Starting phenix.real_space_refine
on Sat Aug 23 04:09:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fmy_29300/08_2025/8fmy_29300.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fmy_29300/08_2025/8fmy_29300.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fmy_29300/08_2025/8fmy_29300.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fmy_29300/08_2025/8fmy_29300.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fmy_29300/08_2025/8fmy_29300.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fmy_29300/08_2025/8fmy_29300.cif"
  }
  resolution = 2.66
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.015
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      57      5.16       5
     C    6036      2.51       5
     N    1611      2.21       5
     O    1893      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9597
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3199
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 420, 3199
          Classifications: {'peptide': 420}
          Link IDs: {'PTRANS': 13, 'TRANS': 406}
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 2.42, per 1000 atoms: 0.25
  Number of scatterers: 9597
  At special positions: 0
  Unit cell: (103, 104, 98, 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      57     16.00
     O    1893      8.00
     N    1611      7.00
     C    6036      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 330 " - pdb=" SG  CYS A 339 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 354 " - pdb=" SG  CYS A 362 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 386 " - pdb=" SG  CYS A 391 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 393 " - pdb=" SG  CYS A 416 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 330 " - pdb=" SG  CYS B 339 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 330 " - pdb=" SG  CYS C 339 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 354 " - pdb=" SG  CYS B 362 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 354 " - pdb=" SG  CYS C 362 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 386 " - pdb=" SG  CYS B 391 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 386 " - pdb=" SG  CYS C 391 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 393 " - pdb=" SG  CYS B 416 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 393 " - pdb=" SG  CYS C 416 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.89
  Conformation dependent library (CDL) restraints added in 459.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2358

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 15 sheets defined
      40.0% alpha, 22.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 33
      removed outlier: 3.556A  pdb=" N   LEU A  32 " --> pdb=" O   HIS A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 70
    Processing helix  chain 'A' and resid 71 through 105
      removed outlier: 3.500A  pdb=" N   GLU A  77 " --> pdb=" O   LYS A  73 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ASN A  80 " --> pdb=" O   ASP A  76 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU A  81 " --> pdb=" O   GLU A  77 " (cutoff:3.500A)
      Proline residue:  A  88  - end of helix
      removed outlier: 3.930A  pdb=" N   MET A  91 " --> pdb=" O   GLU A  87 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ALA A  92 " --> pdb=" O   PRO A  88 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ASN A  99 " --> pdb=" O   THR A  95 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   VAL A 100 " --> pdb=" O   MET A  96 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   GLY A 103 " --> pdb=" O   ASN A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 120
    Processing helix  chain 'A' and resid 124 through 136
      removed outlier: 3.650A  pdb=" N   HIS A 134 " --> pdb=" O   GLY A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 145
      removed outlier: 3.619A  pdb=" N   ALA A 140 " --> pdb=" O   SER A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 152
    Processing helix  chain 'A' and resid 172 through 182
      removed outlier: 3.628A  pdb=" N   GLY A 176 " --> pdb=" O   ASP A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 186
      removed outlier: 3.565A  pdb=" N   ILE A 186 " --> pdb=" O   ILE A 183 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 183 through 186'
    Processing helix  chain 'A' and resid 190 through 219
      removed outlier: 3.668A  pdb=" N   ILE A 200 " --> pdb=" O   LEU A 196 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ARG A 201 " --> pdb=" O   SER A 197 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   THR A 203 " --> pdb=" O   GLY A 199 " (cutoff:3.500A)
      Proline residue:  A 215  - end of helix
      removed outlier: 3.521A  pdb=" N   GLN A 218 " --> pdb=" O   GLY A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 231
    Processing helix  chain 'A' and resid 232 through 235
      removed outlier: 4.100A  pdb=" N   ASN A 235 " --> pdb=" O   SER A 232 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 232 through 235'
    Processing helix  chain 'A' and resid 237 through 245
      removed outlier: 3.763A  pdb=" N   LEU A 241 " --> pdb=" O   ASN A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 258
      removed outlier: 3.619A  pdb=" N   SER A 258 " --> pdb=" O   GLU A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 330
    Processing helix  chain 'A' and resid 348 through 356
    Processing helix  chain 'A' and resid 358 through 362
    Processing helix  chain 'B' and resid 28 through 33
      removed outlier: 3.557A  pdb=" N   LEU B  32 " --> pdb=" O   HIS B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 70
    Processing helix  chain 'B' and resid 71 through 105
