Starting phenix.real_space_refine
on Thu May  1 06:07:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6iww_9743/05_2025/6iww_9743.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6iww_9743/05_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_9743/05_2025/6iww_9743.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6iww_9743/05_2025/6iww_9743.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6iww_9743/05_2025/6iww_9743.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6iww_9743/05_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 6.66, per 1000 atoms: 0.65
  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: 2.99
  Conformation dependent library (CDL) restraints added in 1.4 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: 1.20
  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: 3.32

  Time building geometry restraints manager: 3.44 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:             0.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     28.090
  Find NCS groups from input model:        0.240
  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:3.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.064  10401  Z= 0.333
  Angle     :  1.088   9.417  14118  Z= 0.547
  Chirality :  0.060   0.273   1779
  Planarity :  0.009   0.061   1737
  Dihedral  : 13.483 110.551   3849
  Min Nonbonded Distance : 2.301

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

Rama-Z (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 

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

*********************** 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  : 1.080 
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: 0.2263
  time to fit residues: 123.8165
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  : 1.169 
-------------------------------------------------------------------------------
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 = 44)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.102024 restraints weight = 16215.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.103644 restraints weight = 11031.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.104735 restraints weight = 8681.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
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= 0.156
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03957 (  682)
  hydrogen bonds       : angle       4.78438 ( 2004)
  covalent geometry    : bond        0.00363 (10401)
  covalent geometry    : angle       0.69558 (14118)

*********************** 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  : 1.126 
Fit side-chains
REVERT: A  111 ASN cc_start: 0.8192 (t0) cc_final: 0.7796 (t0)
REVERT: A  159 THR cc_start: 0.8544 (p) cc_final: 0.8252 (p)
REVERT: A  173 THR cc_start: 0.9168 (m) cc_final: 0.8712 (p)
REVERT: A  245 THR cc_start: 0.8068 (m) cc_final: 0.7810 (t)
REVERT: A  248 LYS cc_start: 0.8225 (tppt) cc_final: 0.7979 (pptt)
REVERT: A  292 PHE cc_start: 0.8992 (t80) cc_final: 0.8726 (t80)
REVERT: A  365 ASN cc_start: 0.6738 (OUTLIER) cc_final: 0.6528 (m-40)
REVERT: B   15 MET cc_start: 0.6940 (ttp) cc_final: 0.6600 (ttp)
REVERT: B   42 ARG cc_start: 0.4811 (tmt-80) cc_final: 0.4204 (mtm180)
REVERT: C  109 MET cc_start: 0.7705 (mmm) cc_final: 0.7483 (mmp)
REVERT: C  149 ASP cc_start: 0.8260 (t0) cc_final: 0.8042 (t70)
REVERT: C  159 THR cc_start: 0.8770 (p) cc_final: 0.8390 (p)
REVERT: C  248 LYS cc_start: 0.8273 (tppt) cc_final: 0.8036 (tmmt)
REVERT: C  429 TYR cc_start: 0.7998 (t80) cc_final: 0.7604 (t80)
REVERT: E  110 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7089 (tm-30)
REVERT: E  111 ASN cc_start: 0.8226 (t0) cc_final: 0.7768 (t0)
REVERT: E  248 LYS cc_start: 0.8065 (tppt) cc_final: 0.7763 (tmmt)
REVERT: E  264 GLU cc_start: 0.8056 (tt0) cc_final: 0.7049 (tp30)
REVERT: E  412 ASN cc_start: 0.8589 (t0) cc_final: 0.8382 (t0)
REVERT: F   10 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6653 (mt-10)
  outliers start: 22
  outliers final: 15
  residues processed: 301
  average time/residue: 0.2135
  time to fit residues: 90.9459
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  : 1.084 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 100 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0670
   chunk 115 optimal weight:    3.9990
   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:    0.8980
   overall best weight:    0.7120

-------------------------------------------------------------------------------
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 = 0.3292 r_free = 0.3292 target = 0.118763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.102409 restraints weight = 16474.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.104002 restraints weight = 11135.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.105129 restraints weight = 8640.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.3216

