Starting phenix.real_space_refine
on Sun Feb  8 06:23:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rpd_54161/02_2026/9rpd_54161.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rpd_54161/02_2026/9rpd_54161.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rpd_54161/02_2026/9rpd_54161.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rpd_54161/02_2026/9rpd_54161.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rpd_54161/02_2026/9rpd_54161.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rpd_54161/02_2026/9rpd_54161.cif"
  }
  resolution = 4.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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: 5
    Type Number    sf(0)   Gaussians
     S     146      5.16       5
     C   13784      2.51       5
     N    3724      2.21       5
     O    4142      1.98       5
     H   19714      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 295 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 41510
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "I"
      Number of atoms: 134
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 134
          Classifications: {'peptide': 15}
          Link IDs: {'TRANS': 14}
    Chain: "J"
      Number of atoms: 1228
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1228
          Classifications: {'peptide': 146}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 139}
          Chain breaks: 1
    Chain: "K"
      Number of atoms: 104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 104
          Classifications: {'peptide': 13}
          Link IDs: {'TRANS': 12}
    Chain: "B"
      Number of atoms: 6600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 427, 6600
          Classifications: {'peptide': 427}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406}
    Chain: "A"
      Number of atoms: 6711
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 436, 6711
          Classifications: {'peptide': 436}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 415}
  Restraints were copied for chains:
    C, E, G, D
  Time building chain proxies: 13.14, per 1000 atoms: 0.32
  Number of scatterers: 41510
  At special positions: 0
  Unit cell: (117.59, 122.935, 164.626, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S     146     16.00
     O    4142      8.00
     N    3724      7.00
     C   13784      6.00
     H   19714      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" CD1 PHE D 317 " - pdb=" HE1 PHE D 317 " distance=2.16

  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=15, symmetry=0
  Number of additional bonds: simple=15, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.73
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  5504 Ramachandran restraints generated.
    2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5132

  Finding SS restraints...
    Secondary structure from input PDB file:
      132 helices and 16 sheets defined
      56.0% alpha, 13.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'I' and resid 22 through 36
    Processing helix  chain 'J' and resid 11 through 31
      removed outlier: 3.685A  pdb=" N   VAL J  30 " --> pdb=" O   GLY J  26 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 34 through 39
      removed outlier: 3.510A  pdb=" N   LYS J  39 " --> pdb=" O   ASP J  35 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 50 through 66
    Processing helix  chain 'J' and resid 66 through 74
    Processing helix  chain 'J' and resid 80 through 102
    Processing helix  chain 'J' and resid 111 through 116
    Processing helix  chain 'J' and resid 119 through 145
    Processing helix  chain 'J' and resid 156 through 164
    Processing helix  chain 'K' and resid 64 through 75
    Processing helix  chain 'B' and resid 10 through 28
    Processing helix  chain 'B' and resid 41 through 46
      removed outlier: 4.738A  pdb=" N   ARG B  46 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 49
      No H-bonds generated for 'chain 'B' and resid 47 through 49'
    Processing helix  chain 'B' and resid 70 through 79
    Processing helix  chain 'B' and resid 86 through 88
      No H-bonds generated for 'chain 'B' and resid 86 through 88'
    Processing helix  chain 'B' and resid 100 through 107
      removed outlier: 3.513A  pdb=" N   THR B 107 " --> pdb=" O   LYS B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 125
      removed outlier: 5.118A  pdb=" N   ASP B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
      removed outlier: 5.407A  pdb=" N   SER B 115 " --> pdb=" O   GLU B 111 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   VAL B 119 " --> pdb=" O   SER B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 159
    Processing helix  chain 'B' and resid 180 through 196
      removed outlier: 3.609A  pdb=" N   GLN B 191 " --> pdb=" O   LEU B 187 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLU B 194 " --> pdb=" O   HIS B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 214
    Processing helix  chain 'B' and resid 221 through 237
      removed outlier: 3.525A  pdb=" N   LEU B 228 " --> pdb=" O   ASP B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 242
    Processing helix  chain 'B' and resid 249 through 258
    Processing helix  chain 'B' and resid 285 through 294