      removed outlier: 3.751A  pdb=" N   ASN B  80 " --> pdb=" O   ASP B  76 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU B  81 " --> pdb=" O   GLU B  77 " (cutoff:3.500A)
      Proline residue:  B  88  - end of helix
      removed outlier: 3.930A  pdb=" N   MET B  91 " --> pdb=" O   GLU B  87 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ALA B  92 " --> pdb=" O   PRO B  88 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ASN B  99 " --> pdb=" O   THR B  95 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   VAL B 100 " --> pdb=" O   MET B  96 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   GLY B 103 " --> pdb=" O   ASN B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 120
    Processing helix  chain 'B' and resid 124 through 136
      removed outlier: 3.650A  pdb=" N   HIS B 134 " --> pdb=" O   GLY B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 145
      removed outlier: 3.619A  pdb=" N   ALA B 140 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 152
    Processing helix  chain 'B' and resid 172 through 182
      removed outlier: 3.628A  pdb=" N   GLY B 176 " --> pdb=" O   ASP B 172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 186
      removed outlier: 3.565A  pdb=" N   ILE B 186 " --> pdb=" O   ILE B 183 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 183 through 186'
    Processing helix  chain 'B' and resid 190 through 219
      removed outlier: 3.667A  pdb=" N   ILE B 200 " --> pdb=" O   LEU B 196 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ARG B 201 " --> pdb=" O   SER B 197 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   THR B 203 " --> pdb=" O   GLY B 199 " (cutoff:3.500A)
      Proline residue:  B 215  - end of helix
      removed outlier: 3.521A  pdb=" N   GLN B 218 " --> pdb=" O   GLY B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 231
    Processing helix  chain 'B' and resid 232 through 235
      removed outlier: 4.101A  pdb=" N   ASN B 235 " --> pdb=" O   SER B 232 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 232 through 235'
    Processing helix  chain 'B' and resid 237 through 245
      removed outlier: 3.762A  pdb=" N   LEU B 241 " --> pdb=" O   ASN B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 258
      removed outlier: 3.620A  pdb=" N   SER B 258 " --> pdb=" O   GLU B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 330
    Processing helix  chain 'B' and resid 348 through 356
    Processing helix  chain 'B' and resid 358 through 362
    Processing helix  chain 'C' and resid 28 through 33
      removed outlier: 3.557A  pdb=" N   LEU C  32 " --> pdb=" O   HIS C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 70
    Processing helix  chain 'C' and resid 71 through 105
      removed outlier: 3.750A  pdb=" N   ASN C  80 " --> pdb=" O   ASP C  76 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU C  81 " --> pdb=" O   GLU C  77 " (cutoff:3.500A)
      Proline residue:  C  88  - end of helix
      removed outlier: 3.931A  pdb=" N   MET C  91 " --> pdb=" O   GLU C  87 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ALA C  92 " --> pdb=" O   PRO C  88 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ASN C  99 " --> pdb=" O   THR C  95 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   VAL C 100 " --> pdb=" O   MET C  96 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   GLY C 103 " --> pdb=" O   ASN C  99 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 116 through 120
    Processing helix  chain 'C' and resid 124 through 136
      removed outlier: 3.651A  pdb=" N   HIS C 134 " --> pdb=" O   GLY C 130 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 136 through 145
      removed outlier: 3.618A  pdb=" N   ALA C 140 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 146 through 152
    Processing helix  chain 'C' and resid 172 through 182
      removed outlier: 3.628A  pdb=" N   GLY C 176 " --> pdb=" O   ASP C 172 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 183 through 186
      removed outlier: 3.565A  pdb=" N   ILE C 186 " --> pdb=" O   ILE C 183 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 183 through 186'
    Processing helix  chain 'C' and resid 190 through 219
      removed outlier: 3.667A  pdb=" N   ILE C 200 " --> pdb=" O   LEU C 196 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ARG C 201 " --> pdb=" O   SER C 197 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   THR C 203 " --> pdb=" O   GLY C 199 " (cutoff:3.500A)
      Proline residue:  C 215  - end of helix
      removed outlier: 3.521A  pdb=" N   GLN C 218 " --> pdb=" O   GLY C 214 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 227 through 231
    Processing helix  chain 'C' and resid 232 through 235
      removed outlier: 4.100A  pdb=" N   ASN C 235 " --> pdb=" O   SER C 232 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 232 through 235'
    Processing helix  chain 'C' and resid 237 through 245
      removed outlier: 3.762A  pdb=" N   LEU C 241 " --> pdb=" O   ASN C 237 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 252 through 258
      removed outlier: 3.619A  pdb=" N   SER C 258 " --> pdb=" O   GLU C 254 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 327 through 330
    Processing helix  chain 'C' and resid 348 through 356
    Processing helix  chain 'C' and resid 358 through 362
    Processing sheet with id=AA1, first strand: chain 'A' and resid 331 through 332
      removed outlier: 3.643A  pdb=" N   LYS A  48 " --> pdb=" O   CYS A 339 " (cutoff:3.500A)
      removed outlier: 5.226A  pdb=" N   GLU A 294 " --> pdb=" O   GLY A  40 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   THR A  42 " --> pdb=" O   VAL A 292 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   VAL A 292 " --> pdb=" O   THR A  42 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   ASN A  44 " --> pdb=" O   ALA A 290 " (cutoff:3.500A)