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= 0.130
  Angle     :  0.635   7.829  14118  Z= 0.309
  Chirality :  0.042   0.155   1779
  Planarity :  0.006   0.048   1737
  Dihedral  :  7.100  54.361   1617
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 13.51 %
    Favored  : 84.29 %
  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: -0.74 (0.22), residues: 1374
  helix: -0.06 (0.16), residues: 1035
  sheet:  None (None), residues: 0
  loop : -1.50 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP E  32 
 HIS   0.009   0.001   HIS A 407 
 PHE   0.017   0.001   PHE A 292 
 TYR   0.017   0.002   TYR E 127 
 ARG   0.005   0.000   ARG E 389 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03603 (  682)
  hydrogen bonds       : angle       4.51394 ( 2004)
  covalent geometry    : bond        0.00299 (10401)
  covalent geometry    : angle       0.63462 (14118)

*********************** 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  : 1.115 
Fit side-chains
REVERT: A  111 ASN cc_start: 0.8154 (t0) cc_final: 0.7782 (t0)
REVERT: A  159 THR cc_start: 0.8270 (p) cc_final: 0.8058 (p)
REVERT: A  245 THR cc_start: 0.7521 (m) cc_final: 0.7263 (t)
REVERT: A  248 LYS cc_start: 0.8044 (tppt) cc_final: 0.7805 (pttp)
REVERT: A  360 MET cc_start: 0.8867 (tpp) cc_final: 0.8574 (tpp)
REVERT: B   15 MET cc_start: 0.6860 (ttp) cc_final: 0.6567 (ttp)
REVERT: B   42 ARG cc_start: 0.4875 (tmt-80) cc_final: 0.4234 (mtm180)
REVERT: C  110 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7113 (tm-30)
REVERT: C  149 ASP cc_start: 0.8152 (t0) cc_final: 0.7930 (t70)
REVERT: C  173 THR cc_start: 0.9313 (m) cc_final: 0.8918 (p)
REVERT: C  228 SER cc_start: 0.9112 (m) cc_final: 0.8874 (p)
REVERT: C  264 GLU cc_start: 0.7392 (tt0) cc_final: 0.6786 (tp30)
REVERT: C  406 MET cc_start: 0.7652 (tpp) cc_final: 0.7370 (tpp)
REVERT: C  429 TYR cc_start: 0.8014 (t80) cc_final: 0.7575 (t80)
REVERT: D   10 GLU cc_start: 0.6542 (mt-10) cc_final: 0.6196 (mt-10)
REVERT: E  110 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7040 (tm-30)
REVERT: E  111 ASN cc_start: 0.8254 (t0) cc_final: 0.7839 (t0)
REVERT: E  254 MET cc_start: 0.6250 (mmm) cc_final: 0.6041 (mmm)
REVERT: E  264 GLU cc_start: 0.8067 (tt0) cc_final: 0.7087 (tp30)
REVERT: E  375 LEU cc_start: 0.8743 (mp) cc_final: 0.8535 (mt)
REVERT: E  412 ASN cc_start: 0.8567 (t0) cc_final: 0.8349 (t0)
REVERT: F   10 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6603 (mt-10)
  outliers start: 23
  outliers final: 19
  residues processed: 303
  average time/residue: 0.2049
  time to fit residues: 89.0365
Evaluate side-chains
  263 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 244
  time to evaluate  : 1.119 
-------------------------------------------------------------------------------
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  365 ASN
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  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:    0.6980
   chunk 66 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   chunk 104 optimal weight:    0.7980
   chunk 109 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 121 optimal weight:    0.0030
   chunk 22 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.6390

-------------------------------------------------------------------------------
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

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 = 0.119796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.103360 restraints weight = 16251.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.104964 restraints weight = 10907.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.105949 restraints weight = 8544.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.3579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10401  Z= 0.123
  Angle     :  0.610  12.011  14118  Z= 0.298
  Chirality :  0.041   0.149   1779
  Planarity :  0.005   0.047   1737
  Dihedral  :  6.460  52.223   1617
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 16.95 %
    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   0.007   0.001   TRP C  32 
 HIS   0.009   0.001   HIS A 407 
 PHE   0.014   0.001   PHE A 292 
 TYR   0.014   0.002   TYR E 429 
 ARG   0.006   0.000   ARG E 389 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03356 (  682)
  hydrogen bonds       : angle       4.36940 ( 2004)
  covalent geometry    : bond        0.00281 (10401)
  covalent geometry    : angle       0.61009 (14118)