      removed outlier: 3.563A  pdb=" N   PHE B 294 " --> pdb=" O   THR B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 299
    Processing helix  chain 'B' and resid 304 through 308
    Processing helix  chain 'B' and resid 322 through 337
    Processing helix  chain 'B' and resid 338 through 341
    Processing helix  chain 'B' and resid 374 through 390
      removed outlier: 3.587A  pdb=" N   PHE B 378 " --> pdb=" O   ILE B 374 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   MET B 388 " --> pdb=" O   GLN B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 400
    Processing helix  chain 'B' and resid 404 through 427
      removed outlier: 3.916A  pdb=" N   PHE B 408 " --> pdb=" O   ASP B 404 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 10 through 28
    Processing helix  chain 'D' and resid 41 through 46
      removed outlier: 4.738A  pdb=" N   ARG D  46 " --> pdb=" O   LEU D  42 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 47 through 49
      No H-bonds generated for 'chain 'D' and resid 47 through 49'
    Processing helix  chain 'D' and resid 70 through 79
    Processing helix  chain 'D' and resid 86 through 88
      No H-bonds generated for 'chain 'D' and resid 86 through 88'
    Processing helix  chain 'D' and resid 100 through 107
      removed outlier: 3.514A  pdb=" N   THR D 107 " --> pdb=" O   LYS D 103 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 107 through 125
      removed outlier: 5.118A  pdb=" N   ASP D 114 " --> pdb=" O   ALA D 110 " (cutoff:3.500A)
      removed outlier: 5.407A  pdb=" N   SER D 115 " --> pdb=" O   GLU D 111 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   VAL D 119 " --> pdb=" O   SER D 115 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 142 through 159
    Processing helix  chain 'D' and resid 180 through 196
      removed outlier: 3.610A  pdb=" N   GLN D 191 " --> pdb=" O   LEU D 187 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLU D 194 " --> pdb=" O   HIS D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 204 through 214
    Processing helix  chain 'D' and resid 221 through 237
      removed outlier: 3.524A  pdb=" N   LEU D 228 " --> pdb=" O   ASP D 224 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 237 through 242
    Processing helix  chain 'D' and resid 249 through 258
    Processing helix  chain 'D' and resid 285 through 294
      removed outlier: 3.562A  pdb=" N   PHE D 294 " --> pdb=" O   THR D 290 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 295 through 299
    Processing helix  chain 'D' and resid 304 through 308
    Processing helix  chain 'D' and resid 322 through 337
    Processing helix  chain 'D' and resid 338 through 341
    Processing helix  chain 'D' and resid 374 through 390
      removed outlier: 3.587A  pdb=" N   PHE D 378 " --> pdb=" O   ILE D 374 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   MET D 388 " --> pdb=" O   GLN D 384 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 395 through 400
    Processing helix  chain 'D' and resid 404 through 427
      removed outlier: 3.915A  pdb=" N   PHE D 408 " --> pdb=" O   ASP D 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 10 through 29
    Processing helix  chain 'A' and resid 46 through 51
      removed outlier: 3.929A  pdb=" N   PHE A  49 " --> pdb=" O   ASP A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 81
    Processing helix  chain 'A' and resid 88 through 90
      No H-bonds generated for 'chain 'A' and resid 88 through 90'
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 109 through 127
      removed outlier: 3.897A  pdb=" N   GLU A 113 " --> pdb=" O   THR A 109 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ILE A 114 " --> pdb=" O   ILE A 110 " (cutoff:3.500A)
      removed outlier: 5.065A  pdb=" N   ASP A 116 " --> pdb=" O   LYS A 112 " (cutoff:3.500A)
      removed outlier: 5.535A  pdb=" N   LEU A 117 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 161
      removed outlier: 4.217A  pdb=" N   THR A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 178
      removed outlier: 3.534A  pdb=" N   SER A 178 " --> pdb=" O   PRO A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 195
    Processing helix  chain 'A' and resid 206 through 217
    Processing helix  chain 'A' and resid 223 through 244
      removed outlier: 4.824A  pdb=" N   SER A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 5.246A  pdb=" N   LEU A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 260
      removed outlier: 3.695A  pdb=" N   PHE A 255 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLN A 256 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 281
    Processing helix  chain 'A' and resid 287 through 295
    Processing helix  chain 'A' and resid 296 through 301
      removed outlier: 6.724A  pdb=" N   ALA A 299 " --> pdb=" O   PHE A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 310
    Processing helix  chain 'A' and resid 324 through 339
    Processing helix  chain 'A' and resid 384 through 400
      removed outlier: 3.881A  pdb=" N   TRP A 388 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LYS A 394 " --> pdb=" O   ARG A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 4.146A  pdb=" N   TYR A 408 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 436