      removed outlier: 8.460A  pdb=" N   ALA A 290 " --> pdb=" O   ASN A  44 " (cutoff:3.500A)
      removed outlier: 9.704A  pdb=" N   LYS A  46 " --> pdb=" O   PRO A 288 " (cutoff:3.500A)
      removed outlier: 9.493A  pdb=" N   LYS A  48 " --> pdb=" O   LEU A 286 " (cutoff:3.500A)
      removed outlier: 7.982A  pdb=" N   LEU A 286 " --> pdb=" O   LYS A  48 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   PHE A 314 " --> pdb=" O   ILE A 325 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   ILE A 325 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 157 through 161
      removed outlier: 8.404A  pdb=" N   THR A 167 " --> pdb=" O   THR A  53 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   LEU A  55 " --> pdb=" O   THR A 167 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ASP A 267 " --> pdb=" O   ALA A 276 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   GLU A 278 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 5.792A  pdb=" N   ILE A 265 " --> pdb=" O   GLU A 278 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   GLU A 280 " --> pdb=" O   GLY A 263 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   GLY A 263 " --> pdb=" O   GLU A 280 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 113 through 115
    Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 123
    Processing sheet with id=AA5, first strand: chain 'A' and resid 300 through 302
    Processing sheet with id=AA6, first strand: chain 'A' and resid 409 through 411
    Processing sheet with id=AA7, first strand: chain 'A' and resid 398 through 399
      removed outlier: 7.065A  pdb=" N   LEU A 425 " --> pdb=" O   MET B 114 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 331 through 332
      removed outlier: 3.643A  pdb=" N   LYS B  48 " --> pdb=" O   CYS B 339 " (cutoff:3.500A)
      removed outlier: 5.226A  pdb=" N   GLU B 294 " --> pdb=" O   GLY B  40 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   THR B  42 " --> pdb=" O   VAL B 292 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   VAL B 292 " --> pdb=" O   THR B  42 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   ASN B  44 " --> pdb=" O   ALA B 290 " (cutoff:3.500A)
      removed outlier: 8.460A  pdb=" N   ALA B 290 " --> pdb=" O   ASN B  44 " (cutoff:3.500A)
      removed outlier: 9.705A  pdb=" N   LYS B  46 " --> pdb=" O   PRO B 288 " (cutoff:3.500A)
      removed outlier: 9.494A  pdb=" N   LYS B  48 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 7.984A  pdb=" N   LEU B 286 " --> pdb=" O   LYS B  48 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   PHE B 314 " --> pdb=" O   ILE B 325 " (cutoff:3.500A)
      removed outlier: 4.756A  pdb=" N   ILE B 325 " --> pdb=" O   PHE B 314 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 157 through 161
      removed outlier: 8.403A  pdb=" N   THR B 167 " --> pdb=" O   THR B  53 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   LEU B  55 " --> pdb=" O   THR B 167 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ASP B 267 " --> pdb=" O   ALA B 276 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   GLU B 278 " --> pdb=" O   ILE B 265 " (cutoff:3.500A)
      removed outlier: 5.791A  pdb=" N   ILE B 265 " --> pdb=" O   GLU B 278 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   GLU B 280 " --> pdb=" O   GLY B 263 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   GLY B 263 " --> pdb=" O   GLU B 280 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 300 through 302
    Processing sheet with id=AB2, first strand: chain 'B' and resid 409 through 411
    Processing sheet with id=AB3, first strand: chain 'B' and resid 398 through 399
      removed outlier: 7.080A  pdb=" N   LEU B 425 " --> pdb=" O   MET C 114 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 331 through 332
      removed outlier: 3.642A  pdb=" N   LYS C  48 " --> pdb=" O   CYS C 339 " (cutoff:3.500A)
      removed outlier: 5.226A  pdb=" N   GLU C 294 " --> pdb=" O   GLY C  40 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   THR C  42 " --> pdb=" O   VAL C 292 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   VAL C 292 " --> pdb=" O   THR C  42 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   ASN C  44 " --> pdb=" O   ALA C 290 " (cutoff:3.500A)
      removed outlier: 8.460A  pdb=" N   ALA C 290 " --> pdb=" O   ASN C  44 " (cutoff:3.500A)
      removed outlier: 9.704A  pdb=" N   LYS C  46 " --> pdb=" O   PRO C 288 " (cutoff:3.500A)
      removed outlier: 9.494A  pdb=" N   LYS C  48 " --> pdb=" O   LEU C 286 " (cutoff:3.500A)
      removed outlier: 7.982A  pdb=" N   LEU C 286 " --> pdb=" O   LYS C  48 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   PHE C 314 " --> pdb=" O   ILE C 325 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   ILE C 325 " --> pdb=" O   PHE C 314 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 157 through 161
      removed outlier: 8.403A  pdb=" N   THR C 167 " --> pdb=" O   THR C  53 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   LEU C  55 " --> pdb=" O   THR C 167 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ASP C 267 " --> pdb=" O   ALA C 276 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   GLU C 278 " --> pdb=" O   ILE C 265 " (cutoff:3.500A)
      removed outlier: 5.791A  pdb=" N   ILE C 265 " --> pdb=" O   GLU C 278 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   GLU C 280 " --> pdb=" O   GLY C 263 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   GLY C 263 " --> pdb=" O   GLU C 280 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 300 through 302

    424 hydrogen bonds defined for protein.
