8550 (p)
REVERT: A  360 MET cc_start: 0.8862 (tpp) cc_final: 0.8486 (tpp)
REVERT: C  149 ASP cc_start: 0.8240 (t0) cc_final: 0.7936 (t70)
REVERT: C  173 THR cc_start: 0.9323 (m) cc_final: 0.9089 (p)
REVERT: C  208 ILE cc_start: 0.9507 (OUTLIER) cc_final: 0.9086 (mt)
REVERT: D   36 MET cc_start: 0.7363 (mmp) cc_final: 0.6886 (mmp)
REVERT: E   23 MET cc_start: 0.8497 (mmm) cc_final: 0.8140 (tpt)
REVERT: E  111 ASN cc_start: 0.7896 (t0) cc_final: 0.7397 (t0)
REVERT: E  248 LYS cc_start: 0.8305 (tppt) cc_final: 0.8099 (pttt)
REVERT: E  254 MET cc_start: 0.6068 (mmt) cc_final: 0.5841 (mmt)
REVERT: E  412 ASN cc_start: 0.8671 (t0) cc_final: 0.8464 (t0)
  outliers start: 36
  outliers final: 24
  residues processed: 246
  average time/residue: 0.1953
  time to fit residues: 70.6412
Evaluate side-chains
  243 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 218
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   87 CYS
Chi-restraints excluded: chain A residue  219 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 C residue   14 MET
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   87 CYS
Chi-restraints excluded: chain C residue  154 LEU
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain C residue  228 SER
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  147 MET
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  219 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 70 optimal weight:    4.9990
   chunk 6 optimal weight:   10.0000
   chunk 35 optimal weight:    9.9990
   chunk 75 optimal weight:    0.0570
   chunk 24 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 104 optimal weight:    0.7980
   chunk 111 optimal weight:    3.9990
   chunk 72 optimal weight:    0.0270
   overall best weight:    0.5756

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.118515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.102021 restraints weight = 16462.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.103537 restraints weight = 11247.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.104548 restraints weight = 8860.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.4420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10401  Z= 0.191
  Angle     :  0.688  12.581  14118  Z= 0.326
  Chirality :  0.042   0.173   1779
  Planarity :  0.005   0.045   1737
  Dihedral  :  6.305  53.925   1617
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 24.14 %
    Favored  : 73.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.23), residues: 1374
  helix:  0.97 (0.16), residues: 1038
  sheet:  None (None), residues: 0
  loop : -1.02 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  32 
 HIS   0.005   0.001   HIS C 407 
 PHE   0.013   0.001   PHE A  49 
 TYR   0.029   0.002   TYR C 429 
 ARG   0.008   0.001   ARG A 389 

********************** 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
  257 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 232
  time to evaluate  : 1.167 
Fit side-chains
REVERT: A   90 ASP cc_start: 0.7455 (t70) cc_final: 0.7191 (t0)
REVERT: A  173 THR cc_start: 0.8955 (m) cc_final: 0.8567 (p)
REVERT: A  375 LEU cc_start: 0.8639 (mt) cc_final: 0.8438 (mt)
REVERT: C  149 ASP cc_start: 0.8267 (t0) cc_final: 0.8003 (t70)
REVERT: C  208 ILE cc_start: 0.9445 (OUTLIER) cc_final: 0.8993 (mt)
REVERT: E   23 MET cc_start: 0.8396 (mmm) cc_final: 0.8115 (tpt)
REVERT: E  218 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8382 (tp)
REVERT: E  219 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8965 (tp)
REVERT: E  248 LYS cc_start: 0.8316 (tppt) cc_final: 0.8094 (pttt)
REVERT: F   10 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6291 (mt-10)
  outliers start: 25
  outliers final: 18
  residues processed: 249
  average time/residue: 0.1918
  time to fit residues: 71.4347
Evaluate side-chains
  239 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 218
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   87 CYS
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 C residue   30 LEU
Chi-restraints excluded: chain C residue   87 CYS
Chi-restraints excluded: chain C residue  154 LEU
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain C residue  228 SER
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  210 LEU
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  219 LEU
Chi-restraints excluded: chain E residue  287 LEU
Chi-restraints excluded: chain E residue  416 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 5 optimal weight:    0.0870
   chunk 118 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 104 optimal weight:    0.7980
   chunk 13 optimal weight:    8.9990
   chunk 64 optimal weight:    0.7980
   chunk 8 optimal weight:    5.9990
   chunk 112 optimal weight:    7.9990
   chunk 67 optimal weight:    0.9980
   chunk 122 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.7358

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.119196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.102414 restraints weight = 16302.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.103615 restraints weight = 11315.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.104746 restraints weight = 9098.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.4507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10401  Z= 0.196
  Angle     :  0.703  15.165  14118  Z= 0.329
  Chirality :  0.043   0.176   1779
  Planarity :  0.005   0.045   1737
  Dihedral  :  6.185  52.838   1617
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 13.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 24.14 %
    Favored  : 73.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.23), residues: 1374
  helix:  1.01 (0.16), residues: 1047
  sheet:  None (None), residues: 0
  loop : -1.01 (0.35), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  32 
 HIS   0.002   0.001   HIS A  73 
 PHE   0.013   0.001   PHE A  49 
 TYR   0.027   0.002   TYR E 429 
 ARG   0.003   0.000   ARG A 389 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2839.51 seconds
wall clock time: 51 minutes 50.51 seconds (3110.51 seconds total)