      removed outlier: 4.186A  pdb=" N   PHE A 418 " --> pdb=" O   GLU A 414 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   SER A 419 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 10 through 29
    Processing helix  chain 'C' and resid 46 through 51
      removed outlier: 3.929A  pdb=" N   PHE C  49 " --> pdb=" O   ASP C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 81
    Processing helix  chain 'C' and resid 88 through 90
      No H-bonds generated for 'chain 'C' and resid 88 through 90'
    Processing helix  chain 'C' and resid 102 through 108
    Processing helix  chain 'C' and resid 109 through 127
      removed outlier: 3.898A  pdb=" N   GLU C 113 " --> pdb=" O   THR C 109 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ILE C 114 " --> pdb=" O   ILE C 110 " (cutoff:3.500A)
      removed outlier: 5.066A  pdb=" N   ASP C 116 " --> pdb=" O   LYS C 112 " (cutoff:3.500A)
      removed outlier: 5.534A  pdb=" N   LEU C 117 " --> pdb=" O   GLU C 113 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 143 through 161
      removed outlier: 4.216A  pdb=" N   THR C 150 " --> pdb=" O   GLY C 146 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 174 through 178
      removed outlier: 3.534A  pdb=" N   SER C 178 " --> pdb=" O   PRO C 175 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 182 through 195
    Processing helix  chain 'C' and resid 206 through 217
    Processing helix  chain 'C' and resid 223 through 244
      removed outlier: 4.824A  pdb=" N   SER C 241 " --> pdb=" O   SER C 237 " (cutoff:3.500A)
      removed outlier: 5.246A  pdb=" N   LEU C 242 " --> pdb=" O   ILE C 238 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 251 through 260
      removed outlier: 3.694A  pdb=" N   PHE C 255 " --> pdb=" O   ASP C 251 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLN C 256 " --> pdb=" O   LEU C 252 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 277 through 281
    Processing helix  chain 'C' and resid 287 through 295
    Processing helix  chain 'C' and resid 296 through 301
      removed outlier: 6.723A  pdb=" N   ALA C 299 " --> pdb=" O   PHE C 296 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 306 through 310
    Processing helix  chain 'C' and resid 324 through 339
    Processing helix  chain 'C' and resid 384 through 400
      removed outlier: 3.882A  pdb=" N   TRP C 388 " --> pdb=" O   ILE C 384 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LYS C 394 " --> pdb=" O   ARG C 390 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 404 through 410
      removed outlier: 4.146A  pdb=" N   TYR C 408 " --> pdb=" O   PHE C 404 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 414 through 436
      removed outlier: 4.185A  pdb=" N   PHE C 418 " --> pdb=" O   GLU C 414 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   SER C 419 " --> pdb=" O   GLU C 415 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 10 through 29
    Processing helix  chain 'G' and resid 46 through 51
      removed outlier: 3.930A  pdb=" N   PHE G  49 " --> pdb=" O   ASP G  46 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 72 through 81
    Processing helix  chain 'G' and resid 88 through 90
      No H-bonds generated for 'chain 'G' and resid 88 through 90'
    Processing helix  chain 'G' and resid 102 through 108
    Processing helix  chain 'G' and resid 109 through 127
      removed outlier: 3.898A  pdb=" N   GLU G 113 " --> pdb=" O   THR G 109 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ILE G 114 " --> pdb=" O   ILE G 110 " (cutoff:3.500A)
      removed outlier: 5.066A  pdb=" N   ASP G 116 " --> pdb=" O   LYS G 112 " (cutoff:3.500A)
      removed outlier: 5.534A  pdb=" N   LEU G 117 " --> pdb=" O   GLU G 113 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 143 through 161
      removed outlier: 4.216A  pdb=" N   THR G 150 " --> pdb=" O   GLY G 146 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 174 through 178
      removed outlier: 3.534A  pdb=" N   SER G 178 " --> pdb=" O   PRO G 175 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 182 through 195
    Processing helix  chain 'G' and resid 206 through 217
    Processing helix  chain 'G' and resid 223 through 244
      removed outlier: 4.824A  pdb=" N   SER G 241 " --> pdb=" O   SER G 237 " (cutoff:3.500A)
      removed outlier: 5.246A  pdb=" N   LEU G 242 " --> pdb=" O   ILE G 238 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 251 through 260
      removed outlier: 3.695A  pdb=" N   PHE G 255 " --> pdb=" O   ASP G 251 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLN G 256 " --> pdb=" O   LEU G 252 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 277 through 281
    Processing helix  chain 'G' and resid 287 through 295
    Processing helix  chain 'G' and resid 296 through 301
      removed outlier: 6.724A  pdb=" N   ALA G 299 " --> pdb=" O   PHE G 296 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 306 through 310
    Processing helix  chain 'G' and resid 324 through 339
    Processing helix  chain 'G' and resid 384 through 400
      removed outlier: 3.882A  pdb=" N   TRP G 388 " --> pdb=" O   ILE G 384 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LYS G 394 " --> pdb=" O   ARG G 390 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 404 through 410