    1146 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.76

  Time building geometry restraints manager: 1.20 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2997
        1.34 -     1.46: 1888
        1.46 -     1.59: 4757
        1.59 -     1.72: 0
        1.72 -     1.84: 84
  Bond restraints: 9726
  Sorted by residual:
  bond pdb=" N   ASP C 172 "
       pdb=" CA  ASP C 172 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.037 2.20e-02 2.07e+03 2.76e+00
  bond pdb=" N   ASP A 172 "
       pdb=" CA  ASP A 172 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.036 2.20e-02 2.07e+03 2.75e+00
  bond pdb=" N   ASP B 172 "
       pdb=" CA  ASP B 172 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.036 2.20e-02 2.07e+03 2.67e+00
  bond pdb=" CA  THR B 173 "
       pdb=" C   THR B 173 "
    ideal  model  delta    sigma   weight residual
    1.524  1.542 -0.019 1.27e-02 6.20e+03 2.12e+00
  bond pdb=" CA  THR C 173 "
       pdb=" C   THR C 173 "
    ideal  model  delta    sigma   weight residual
    1.524  1.542 -0.018 1.27e-02 6.20e+03 2.02e+00
  ... (remaining 9721 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.48: 11284
        1.48 -     2.96: 1502
        2.96 -     4.43: 339
        4.43 -     5.91: 76
        5.91 -     7.39: 23
  Bond angle restraints: 13224
  Sorted by residual:
  angle pdb=" N   THR B 173 "
        pdb=" CA  THR B 173 "
        pdb=" C   THR B 173 "
      ideal   model   delta    sigma   weight residual
     111.07  115.94   -4.87 1.07e+00 8.73e-01 2.07e+01
  angle pdb=" N   THR C 173 "
        pdb=" CA  THR C 173 "
        pdb=" C   THR C 173 "
      ideal   model   delta    sigma   weight residual
     111.07  115.93   -4.86 1.07e+00 8.73e-01 2.06e+01
  angle pdb=" N   THR A 173 "
        pdb=" CA  THR A 173 "
        pdb=" C   THR A 173 "
      ideal   model   delta    sigma   weight residual
     111.07  115.89   -4.82 1.07e+00 8.73e-01 2.03e+01
  angle pdb=" N   LYS B  68 "
        pdb=" CA  LYS B  68 "
        pdb=" C   LYS B  68 "
      ideal   model   delta    sigma   weight residual
     111.33  116.31   -4.98 1.21e+00 6.83e-01 1.70e+01
  angle pdb=" N   LYS C  68 "
        pdb=" CA  LYS C  68 "
        pdb=" C   LYS C  68 "
      ideal   model   delta    sigma   weight residual
     111.33  116.29   -4.96 1.21e+00 6.83e-01 1.68e+01
  ... (remaining 13219 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.33: 5514
       15.33 -    30.65: 342
       30.65 -    45.98: 62
       45.98 -    61.31: 31
       61.31 -    76.64: 18
  Dihedral angle restraints: 5967
    sinusoidal: 2298
      harmonic: 3669
  Sorted by residual:
  dihedral pdb=" CB  CYS B 393 "
           pdb=" SG  CYS B 393 "
           pdb=" SG  CYS B 416 "
           pdb=" CB  CYS B 416 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.09  -60.09     1      1.00e+01 1.00e-02 4.81e+01
  dihedral pdb=" CB  CYS C 393 "
           pdb=" SG  CYS C 393 "
           pdb=" SG  CYS C 416 "
           pdb=" CB  CYS C 416 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.09  -60.09     1      1.00e+01 1.00e-02 4.81e+01
  dihedral pdb=" CB  CYS A 393 "
           pdb=" SG  CYS A 393 "
           pdb=" SG  CYS A 416 "
           pdb=" CB  CYS A 416 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.08  -60.08     1      1.00e+01 1.00e-02 4.81e+01
  ... (remaining 5964 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 782
       0.039 -    0.077: 496
       0.077 -    0.116: 233
       0.116 -    0.155: 85
       0.155 -    0.193: 18
  Chirality restraints: 1614
  Sorted by residual:
  chirality pdb=" CA  ILE C 183 "
            pdb=" N   ILE C 183 "
            pdb=" C   ILE C 183 "
            pdb=" CB  ILE C 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.24    0.19 2.00e-01 2.50e+01 9.33e-01
  chirality pdb=" CA  ILE A 183 "
            pdb=" N   ILE A 183 "
            pdb=" C   ILE A 183 "
            pdb=" CB  ILE A 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.24    0.19 2.00e-01 2.50e+01 9.11e-01
  chirality pdb=" CA  ILE B 183 "
            pdb=" N   ILE B 183 "
            pdb=" C   ILE B 183 "
            pdb=" CB  ILE B 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.24    0.19 2.00e-01 2.50e+01 9.00e-01
  ... (remaining 1611 not shown)

  Planarity restraints: 1695
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 210 "   -0.017 2.00e-02 2.50e+03   3.44e-02 1.19e+01
        pdb=" C   ILE A 210 "    0.060 2.00e-02 2.50e+03
        pdb=" O   ILE A 210 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   THR A 211 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 210 "   -0.017 2.00e-02 2.50e+03   3.43e-02 1.17e+01
        pdb=" C   ILE B 210 "    0.059 2.00e-02 2.50e+03
        pdb=" O   ILE B 210 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   THR B 211 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE C 210 "    0.017 2.00e-02 2.50e+03   3.42e-02 1.17e+01
        pdb=" C   ILE C 210 "   -0.059 2.00e-02 2.50e+03
        pdb=" O   ILE C 210 "    0.022 2.00e-02 2.50e+03
        pdb=" N   THR C 211 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1692 not shown)

  Histogram of nonbonded interaction distances:
        2.42 -     2.91: 3594
        2.91 -     3.41: 8340
        3.41 -     3.91: 14234
        3.91 -     4.40: 15737
        4.40 -     4.90: 27878
  Nonbonded interactions: 69783
  Sorted by model distance:
  nonbonded pdb=" O   THR A 319 "
            pdb=" OG1 THR A 320 "
     model   vdw
     2.417 3.040
  nonbonded pdb=" O   THR B 319 "
            pdb=" OG1 THR B 320 "
     model   vdw
     2.417 3.040
  nonbonded pdb=" O   THR C 319 "
            pdb=" OG1 THR C 320 "
     model   vdw
     2.417 3.040
  nonbonded pdb=" OD1 ASN A  44 "
            pdb=" OG  SER A 336 "
     model   vdw
     2.505 3.040
  nonbonded pdb=" OD1 ASN B  44 "