*********************** 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
  310 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 281
  time to evaluate  : 1.184 
Fit side-chains
REVERT: A  111 ASN cc_start: 0.8068 (t0) cc_final: 0.7717 (t0)
REVERT: A  426 MET cc_start: 0.8254 (ttm) cc_final: 0.7971 (mtp)
REVERT: B   15 MET cc_start: 0.6932 (ttp) cc_final: 0.6667 (ttp)
REVERT: B   42 ARG cc_start: 0.4984 (tmt-80) cc_final: 0.4193 (mtm180)
REVERT: C  110 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7529 (tm-30)
REVERT: C  149 ASP cc_start: 0.8319 (t0) cc_final: 0.8037 (t70)
REVERT: C  173 THR cc_start: 0.9338 (m) cc_final: 0.9080 (p)
REVERT: C  263 ARG cc_start: 0.7208 (mmt180) cc_final: 0.6746 (tpt170)
REVERT: C  264 GLU cc_start: 0.7303 (tt0) cc_final: 0.6739 (tp30)
REVERT: C  375 LEU cc_start: 0.8847 (mm) cc_final: 0.8519 (mp)
REVERT: C  406 MET cc_start: 0.7583 (tpp) cc_final: 0.7337 (tpp)
REVERT: C  429 TYR cc_start: 0.8000 (t80) cc_final: 0.7523 (t80)
REVERT: E   23 MET cc_start: 0.8664 (mmm) cc_final: 0.8267 (tpt)
REVERT: E  110 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7132 (tm-30)
REVERT: E  111 ASN cc_start: 0.8131 (t0) cc_final: 0.7790 (t0)
REVERT: E  248 LYS cc_start: 0.8414 (tppt) cc_final: 0.7865 (pttp)
REVERT: E  264 GLU cc_start: 0.8019 (tt0) cc_final: 0.7004 (tp30)
REVERT: E  375 LEU cc_start: 0.8755 (mp) cc_final: 0.8533 (mt)
REVERT: E  412 ASN cc_start: 0.8656 (t0) cc_final: 0.8320 (t0)
  outliers start: 29
  outliers final: 19
  residues processed: 299
  average time/residue: 0.2215
  time to fit residues: 96.1532
Evaluate side-chains
  259 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 240
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
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  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  296 MET
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:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 65 optimal weight:    0.7980
   chunk 103 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 89 optimal weight:    6.9990
   chunk 13 optimal weight:    9.9990
   chunk 74 optimal weight:    3.9990
   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 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 407 HIS
C 370 ASN
** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.117927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.101522 restraints weight = 16411.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.102863 restraints weight = 11204.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.104070 restraints weight = 8874.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.3805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10401  Z= 0.139
  Angle     :  0.618   9.080  14118  Z= 0.302
  Chirality :  0.042   0.163   1779
  Planarity :  0.005   0.045   1737
  Dihedral  :  6.370  49.150   1617
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 18.10 %
    Favored  : 78.45 %
  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:  0.24 (0.23), residues: 1374
  helix:  0.68 (0.17), residues: 1032
  sheet:  None (None), residues: 0
  loop : -1.26 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  32 
 HIS   0.005   0.001   HIS A 407 
 PHE   0.019   0.001   PHE A 292 
 TYR   0.018   0.002   TYR E 429 
 ARG   0.002   0.000   ARG C 253 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03395 (  682)
  hydrogen bonds       : angle       4.35195 ( 2004)
  covalent geometry    : bond        0.00328 (10401)
  covalent geometry    : angle       0.61814 (14118)