      removed outlier: 4.147A  pdb=" N   TYR G 408 " --> pdb=" O   PHE G 404 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 414 through 436
      removed outlier: 4.186A  pdb=" N   PHE G 418 " --> pdb=" O   GLU G 414 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   SER G 419 " --> pdb=" O   GLU G 415 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 10 through 29
    Processing helix  chain 'E' and resid 46 through 51
      removed outlier: 3.930A  pdb=" N   PHE E  49 " --> pdb=" O   ASP E  46 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 72 through 81
    Processing helix  chain 'E' and resid 88 through 90
      No H-bonds generated for 'chain 'E' and resid 88 through 90'
    Processing helix  chain 'E' and resid 102 through 108
    Processing helix  chain 'E' and resid 109 through 127
      removed outlier: 3.898A  pdb=" N   GLU E 113 " --> pdb=" O   THR E 109 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ILE E 114 " --> pdb=" O   ILE E 110 " (cutoff:3.500A)
      removed outlier: 5.066A  pdb=" N   ASP E 116 " --> pdb=" O   LYS E 112 " (cutoff:3.500A)
      removed outlier: 5.535A  pdb=" N   LEU E 117 " --> pdb=" O   GLU E 113 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 143 through 161
      removed outlier: 4.217A  pdb=" N   THR E 150 " --> pdb=" O   GLY E 146 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 174 through 178
      removed outlier: 3.534A  pdb=" N   SER E 178 " --> pdb=" O   PRO E 175 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 182 through 195
    Processing helix  chain 'E' and resid 206 through 217
    Processing helix  chain 'E' and resid 223 through 244
      removed outlier: 4.824A  pdb=" N   SER E 241 " --> pdb=" O   SER E 237 " (cutoff:3.500A)
      removed outlier: 5.246A  pdb=" N   LEU E 242 " --> pdb=" O   ILE E 238 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 251 through 260
      removed outlier: 3.695A  pdb=" N   PHE E 255 " --> pdb=" O   ASP E 251 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLN E 256 " --> pdb=" O   LEU E 252 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 277 through 281
    Processing helix  chain 'E' and resid 287 through 295
    Processing helix  chain 'E' and resid 296 through 301
      removed outlier: 6.723A  pdb=" N   ALA E 299 " --> pdb=" O   PHE E 296 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 306 through 310
    Processing helix  chain 'E' and resid 324 through 339
    Processing helix  chain 'E' and resid 384 through 400
      removed outlier: 3.882A  pdb=" N   TRP E 388 " --> pdb=" O   ILE E 384 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LYS E 394 " --> pdb=" O   ARG E 390 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 404 through 410
      removed outlier: 4.147A  pdb=" N   TYR E 408 " --> pdb=" O   PHE E 404 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 414 through 436
      removed outlier: 4.187A  pdb=" N   PHE E 418 " --> pdb=" O   GLU E 414 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   SER E 419 " --> pdb=" O   GLU E 415 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 90 through 92
      removed outlier: 7.998A  pdb=" N   VAL B  91 " --> pdb=" O   ALA B  63 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   LEU B  65 " --> pdb=" O   VAL B  91 " (cutoff:3.500A)
      removed outlier: 8.380A  pdb=" N   ILE B  64 " --> pdb=" O   ILE B   4 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   HIS B   6 " --> pdb=" O   ILE B  64 " (cutoff:3.500A)
      removed outlier: 7.758A  pdb=" N   VAL B  66 " --> pdb=" O   HIS B   6 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   GLN B   8 " --> pdb=" O   VAL B  66 " (cutoff:3.500A)
      removed outlier: 6.036A  pdb=" N   GLU B   3 " --> pdb=" O   LEU B 130 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   GLY B 132 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   SER B 138 " --> pdb=" O   ALA B   9 " (cutoff:3.500A)
      removed outlier: 7.172A  pdb=" N   GLN B 131 " --> pdb=" O   ILE B 163 " (cutoff:3.500A)
      removed outlier: 8.209A  pdb=" N   ASN B 165 " --> pdb=" O   GLN B 131 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   PHE B 133 " --> pdb=" O   ASN B 165 " (cutoff:3.500A)
      removed outlier: 7.929A  pdb=" N   PHE B 167 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   LEU B 135 " --> pdb=" O   PHE B 167 " (cutoff:3.500A)
      removed outlier: 7.427A  pdb=" N   VAL B 169 " --> pdb=" O   LEU B 135 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   HIS B 137 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   MET B 164 " --> pdb=" O   GLU B 198 " (cutoff:3.500A)
      removed outlier: 8.131A  pdb=" N   TYR B 200 " --> pdb=" O   MET B 164 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   THR B 166 " --> pdb=" O   TYR B 200 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   ILE B 202 " --> pdb=" O   THR B 166 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   SER B 168 " --> pdb=" O   ILE B 202 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   THR B 199 " --> pdb=" O   PHE B 266 " (cutoff:3.500A)
      removed outlier: 7.485A  pdb=" N   CYS B 201 " --> pdb=" O   PRO B 268 " (cutoff:3.500A)
      removed outlier: 10.197A  pdb=" N   PHE B 270 " --> pdb=" O   CYS B 201 " (cutoff:3.500A)