            pdb=" OG  SER B 336 "
     model   vdw
     2.505 3.040
  ... (remaining 69778 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.370
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.860
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  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:6.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
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   0.050   9738  Z= 0.401
  Angle     :  1.164   7.388  13248  Z= 0.716
  Chirality :  0.062   0.193   1614
  Planarity :  0.007   0.049   1695
  Dihedral  : 12.096  76.635   3573
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 0.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.16 (0.21), residues: 1254
  helix: -1.03 (0.21), residues: 402
  sheet:  0.31 (0.31), residues: 258
  loop : -0.98 (0.23), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.002   ARG A 364 
 TYR   0.042   0.006   TYR A  45 
 PHE   0.023   0.005   PHE C 281 
 TRP   0.028   0.007   TRP B 307 
 HIS   0.006   0.002   HIS B 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00831 ( 9726)
  covalent geometry    : angle       1.15894 (13224)
  SS BOND              : bond        0.00989 (   12)
  SS BOND              : angle       2.74375 (   24)
  hydrogen bonds       : bond        0.19047 (  424)
  hydrogen bonds       : angle       6.99219 ( 1146)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.473 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.9221
  time to fit residues: 55.3969
Evaluate side-chains
  32 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    0.9980
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 123 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
B 349 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.070575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.056483 restraints weight = 21994.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.2838 rms_B_bonded: 3.51
r_work: 0.2693 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.1589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9738  Z= 0.169
  Angle     :  0.627   5.459  13248  Z= 0.359
  Chirality :  0.045   0.138   1614
  Planarity :  0.004   0.050   1695
  Dihedral  :  4.990  17.736   1350
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  4.04 %
    Favored  : 95.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.23), residues: 1254
  helix:  1.11 (0.25), residues: 405
  sheet:  0.50 (0.32), residues: 249
  loop : -0.36 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 108 
 TYR   0.013   0.002   TYR A  45 
 PHE   0.011   0.002   PHE A 234 
 TRP   0.010   0.002   TRP C 307 
 HIS   0.003   0.001   HIS B 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 9726)
  covalent geometry    : angle       0.62570 (13224)
  SS BOND              : bond        0.00213 (   12)
  SS BOND              : angle       1.10812 (   24)
  hydrogen bonds       : bond        0.06548 (  424)
  hydrogen bonds       : angle       5.30635 ( 1146)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 33
  time to evaluate  : 0.378 
Fit side-chains
REVERT: A  296 MET cc_start: 0.8682 (mtm) cc_final: 0.8472 (mtp)
  outliers start: 9
  outliers final: 2
  residues processed: 38
  average time/residue: 0.5932
  time to fit residues: 24.6347
Evaluate side-chains
  31 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 29
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain C residue  349 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 92 optimal weight:    6.9990
   chunk 118 optimal weight:    0.0270
   chunk 122 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 13 optimal weight:    0.4980
   chunk 72 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    1.9044

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.068350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.054374 restraints weight = 22349.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.2802 rms_B_bonded: 3.52
r_work: 0.2652 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.2007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9738  Z= 0.179
  Angle     :  0.595   7.484  13248  Z= 0.335
  Chirality :  0.045   0.145   1614
  Planarity :  0.004   0.034   1695
  Dihedral  :  4.841  17.143   1350
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 1.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  4.59 %
    Favored  : 94.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.24), residues: 1254
  helix:  2.12 (0.28), residues: 369
  sheet:  0.31 (0.32), residues: 246
  loop : -0.40 (0.25), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 201 
 TYR   0.014   0.002   TYR A 274 
 PHE   0.012   0.002   PHE A 234 
 TRP   0.011   0.002   TRP C 307 
 HIS   0.002   0.001   HIS C 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 9726)
  covalent geometry    : angle       0.59397 (13224)
  SS BOND              : bond        0.00276 (   12)
  SS BOND              : angle       1.01974 (   24)
  hydrogen bonds       : bond        0.06207 (  424)
  hydrogen bonds       : angle       5.12596 ( 1146)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 30
  time to evaluate  : 0.397 
Fit side-chains
REVERT: B  426 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8263 (tt)
  outliers start: 9
  outliers final: 1
  residues processed: 36
  average time/residue: 0.6613
  time to fit residues: 25.8965
Evaluate side-chains
  29 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 27
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain B residue  426 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   chunk 46 optimal weight:    0.3980
   chunk 35 optimal weight:    0.7980
   chunk 37 optimal weight:    0.2980
   chunk 88 optimal weight:    0.2980
   chunk 107 optimal weight:    0.9990
   chunk 110 optimal weight:    4.9990