*********************** 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
  289 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 253
  time to evaluate  : 1.042 
Fit side-chains
REVERT: B   42 ARG cc_start: 0.4888 (tmt-80) cc_final: 0.4092 (mtm180)
REVERT: C  110 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7337 (tm-30)
REVERT: C  149 ASP cc_start: 0.8378 (t0) cc_final: 0.8054 (t70)
REVERT: C  208 ILE cc_start: 0.9486 (OUTLIER) cc_final: 0.9017 (mt)
REVERT: C  219 LEU cc_start: 0.9445 (tp) cc_final: 0.9189 (tp)
REVERT: C  264 GLU cc_start: 0.7299 (tt0) cc_final: 0.6795 (tp30)
REVERT: C  375 LEU cc_start: 0.8760 (mm) cc_final: 0.8475 (mt)
REVERT: C  406 MET cc_start: 0.7507 (tpp) cc_final: 0.7265 (tpp)
REVERT: E   23 MET cc_start: 0.8642 (mmm) cc_final: 0.8051 (tpt)
REVERT: E   43 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8578 (tt)
REVERT: E  110 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7197 (tm-30)
REVERT: E  111 ASN cc_start: 0.8241 (t0) cc_final: 0.7871 (t0)
REVERT: E  412 ASN cc_start: 0.8537 (t0) cc_final: 0.8266 (t0)
  outliers start: 36
  outliers final: 23
  residues processed: 275
  average time/residue: 0.1905
  time to fit residues: 76.4055
Evaluate side-chains
  260 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 235
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
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  384 VAL
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   64 THR
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  370 ASN
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue   64 THR
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  161 LEU
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  219 LEU
Chi-restraints excluded: chain E residue  282 ASP
Chi-restraints excluded: chain E residue  296 MET
Chi-restraints excluded: chain E residue  416 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 80 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   chunk 136 optimal weight:    1.9990
   chunk 131 optimal weight:    0.9980
   chunk 125 optimal weight:    0.9990
   chunk 99 optimal weight:   10.0000
   chunk 130 optimal weight:    3.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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
** C 412 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 = 0.3300 r_free = 0.3300 target = 0.118755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.102348 restraints weight = 16401.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.103965 restraints weight = 11099.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.105018 restraints weight = 8664.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.3981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10401  Z= 0.134
  Angle     :  0.634  12.885  14118  Z= 0.306
  Chirality :  0.042   0.166   1779
  Planarity :  0.005   0.050   1737
  Dihedral  :  6.280  49.201   1617
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 19.35 %
    Favored  : 77.49 %
  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:  0.38 (0.23), residues: 1374
  helix:  0.78 (0.17), residues: 1032
  sheet:  None (None), residues: 0
  loop : -1.20 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  32 
 HIS   0.008   0.001   HIS C 407 
 PHE   0.014   0.001   PHE A 292 
 TYR   0.017   0.002   TYR C 127 
 ARG   0.006   0.000   ARG E 389 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03323 (  682)
  hydrogen bonds       : angle       4.33989 ( 2004)
  covalent geometry    : bond        0.00317 (10401)
  covalent geometry    : angle       0.63413 (14118)

*********************** 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
  294 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 261
  time to evaluate  : 1.016 
Fit side-chains
REVERT: A  173 THR cc_start: 0.8953 (m) cc_final: 0.8504 (p)
REVERT: B   42 ARG cc_start: 0.4869 (tmt-80) cc_final: 0.4072 (mtm180)
REVERT: C  149 ASP cc_start: 0.8497 (t0) cc_final: 0.8115 (t70)
REVERT: C  173 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8950 (p)
REVERT: C  208 ILE cc_start: 0.9453 (OUTLIER) cc_final: 0.8961 (mt)
REVERT: C  219 LEU cc_start: 0.9424 (tp) cc_final: 0.9199 (tp)
REVERT: C  263 ARG cc_start: 0.7205 (mmt180) cc_final: 0.6685 (tpt170)
REVERT: C  264 GLU cc_start: 0.7446 (tt0) cc_final: 0.6705 (tp30)
REVERT: C  375 LEU cc_start: 0.8888 (mm) cc_final: 0.8547 (mt)
REVERT: C  417 ILE cc_start: 0.9337 (mm) cc_final: 0.9137 (mt)
REVERT: D   36 MET cc_start: 0.7297 (mmp) cc_final: 0.6898 (mmp)
REVERT: E   23 MET cc_start: 0.8611 (mmm) cc_final: 0.8082 (tpt)
REVERT: E   43 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8607 (tt)
REVERT: E  111 ASN cc_start: 0.8221 (t0) cc_final: 0.7825 (t0)
REVERT: E  115 ASP cc_start: 0.8045 (m-30) cc_final: 0.7827 (m-30)
REVERT: E  248 LYS cc_start: 0.8408 (tppt) cc_final: 0.7866 (pttp)
REVERT: E  264 GLU cc_start: 0.7945 (tt0) cc_final: 0.7014 (tp30)
REVERT: E  378 SER cc_start: 0.8699 (p) cc_final: 0.8418 (t)
REVERT: E  389 ARG cc_start: 0.8078 (mtp-110) cc_final: 0.7854 (mtp180)
REVERT: E  412 ASN cc_start: 0.8497 (t0) cc_final: 0.8205 (t0)
  outliers start: 33
  outliers final: 23
  residues processed: 280
  average time/residue: 0.1834
  time to fit residues: 75.4358
Evaluate side-chains
  264 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 238
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
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 C residue   30 LEU
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue  173 THR
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  370 ASN
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue   64 THR
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  161 LEU
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  219 LEU
Chi-restraints excluded: chain E residue  282 ASP
Chi-restraints excluded: chain E residue  296 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 67 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 98 optimal weight:    7.9990
   chunk 81 optimal weight:    9.9990
   chunk 104 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 6 optimal weight:   10.0000
   chunk 47 optimal weight:    2.9990
   chunk 129 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
A 407 HIS
C 370 ASN
C 407 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.116291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.099603 restraints weight = 16604.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.101064 restraints weight = 11266.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.102190 restraints weight = 8851.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.4053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10401  Z= 0.160
  Angle     :  0.663  11.411  14118  Z= 0.320
  Chirality :  0.043   0.181   1779
  Planarity :  0.005   0.051   1737
  Dihedral  :  6.333  48.423   1617
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 19.25 %
    Favored  : 76.82 %
  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:  0.40 (0.23), residues: 1374
  helix:  0.81 (0.17), residues: 1032
  sheet:  None (None), residues: 0
  loop : -1.26 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  32 
 HIS   0.006   0.001   HIS C 407 
 PHE   0.012   0.001   PHE A  49 
 TYR   0.022   0.002   TYR E 429 
 ARG   0.007   0.001   ARG A 389 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03473 (  682)
  hydrogen bonds       : angle       4.41199 ( 2004)
  covalent geometry    : bond        0.00388 (10401)
  covalent geometry    : angle       0.66327 (14118)