      removed outlier: 13.286A  pdb=" N   ASP B 203 " --> pdb=" O   PHE B 270 " (cutoff:3.500A)
      removed outlier: 7.293A  pdb=" N   PHE B 265 " --> pdb=" O   SER B 371 " (cutoff:3.500A)
      removed outlier: 4.791A  pdb=" N   SER B 371 " --> pdb=" O   PHE B 265 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 54
    Processing sheet with id=AA3, first strand: chain 'D' and resid 90 through 92
      removed outlier: 7.999A  pdb=" N   VAL D  91 " --> pdb=" O   ALA D  63 " (cutoff:3.500A)
      removed outlier: 6.103A  pdb=" N   LEU D  65 " --> pdb=" O   VAL D  91 " (cutoff:3.500A)
      removed outlier: 8.380A  pdb=" N   ILE D  64 " --> pdb=" O   ILE D   4 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   HIS D   6 " --> pdb=" O   ILE D  64 " (cutoff:3.500A)
      removed outlier: 7.758A  pdb=" N   VAL D  66 " --> pdb=" O   HIS D   6 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   GLN D   8 " --> pdb=" O   VAL D  66 " (cutoff:3.500A)
      removed outlier: 6.036A  pdb=" N   GLU D   3 " --> pdb=" O   LEU D 130 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   GLY D 132 " --> pdb=" O   GLU D   3 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   SER D 138 " --> pdb=" O   ALA D   9 " (cutoff:3.500A)
      removed outlier: 7.172A  pdb=" N   GLN D 131 " --> pdb=" O   ILE D 163 " (cutoff:3.500A)
      removed outlier: 8.209A  pdb=" N   ASN D 165 " --> pdb=" O   GLN D 131 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   PHE D 133 " --> pdb=" O   ASN D 165 " (cutoff:3.500A)
      removed outlier: 7.929A  pdb=" N   PHE D 167 " --> pdb=" O   PHE D 133 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   LEU D 135 " --> pdb=" O   PHE D 167 " (cutoff:3.500A)
      removed outlier: 7.426A  pdb=" N   VAL D 169 " --> pdb=" O   LEU D 135 " (cutoff:3.500A)
      removed outlier: 7.168A  pdb=" N   HIS D 137 " --> pdb=" O   VAL D 169 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   MET D 164 " --> pdb=" O   GLU D 198 " (cutoff:3.500A)
      removed outlier: 8.130A  pdb=" N   TYR D 200 " --> pdb=" O   MET D 164 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   THR D 166 " --> pdb=" O   TYR D 200 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   ILE D 202 " --> pdb=" O   THR D 166 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   SER D 168 " --> pdb=" O   ILE D 202 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   THR D 199 " --> pdb=" O   PHE D 266 " (cutoff:3.500A)
      removed outlier: 7.485A  pdb=" N   CYS D 201 " --> pdb=" O   PRO D 268 " (cutoff:3.500A)
      removed outlier: 10.198A  pdb=" N   PHE D 270 " --> pdb=" O   CYS D 201 " (cutoff:3.500A)
      removed outlier: 13.286A  pdb=" N   ASP D 203 " --> pdb=" O   PHE D 270 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   PHE D 265 " --> pdb=" O   SER D 371 " (cutoff:3.500A)
      removed outlier: 4.791A  pdb=" N   SER D 371 " --> pdb=" O   PHE D 265 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 51 through 54
    Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 94
      removed outlier: 8.117A  pdb=" N   ILE A  93 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   PHE A  67 " --> pdb=" O   ILE A  93 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   VAL A  66 " --> pdb=" O   CYS A   4 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   SER A   6 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   VAL A  68 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 6.185A  pdb=" N   HIS A   8 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   SER A 140 " --> pdb=" O   VAL A   9 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   LYS A 166 " --> pdb=" O   CYS A 200 " (cutoff:3.500A)
      removed outlier: 8.144A  pdb=" N   PHE A 202 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   GLU A 168 " --> pdb=" O   PHE A 202 " (cutoff:3.500A)
      removed outlier: 7.618A  pdb=" N   VAL A 204 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   SER A 170 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 53 through 55
    Processing sheet with id=AA7, first strand: chain 'A' and resid 269 through 273
      removed outlier: 6.725A  pdb=" N   ALA A 374 " --> pdb=" O   TYR A 319 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   TYR A 319 " --> pdb=" O   ALA A 374 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   CYS A 376 " --> pdb=" O   LEU A 317 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   LEU A 317 " --> pdb=" O   CYS A 376 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   LEU A 378 " --> pdb=" O   CYS A 315 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   CYS A 315 " --> pdb=" O   LEU A 378 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   ASN A 380 " --> pdb=" O   MET A 313 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 92 through 94
      removed outlier: 8.116A  pdb=" N   ILE C  93 " --> pdb=" O   ALA C  65 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   PHE C  67 " --> pdb=" O   ILE C  93 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   VAL C  66 " --> pdb=" O   CYS C   4 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   SER C   6 " --> pdb=" O   VAL C  66 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   VAL C  68 " --> pdb=" O   SER C   6 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   HIS C   8 " --> pdb=" O   VAL C  68 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   SER C 140 " --> pdb=" O   VAL C   9 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   LYS C 166 " --> pdb=" O   CYS C 200 " (cutoff:3.500A)