   chunk 114 optimal weight:    2.9990
   chunk 112 optimal weight:    3.9990
   overall best weight:    0.5582

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

Flipped N/Q/H residues before XYZ refinement:
A 301 ASN
B 301 ASN
C 301 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.072733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.058838 restraints weight = 22092.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.2901 rms_B_bonded: 3.53
r_work: 0.2757 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9738  Z= 0.098
  Angle     :  0.467   5.676  13248  Z= 0.262
  Chirality :  0.043   0.144   1614
  Planarity :  0.003   0.037   1695
  Dihedral  :  4.381  15.620   1350
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 1.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  5.51 %
    Favored  : 94.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.24), residues: 1254
  helix:  2.30 (0.27), residues: 375
  sheet:  0.45 (0.29), residues: 288
  loop : -0.31 (0.26), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 415 
 TYR   0.009   0.001   TYR C 274 
 PHE   0.006   0.001   PHE B 375 
 TRP   0.002   0.000   TRP A 307 
 HIS   0.001   0.000   HIS C 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00186 ( 9726)
  covalent geometry    : angle       0.46663 (13224)
  SS BOND              : bond        0.00131 (   12)
  SS BOND              : angle       0.67799 (   24)
  hydrogen bonds       : bond        0.03840 (  424)
  hydrogen bonds       : angle       4.49011 ( 1146)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 30
  time to evaluate  : 0.397 
Fit side-chains
REVERT: C  146 MET cc_start: 0.7522 (mmp) cc_final: 0.7310 (mmm)
  outliers start: 4
  outliers final: 1
  residues processed: 33
  average time/residue: 0.6504
  time to fit residues: 23.4212
Evaluate side-chains
  29 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 28
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  349 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    0.2980
   chunk 84 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 112 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9980
   chunk 104 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9990
   chunk 105 optimal weight:    0.9990
   overall best weight:    0.7582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.072093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.058291 restraints weight = 22254.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.2900 rms_B_bonded: 3.51
r_work: 0.2758 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.2585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   9738  Z= 0.101
  Angle     :  0.470   9.442  13248  Z= 0.261
  Chirality :  0.042   0.127   1614
  Planarity :  0.003   0.034   1695
  Dihedral  :  4.186  15.792   1350
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 1.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  6.15 %
    Favored  : 93.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.24), residues: 1254
  helix:  2.54 (0.27), residues: 375
  sheet:  0.43 (0.29), residues: 288
  loop : -0.34 (0.26), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 108 
 TYR   0.010   0.001   TYR C 274 
 PHE   0.007   0.001   PHE B 238 
 TRP   0.004   0.001   TRP A 307 
 HIS   0.001   0.000   HIS C 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 9726)
  covalent geometry    : angle       0.46978 (13224)
  SS BOND              : bond        0.00165 (   12)
  SS BOND              : angle       0.64964 (   24)
  hydrogen bonds       : bond        0.04127 (  424)
  hydrogen bonds       : angle       4.40296 ( 1146)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 28
  time to evaluate  : 0.402 
Fit side-chains
REVERT: A  146 MET cc_start: 0.7382 (mmp) cc_final: 0.7150 (mmm)
REVERT: B  245 MET cc_start: 0.8285 (mtt) cc_final: 0.8059 (mtt)
REVERT: B  426 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8196 (tt)
  outliers start: 8
  outliers final: 2
  residues processed: 35
  average time/residue: 0.6212
  time to fit residues: 23.6919
Evaluate side-chains
  31 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 28
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain C residue  225 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 115 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 40 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   chunk 78 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9990
   chunk 99 optimal weight:    0.3980
   overall best weight:    1.0184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.071330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.057579 restraints weight = 22117.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.2888 rms_B_bonded: 3.50
r_work: 0.2744 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.2618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9738  Z= 0.111
  Angle     :  0.472   9.126  13248  Z= 0.263
  Chirality :  0.042   0.128   1614
  Planarity :  0.003   0.035   1695
  Dihedral  :  4.166  15.951   1350
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 1.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  6.80 %
    Favored  : 92.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (0.24), residues: 1254
  helix:  2.59 (0.27), residues: 375
  sheet:  0.39 (0.29), residues: 288
  loop : -0.38 (0.26), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 415 
 TYR   0.012   0.001   TYR C 274 
 PHE   0.008   0.001   PHE B 238 
 TRP   0.005   0.001   TRP A 307 
 HIS   0.002   0.000   HIS A 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 9726)
  covalent geometry    : angle       0.47167 (13224)
  SS BOND              : bond        0.00179 (   12)
  SS BOND              : angle       0.64838 (   24)
  hydrogen bonds       : bond        0.04349 (  424)