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

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

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

  2748 Ramachandran restraints generated.
    1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 248
  time to evaluate  : 1.139 
Fit side-chains
REVERT: A   96 GLU cc_start: 0.7754 (mp0) cc_final: 0.7471 (mp0)
REVERT: A  173 THR cc_start: 0.8913 (m) cc_final: 0.8557 (p)
REVERT: A  264 GLU cc_start: 0.7628 (tt0) cc_final: 0.6699 (tp30)
REVERT: A  287 LEU cc_start: 0.9214 (mt) cc_final: 0.9012 (mt)
REVERT: C  149 ASP cc_start: 0.8373 (t0) cc_final: 0.7950 (t70)
REVERT: C  173 THR cc_start: 0.9307 (p) cc_final: 0.9054 (p)
REVERT: C  208 ILE cc_start: 0.9488 (OUTLIER) cc_final: 0.9029 (mt)
REVERT: C  219 LEU cc_start: 0.9451 (tp) cc_final: 0.9242 (tp)
REVERT: C  264 GLU cc_start: 0.7590 (tt0) cc_final: 0.6600 (tp30)
REVERT: C  375 LEU cc_start: 0.8929 (mm) cc_final: 0.8653 (mt)
REVERT: C  417 ILE cc_start: 0.9298 (mm) cc_final: 0.9094 (mt)
REVERT: E   23 MET cc_start: 0.8530 (mmm) cc_final: 0.7985 (tpt)
REVERT: E   43 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8666 (tt)
REVERT: E  111 ASN cc_start: 0.8107 (t0) cc_final: 0.7639 (t0)
REVERT: E  218 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8637 (tp)
REVERT: E  378 SER cc_start: 0.8672 (OUTLIER) cc_final: 0.8404 (t)
REVERT: E  412 ASN cc_start: 0.8553 (t0) cc_final: 0.8277 (t0)
  outliers start: 41
  outliers final: 32
  residues processed: 271
  average time/residue: 0.1873
  time to fit residues: 75.8073
Evaluate side-chains
  259 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 223
  time to evaluate  : 1.154 
-------------------------------------------------------------------------------
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 A residue  384 VAL
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   87 CYS
Chi-restraints excluded: chain C residue  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  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 C residue  386 MET
Chi-restraints excluded: chain D residue   15 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  161 LEU
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  296 MET
Chi-restraints excluded: chain E residue  378 SER
Chi-restraints excluded: chain E residue  386 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:    9.9990
   chunk 128 optimal weight:    0.2980
   chunk 26 optimal weight:    0.8980
   chunk 98 optimal weight:    7.9990
   chunk 93 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0970
   chunk 61 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.6178

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.119364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.102305 restraints weight = 16429.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.103821 restraints weight = 10841.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.105193 restraints weight = 8427.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.4287