      removed outlier: 8.144A  pdb=" N   PHE C 202 " --> pdb=" O   LYS C 166 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   GLU C 168 " --> pdb=" O   PHE C 202 " (cutoff:3.500A)
      removed outlier: 7.619A  pdb=" N   VAL C 204 " --> pdb=" O   GLU C 168 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   SER C 170 " --> pdb=" O   VAL C 204 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 55
    Processing sheet with id=AB1, first strand: chain 'C' and resid 269 through 273
      removed outlier: 6.725A  pdb=" N   ALA C 374 " --> pdb=" O   TYR C 319 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   TYR C 319 " --> pdb=" O   ALA C 374 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   CYS C 376 " --> pdb=" O   LEU C 317 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   LEU C 317 " --> pdb=" O   CYS C 376 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   LEU C 378 " --> pdb=" O   CYS C 315 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   CYS C 315 " --> pdb=" O   LEU C 378 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   ASN C 380 " --> pdb=" O   MET C 313 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'G' and resid 92 through 94
      removed outlier: 8.117A  pdb=" N   ILE G  93 " --> pdb=" O   ALA G  65 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   PHE G  67 " --> pdb=" O   ILE G  93 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   VAL G  66 " --> pdb=" O   CYS G   4 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   SER G   6 " --> pdb=" O   VAL G  66 " (cutoff:3.500A)
      removed outlier: 7.871A  pdb=" N   VAL G  68 " --> pdb=" O   SER G   6 " (cutoff:3.500A)
      removed outlier: 6.185A  pdb=" N   HIS G   8 " --> pdb=" O   VAL G  68 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   SER G 140 " --> pdb=" O   VAL G   9 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   LYS G 166 " --> pdb=" O   CYS G 200 " (cutoff:3.500A)
      removed outlier: 8.143A  pdb=" N   PHE G 202 " --> pdb=" O   LYS G 166 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   GLU G 168 " --> pdb=" O   PHE G 202 " (cutoff:3.500A)
      removed outlier: 7.619A  pdb=" N   VAL G 204 " --> pdb=" O   GLU G 168 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   SER G 170 " --> pdb=" O   VAL G 204 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'G' and resid 53 through 55
    Processing sheet with id=AB4, first strand: chain 'G' and resid 269 through 273
      removed outlier: 6.726A  pdb=" N   ALA G 374 " --> pdb=" O   TYR G 319 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   TYR G 319 " --> pdb=" O   ALA G 374 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   CYS G 376 " --> pdb=" O   LEU G 317 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   LEU G 317 " --> pdb=" O   CYS G 376 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   LEU G 378 " --> pdb=" O   CYS G 315 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   CYS G 315 " --> pdb=" O   LEU G 378 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   ASN G 380 " --> pdb=" O   MET G 313 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 92 through 94
      removed outlier: 8.117A  pdb=" N   ILE E  93 " --> pdb=" O   ALA E  65 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   PHE E  67 " --> pdb=" O   ILE E  93 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   VAL E  66 " --> pdb=" O   CYS E   4 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   SER E   6 " --> pdb=" O   VAL E  66 " (cutoff:3.500A)
      removed outlier: 7.871A  pdb=" N   VAL E  68 " --> pdb=" O   SER E   6 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   HIS E   8 " --> pdb=" O   VAL E  68 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   SER E 140 " --> pdb=" O   VAL E   9 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   LYS E 166 " --> pdb=" O   CYS E 200 " (cutoff:3.500A)
      removed outlier: 8.143A  pdb=" N   PHE E 202 " --> pdb=" O   LYS E 166 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   GLU E 168 " --> pdb=" O   PHE E 202 " (cutoff:3.500A)
      removed outlier: 7.618A  pdb=" N   VAL E 204 " --> pdb=" O   GLU E 168 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   SER E 170 " --> pdb=" O   VAL E 204 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 53 through 55
    Processing sheet with id=AB7, first strand: chain 'E' and resid 269 through 273
      removed outlier: 6.725A  pdb=" N   ALA E 374 " --> pdb=" O   TYR E 319 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   TYR E 319 " --> pdb=" O   ALA E 374 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   CYS E 376 " --> pdb=" O   LEU E 317 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   LEU E 317 " --> pdb=" O   CYS E 376 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   LEU E 378 " --> pdb=" O   CYS E 315 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   CYS E 315 " --> pdb=" O   LEU E 378 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   ASN E 380 " --> pdb=" O   MET E 313 " (cutoff:3.500A)

    1125 hydrogen bonds defined for protein.