  hydrogen bonds       : angle       4.44526 ( 1146)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 29
  time to evaluate  : 0.361 
Fit side-chains
REVERT: A   91 MET cc_start: 0.8098 (mmp) cc_final: 0.7878 (tpp)
REVERT: A  146 MET cc_start: 0.7472 (mmp) cc_final: 0.7261 (mmm)
REVERT: B  245 MET cc_start: 0.8280 (mtt) cc_final: 0.8043 (mtt)
REVERT: B  426 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8201 (tt)
  outliers start: 7
  outliers final: 3
  residues processed: 34
  average time/residue: 0.6412
  time to fit residues: 23.7702
Evaluate side-chains
  33 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 29
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  349 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 98 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   chunk 55 optimal weight:    5.9990
   chunk 40 optimal weight:    0.0470
   chunk 95 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   overall best weight:    2.4086

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

Flipped N/Q/H residues before XYZ refinement:
C 349 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.067111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.053391 restraints weight = 22392.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.2796 rms_B_bonded: 3.51
r_work: 0.2647 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.2466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   9738  Z= 0.205
  Angle     :  0.578  10.070  13248  Z= 0.323
  Chirality :  0.045   0.143   1614
  Planarity :  0.004   0.037   1695
  Dihedral  :  4.563  16.635   1350
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 1.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  6.98 %
    Favored  : 92.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.74 (0.24), residues: 1254
  helix:  2.54 (0.28), residues: 372
  sheet:  0.09 (0.31), residues: 255
  loop : -0.60 (0.25), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 201 
 TYR   0.016   0.002   TYR A 274 
 PHE   0.013   0.002   PHE C 238 
 TRP   0.010   0.003   TRP B 307 
 HIS   0.003   0.001   HIS A 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 ( 9726)
  covalent geometry    : angle       0.57713 (13224)
  SS BOND              : bond        0.00305 (   12)
  SS BOND              : angle       0.97501 (   24)
  hydrogen bonds       : bond        0.06378 (  424)
  hydrogen bonds       : angle       5.02456 ( 1146)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 30
  time to evaluate  : 0.432 
Fit side-chains
REVERT: B  426 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8265 (tt)
  outliers start: 8
  outliers final: 4
  residues processed: 36
  average time/residue: 0.6226
  time to fit residues: 24.4768
Evaluate side-chains
  33 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 28
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  349 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 65 optimal weight:    0.7980
   chunk 97 optimal weight:    1.9990
   chunk 111 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 116 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 56 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
C 349 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.070082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.056460 restraints weight = 22187.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.2861 rms_B_bonded: 3.49
r_work: 0.2715 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.2678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9738  Z= 0.106
  Angle     :  0.479  10.653  13248  Z= 0.267
  Chirality :  0.042   0.127   1614
  Planarity :  0.003   0.033   1695
  Dihedral  :  4.322  16.400   1350
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 1.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  6.98 %
    Favored  : 92.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.76 (0.24), residues: 1254
  helix:  2.50 (0.28), residues: 375
  sheet:  0.09 (0.31), residues: 258
  loop : -0.56 (0.25), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 415 
 TYR   0.009   0.001   TYR A 274 
 PHE   0.006   0.001   PHE A 281 
 TRP   0.004   0.001   TRP A 307 
 HIS   0.005   0.001   HIS C 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 9726)
  covalent geometry    : angle       0.47864 (13224)
  SS BOND              : bond        0.00162 (   12)
  SS BOND              : angle       0.66465 (   24)
  hydrogen bonds       : bond        0.04547 (  424)
  hydrogen bonds       : angle       4.59571 ( 1146)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 28
  time to evaluate  : 0.427 
Fit side-chains
REVERT: A  146 MET cc_start: 0.7657 (mmp) cc_final: 0.7435 (mmm)
REVERT: B  426 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8250 (tt)
  outliers start: 8
  outliers final: 2
  residues processed: 35
  average time/residue: 0.5776
  time to fit residues: 22.0997
Evaluate side-chains
  32 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 29
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain C residue  225 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 91 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 90 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.9182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.070665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.057010 restraints weight = 22085.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.2874 rms_B_bonded: 3.49
r_work: 0.2729 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.2795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9738  Z= 0.106
  Angle     :  0.473  11.330  13248  Z= 0.261
  Chirality :  0.042   0.127   1614
  Planarity :  0.003   0.035   1695
  Dihedral  :  4.153  16.163   1350
  Min Nonbonded Distance : 2.649

Molprobity Statistics.