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= 0.127
  Angle     :  0.655  12.217  14118  Z= 0.314
  Chirality :  0.042   0.199   1779
  Planarity :  0.005   0.050   1737
  Dihedral  :  6.164  50.767   1617
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 20.88 %
    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:  0.63 (0.23), residues: 1374
  helix:  0.96 (0.17), residues: 1026
  sheet:  None (None), residues: 0
  loop : -1.05 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  32 
 HIS   0.004   0.001   HIS C 407 
 PHE   0.014   0.001   PHE C 292 
 TYR   0.025   0.002   TYR E 429 
 ARG   0.006   0.000   ARG A 389 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03341 (  682)
  hydrogen bonds       : angle       4.38803 ( 2004)
  covalent geometry    : bond        0.00292 (10401)
  covalent geometry    : angle       0.65506 (14118)

*********************** 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
  291 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 259
  time to evaluate  : 1.090 
Fit side-chains
REVERT: A  173 THR cc_start: 0.8928 (m) cc_final: 0.8521 (p)
REVERT: C  110 GLU cc_start: 0.8517 (tp30) cc_final: 0.8143 (tp30)
REVERT: C  149 ASP cc_start: 0.8378 (t0) cc_final: 0.7952 (t70)
REVERT: C  173 THR cc_start: 0.9279 (OUTLIER) cc_final: 0.9047 (p)
REVERT: C  208 ILE cc_start: 0.9436 (OUTLIER) cc_final: 0.8987 (mt)
REVERT: C  264 GLU cc_start: 0.7646 (tt0) cc_final: 0.6674 (tp30)
REVERT: C  375 LEU cc_start: 0.8940 (mm) cc_final: 0.8626 (mt)
REVERT: E   23 MET cc_start: 0.8396 (mmm) cc_final: 0.8054 (tpt)
REVERT: E   43 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8628 (tt)
REVERT: E  110 GLU cc_start: 0.7939 (tm-30) cc_final: 0.6614 (tm-30)
REVERT: E  111 ASN cc_start: 0.8055 (t0) cc_final: 0.7720 (t0)
REVERT: E  218 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8559 (tp)
REVERT: E  248 LYS cc_start: 0.8447 (tppt) cc_final: 0.7892 (pttp)
REVERT: E  412 ASN cc_start: 0.8504 (t0) cc_final: 0.8227 (t0)
REVERT: F   10 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6196 (mt-10)
  outliers start: 32
  outliers final: 24
  residues processed: 279
  average time/residue: 0.1910
  time to fit residues: 77.9436
Evaluate side-chains
  253 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 225
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
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  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  173 THR
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   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  218 LEU
Chi-restraints excluded: chain E residue  219 LEU
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:    6.9990
   chunk 63 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 93 optimal weight:    0.7980
   chunk 116 optimal weight:    0.1980
   chunk 67 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 84 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9990
   chunk 42 optimal weight:   10.0000
   chunk 10 optimal weight:    0.0050
   overall best weight:    0.9998

-------------------------------------------------------------------------------
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 = 0.3296 r_free = 0.3296 target = 0.118194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.101637 restraints weight = 16551.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.102860 restraints weight = 11551.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.104016 restraints weight = 9300.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.4378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10401  Z= 0.140
  Angle     :  0.690  11.871  14118  Z= 0.325
  Chirality :  0.043   0.179   1779
  Planarity :  0.005   0.043   1737
  Dihedral  :  6.173  49.114   1617
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 22.70 %
    Favored  : 74.52 %
  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:  0.64 (0.23), residues: 1374
  helix:  0.97 (0.16), residues: 1032
  sheet:  None (None), residues: 0
  loop : -1.10 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  32 
 HIS   0.004   0.001   HIS A 407 
 PHE   0.013   0.001   PHE A  49 
 TYR   0.027   0.002   TYR C 429 
 ARG   0.009   0.000   ARG A 389 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03427 (  682)
  hydrogen bonds       : angle       4.46251 ( 2004)
  covalent geometry    : bond        0.00328 (10401)
  covalent geometry    : angle       0.69011 (14118)