    3213 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: 10.38

  Time building geometry restraints manager: 4.90 seconds

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

  Histogram of bond lengths:
        0.96 -     1.13: 19650
        1.13 -     1.31: 4098
        1.31 -     1.48: 8773
        1.48 -     1.66: 9257
        1.66 -     1.84: 228
  Bond restraints: 42006
  Sorted by residual:
  bond pdb=" C   ALA J 107 "
       pdb=" N   ASN J 108 "
    ideal  model  delta    sigma   weight residual
    1.333  1.198  0.135 1.42e-02 4.96e+03 9.05e+01
  bond pdb=" C   LEU J  40 "
       pdb=" N   ILE J  41 "
    ideal  model  delta    sigma   weight residual
    1.331  1.236  0.096 1.11e-02 8.12e+03 7.41e+01
  bond pdb=" C   PHE J  54 "
       pdb=" N   VAL J  55 "
    ideal  model  delta    sigma   weight residual
    1.335  1.234  0.100 1.26e-02 6.30e+03 6.36e+01
  bond pdb=" C   ASP I  22 "
       pdb=" N   ASP I  23 "
    ideal  model  delta    sigma   weight residual
    1.332  1.224  0.108 1.40e-02 5.10e+03 5.98e+01
  bond pdb=" C   HIS J  31 "
       pdb=" N   PRO J  32 "
    ideal  model  delta    sigma   weight residual
    1.332  1.229  0.103 1.34e-02 5.57e+03 5.91e+01
  ... (remaining 42001 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.13: 67230
        3.13 -     6.25: 6429
        6.25 -     9.38: 1235
        9.38 -    12.50: 66
       12.50 -    15.63: 26
  Bond angle restraints: 74986
  Sorted by residual:
  angle pdb=" O   MET J 116 "
        pdb=" C   MET J 116 "
        pdb=" N   PRO J 117 "
      ideal   model   delta    sigma   weight residual
     121.34  129.60   -8.26 8.90e-01 1.26e+00 8.62e+01
  angle pdb=" C   LEU J 113 "
        pdb=" N   VAL J 114 "
        pdb=" CA  VAL J 114 "
      ideal   model   delta    sigma   weight residual
     122.16  112.19    9.97 1.26e+00 6.30e-01 6.27e+01
  angle pdb=" CA  MET J 116 "
        pdb=" C   MET J 116 "
        pdb=" N   PRO J 117 "
      ideal   model   delta    sigma   weight residual
     117.59  109.73    7.86 1.03e+00 9.43e-01 5.82e+01
  angle pdb=" CA  LEU J 113 "
        pdb=" C   LEU J 113 "
        pdb=" N   VAL J 114 "
      ideal   model   delta    sigma   weight residual
     118.14  108.77    9.37 1.31e+00 5.83e-01 5.11e+01
  angle pdb=" OE1 GLN D 131 "
        pdb=" CD  GLN D 131 "
        pdb=" NE2 GLN D 131 "
      ideal   model   delta    sigma   weight residual
     122.60  115.73    6.87 1.00e+00 1.00e+00 4.73e+01
  ... (remaining 74981 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.20: 18402
       17.20 -    34.40: 871
       34.40 -    51.60: 435
       51.60 -    68.80: 421
       68.80 -    86.00: 13
  Dihedral angle restraints: 20142
    sinusoidal: 10743
      harmonic: 9399
  Sorted by residual:
  dihedral pdb=" CB  PHE D 317 "
           pdb=" CD1 PHE D 317 "
           pdb=" HE1 PHE D 317 "
           pdb=" CB  PHE D 317 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -0.00  -86.00     1      1.00e+01 1.00e-02 8.93e+01
  dihedral pdb=" CD2 HIS E 197 "
           pdb=" CG  HIS E 197 "
           pdb=" ND1 HIS E 197 "
           pdb=" HD1 HIS E 197 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.53  -23.47     0      5.00e+00 4.00e-02 2.20e+01
  dihedral pdb=" CD2 HIS A 197 "
           pdb=" CG  HIS A 197 "
           pdb=" ND1 HIS A 197 "
           pdb=" HD1 HIS A 197 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.57  -23.43     0      5.00e+00 4.00e-02 2.20e+01
  ... (remaining 20139 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 2135
       0.072 -    0.143: 938
       0.143 -    0.214: 179
       0.214 -    0.286: 51
       0.286 -    0.357: 2
  Chirality restraints: 3305
  Sorted by residual:
  chirality pdb=" CA  THR B 107 "
            pdb=" N   THR B 107 "
            pdb=" C   THR B 107 "
            pdb=" CB  THR B 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.17    0.36 2.00e-01 2.50e+01 3.19e+00
  chirality pdb=" CA  THR D 107 "
            pdb=" N   THR D 107 "
            pdb=" C   THR D 107 "
            pdb=" CB  THR D 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.17    0.35 2.00e-01 2.50e+01 3.11e+00
  chirality pdb=" CB  THR D  33 "
            pdb=" CA  THR D  33 "
            pdb=" OG1 THR D  33 "
            pdb=" CG2 THR D  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.27    0.29 2.00e-01 2.50e+01 2.03e+00
  ... (remaining 3302 not shown)

  Planarity restraints: 6432
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D   2 "    0.623 9.50e-02 1.11e+02   2.79e-01 8.21e+02
        pdb=" NE  ARG D   2 "    0.239 2.00e-02 2.50e+03
        pdb=" CZ  ARG D   2 "    0.018 2.00e-02 2.50e+03
        pdb=" NH1 ARG D   2 "   -0.192 2.00e-02 2.50e+03
        pdb=" NH2 ARG D   2 "    0.057 2.00e-02 2.50e+03
        pdb="HH11 ARG D   2 "   -0.163 2.00e-02 2.50e+03
        pdb="HH12 ARG D   2 "    0.128 2.00e-02 2.50e+03
        pdb="HH21 ARG D   2 "    0.229 2.00e-02 2.50e+03