  All-atom Clashscore : 1.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  7.25 %
    Favored  : 92.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.24), residues: 1254
  helix:  2.62 (0.28), residues: 375
  sheet:  0.10 (0.31), residues: 258
  loop : -0.53 (0.25), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 108 
 TYR   0.011   0.001   TYR C 274 
 PHE   0.007   0.001   PHE B 238 
 TRP   0.005   0.001   TRP B 307 
 HIS   0.002   0.001   HIS C 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 9726)
  covalent geometry    : angle       0.47277 (13224)
  SS BOND              : bond        0.00167 (   12)
  SS BOND              : angle       0.59595 (   24)
  hydrogen bonds       : bond        0.04321 (  424)
  hydrogen bonds       : angle       4.46483 ( 1146)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 30
  time to evaluate  : 0.411 
Fit side-chains
REVERT: A  146 MET cc_start: 0.7614 (mmp) cc_final: 0.7396 (mmm)
REVERT: B  426 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8190 (tt)
  outliers start: 7
  outliers final: 4
  residues processed: 37
  average time/residue: 0.6042
  time to fit residues: 24.3705
Evaluate side-chains
  34 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 29
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  404 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 83 optimal weight:    9.9990
   chunk 23 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 82 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 98 optimal weight:    0.6980
   chunk 86 optimal weight:    0.7980
   overall best weight:    1.6986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.068557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.054928 restraints weight = 22094.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.2828 rms_B_bonded: 3.49
r_work: 0.2682 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.2699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9738  Z= 0.153
  Angle     :  0.540  12.361  13248  Z= 0.294
  Chirality :  0.043   0.136   1614
  Planarity :  0.003   0.035   1695
  Dihedral  :  4.330  16.559   1350
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 1.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  7.53 %
    Favored  : 91.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.76 (0.24), residues: 1254
  helix:  2.61 (0.28), residues: 375
  sheet:  0.12 (0.32), residues: 255
  loop : -0.65 (0.25), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 108 
 TYR   0.014   0.001   TYR A 274 
 PHE   0.012   0.002   PHE B 238 
 TRP   0.007   0.002   TRP A 307 
 HIS   0.002   0.001   HIS C 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 9726)
  covalent geometry    : angle       0.53916 (13224)
  SS BOND              : bond        0.00237 (   12)
  SS BOND              : angle       0.76152 (   24)
  hydrogen bonds       : bond        0.05407 (  424)
  hydrogen bonds       : angle       4.74756 ( 1146)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 31
  time to evaluate  : 0.399 
Fit side-chains
REVERT: A  146 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.7551 (mmm)
REVERT: B  426 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8260 (tt)
  outliers start: 8
  outliers final: 4
  residues processed: 36
  average time/residue: 0.6182
  time to fit residues: 24.3338
Evaluate side-chains
  37 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 MET
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain C residue  225 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 56 optimal weight:    3.9990
   chunk 101 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9990
   chunk 69 optimal weight:    5.9990
   chunk 123 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0870
   chunk 63 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.6158

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.071496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.057882 restraints weight = 21834.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.2893 rms_B_bonded: 3.47
r_work: 0.2750 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.2929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9738  Z= 0.093
  Angle     :  0.469  11.833  13248  Z= 0.253
  Chirality :  0.042   0.125   1614
  Planarity :  0.003   0.032   1695
  Dihedral  :  4.101  16.106   1350
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 1.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  8.36 %
    Favored  : 91.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.25), residues: 1254
  helix:  2.65 (0.28), residues: 375
  sheet:  0.33 (0.30), residues: 288
  loop : -0.51 (0.26), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 415 
 TYR   0.009   0.001   TYR A 274 
 PHE   0.005   0.001   PHE B 375 
 TRP   0.003   0.001   TRP A 307 
 HIS   0.001   0.000   HIS C 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00189 ( 9726)
  covalent geometry    : angle       0.46855 (13224)
  SS BOND              : bond        0.00122 (   12)
  SS BOND              : angle       0.61164 (   24)
  hydrogen bonds       : bond        0.03857 (  424)
  hydrogen bonds       : angle       4.36695 ( 1146)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2260.91 seconds
wall clock time: 39 minutes 31.28 seconds (2371.28 seconds total)