*********************** 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
  274 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 245
  time to evaluate  : 1.108 
Fit side-chains
REVERT: A  173 THR cc_start: 0.8925 (m) cc_final: 0.8543 (p)
REVERT: A  254 MET cc_start: 0.5928 (mmt) cc_final: 0.5724 (mmt)
REVERT: A  426 MET cc_start: 0.8280 (ttm) cc_final: 0.7936 (mtp)
REVERT: C   52 LEU cc_start: 0.9358 (mt) cc_final: 0.9149 (tp)
REVERT: C  110 GLU cc_start: 0.8268 (tp30) cc_final: 0.8046 (tp30)
REVERT: C  149 ASP cc_start: 0.8370 (t0) cc_final: 0.7991 (t70)
REVERT: C  173 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.9075 (p)
REVERT: C  208 ILE cc_start: 0.9450 (OUTLIER) cc_final: 0.9010 (mt)
REVERT: C  264 GLU cc_start: 0.7680 (tt0) cc_final: 0.6678 (tp30)
REVERT: C  375 LEU cc_start: 0.9024 (mm) cc_final: 0.8740 (mt)
REVERT: E   23 MET cc_start: 0.8402 (mmm) cc_final: 0.8084 (tpt)
REVERT: E   43 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8617 (tt)
REVERT: E  111 ASN cc_start: 0.8004 (t0) cc_final: 0.7582 (t0)
REVERT: E  412 ASN cc_start: 0.8515 (t0) cc_final: 0.8195 (t0)
  outliers start: 29
  outliers final: 25
  residues processed: 260
  average time/residue: 0.1911
  time to fit residues: 72.6730
Evaluate side-chains
  255 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 227
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
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  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   87 CYS
Chi-restraints excluded: chain C residue  154 LEU
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  173 THR
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 C residue  386 MET
Chi-restraints excluded: chain E residue   28 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  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
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 68.705 > 50:
  distance: 4 - 18:   3.230
  distance: 7 - 26:  16.951
  distance: 13 - 31:  31.427
  distance: 17 - 36:  19.816
  distance: 20 - 26:  19.308
  distance: 21 - 45:  17.549
  distance: 26 - 27:  27.393
  distance: 27 - 28:  30.000
  distance: 27 - 30:  23.238
  distance: 28 - 29:  16.731
  distance: 29 - 53:  49.119
  distance: 31 - 32:  13.905
  distance: 32 - 33:  23.020
  distance: 32 - 35:  48.085
  distance: 33 - 34:  29.721
  distance: 33 - 36:  16.307
  distance: 36 - 37:  11.051
  distance: 37 - 38:  39.748
  distance: 37 - 40:  33.193
  distance: 38 - 39:  13.160
  distance: 38 - 45:  31.291
  distance: 40 - 41:  27.611
  distance: 41 - 42:  28.492
  distance: 42 - 43:   5.133
  distance: 43 - 44:  25.209
  distance: 45 - 46:  21.967
  distance: 46 - 47:  16.748
  distance: 46 - 49:  22.374
  distance: 47 - 48:  13.556
  distance: 47 - 53:  38.671
  distance: 49 - 50:  29.725
  distance: 50 - 51:  23.984
  distance: 50 - 52:  22.366
  distance: 53 - 54:  37.420
  distance: 54 - 55:   9.119
  distance: 54 - 57:  44.455
  distance: 55 - 56:  20.500
  distance: 55 - 61:   6.494
  distance: 57 - 58:  17.854
  distance: 58 - 59:  24.053
  distance: 58 - 60:  25.287
  distance: 61 - 62:  12.506
  distance: 62 - 63:  14.835
  distance: 62 - 65:  45.324
  distance: 63 - 64:  40.022
  distance: 65 - 66:  40.412
  distance: 67 - 68:  27.336
  distance: 68 - 69:  20.410
  distance: 68 - 71:  25.531
  distance: 69 - 70:  25.998
  distance: 69 - 72:  36.492
  distance: 72 - 73:   3.715
  distance: 72 - 78:  29.207
  distance: 73 - 74:  15.517
  distance: 73 - 76:  37.011
  distance: 74 - 79:  18.131
  distance: 76 - 77:  13.544
  distance: 77 - 78:  11.355
  distance: 79 - 80:  34.321
  distance: 80 - 81:  37.330
  distance: 80 - 83:  14.962
  distance: 81 - 82:   6.215
  distance: 81 - 87:  26.568
  distance: 83 - 84:   9.239
  distance: 84 - 85:  37.789
  distance: 84 - 86:  43.473
  distance: 87 - 88:  20.198
  distance: 88 - 89:  11.803
  distance: 88 - 91:  32.106
  distance: 89 - 90:   4.842
  distance: 89 - 94:  32.001
  distance: 91 - 92:  18.870
  distance: 91 - 93:  20.949