        pdb="HH22 ARG D   2 "   -0.344 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B   2 "   -0.622 9.50e-02 1.11e+02   2.78e-01 8.19e+02
        pdb=" NE  ARG B   2 "   -0.239 2.00e-02 2.50e+03
        pdb=" CZ  ARG B   2 "   -0.017 2.00e-02 2.50e+03
        pdb=" NH1 ARG B   2 "    0.192 2.00e-02 2.50e+03
        pdb=" NH2 ARG B   2 "   -0.057 2.00e-02 2.50e+03
        pdb="HH11 ARG B   2 "    0.162 2.00e-02 2.50e+03
        pdb="HH12 ARG B   2 "   -0.128 2.00e-02 2.50e+03
        pdb="HH21 ARG B   2 "   -0.229 2.00e-02 2.50e+03
        pdb="HH22 ARG B   2 "    0.343 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 165 "    0.188 2.00e-02 2.50e+03   1.97e-01 5.80e+02
        pdb=" CG  ASN B 165 "   -0.067 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 165 "   -0.096 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 165 "   -0.232 2.00e-02 2.50e+03
        pdb="HD21 ASN B 165 "   -0.128 2.00e-02 2.50e+03
        pdb="HD22 ASN B 165 "    0.336 2.00e-02 2.50e+03
  ... (remaining 6429 not shown)

  Histogram of nonbonded interaction distances:
        0.17 -     1.05: 159
        1.05 -     1.94: 1683
        1.94 -     2.83: 85593
        2.83 -     3.71: 188544
        3.71 -     4.60: 318309
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 594288
  Sorted by model distance:
  nonbonded pdb=" CG  LYS D 324 "
            pdb=" HA  ARG G 221 "
     model   vdw
     0.168 2.920
  nonbonded pdb=" CG  LYS B 324 "
            pdb=" HA  ARG E 221 "
     model   vdw
     0.169 2.920
  nonbonded pdb=" HE2 LYS B 324 "
            pdb=" O   GLU E 220 "
     model   vdw
     0.341 2.620
  nonbonded pdb=" HE2 LYS D 324 "
            pdb=" O   GLU G 220 "
     model   vdw
     0.342 2.620
  nonbonded pdb=" HB2 ASN B 247 "
            pdb=" OE2 GLU E  71 "
     model   vdw
     0.435 2.620
  ... (remaining 594283 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

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:             1.080
  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:             0.310
  Extract box with map and model:          0.570
  Check model and map are aligned:         0.120
  Set scattering table:                    0.100
  Process input model:                     43.650
  Find NCS groups from input model:        0.490
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4804
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      :  0.016   0.381  22307  Z= 1.202
  Angle     :  1.618  10.387  30216  Z= 1.104
  Chirality :  0.080   0.357   3305
  Planarity :  0.014   0.157   3960
  Dihedral  : 11.461  76.406   8159
  Min Nonbonded Distance : 0.818

Molprobity Statistics.
  All-atom Clashscore : 16.28
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.76 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  0.72 %
    Favored  : 98.17 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.38 (0.14), residues: 2752
  helix: -0.06 (0.13), residues: 1274
  sheet:  0.06 (0.25), residues: 388
  loop : -0.41 (0.17), residues: 1090

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.002   ARG D 213 
 TYR   0.094   0.013   TYR D 106 
 PHE   0.058   0.009   PHE G 141 
 TRP   0.064   0.020   TRP B 344 
 HIS   0.024   0.006   HIS G 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.01296 (22292)
  covalent geometry    : angle       1.61782 (30216)
  hydrogen bonds       : bond        0.17969 ( 1125)
  hydrogen bonds       : angle       6.99722 ( 3213)
  Misc. bond           : bond        0.35297 (   15)

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

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

  5504 Ramachandran restraints generated.
    2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5504 Ramachandran restraints generated.
    2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  754 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 728
  time to evaluate  : 1.197 
Fit side-chains
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REVERT: J   54 PHE cc_start: 0.8348 (t80) cc_final: 0.8030 (t80)
REVERT: J   70 PHE cc_start: 0.7841 (t80) cc_final: 0.7454 (t80)
REVERT: B  232 THR cc_start: 0.8247 (m) cc_final: 0.7957 (m)
REVERT: B  266 PHE cc_start: 0.7706 (m-10) cc_final: 0.7466 (m-10)
REVERT: D   73 MET cc_start: 0.8509 (mtp) cc_final: 0.8283 (mmm)
REVERT: D  237 THR cc_start: 0.8266 (p) cc_final: 0.7892 (p)
REVERT: D  266 PHE cc_start: 0.7651 (m-10) cc_final: 0.7028 (m-80)
REVERT: A   20 CYS cc_start: 0.8185 (m) cc_final: 0.7042 (m)
REVERT: A   73 THR cc_start: 0.7536 (m) cc_final: 0.7233 (p)
REVERT: A  101 ASN cc_start: 0.5257 (m-40) cc_final: 0.4974 (p0)
REVERT: A  149 PHE cc_start: 0.8215 (t80) cc_final: 0.7801 (t80)
REVERT: C  149 PHE cc_start: 0.8100 (t80) cc_final: 0.7541 (t80)
REVERT: C  167 LEU cc_start: 0.8766 (mp) cc_final: 0.8513 (tp)
REVERT: C  328 VAL cc_start: 0.9157 (t) cc_final: 0.8723 (t)
REVERT: G  167 LEU cc_start: 0.8902 (mp) cc_final: 0.8525 (mp)
REVERT: E  150 THR cc_start: 0.8630 (m) cc_final: 0.8066 (p)
REVERT: E  238 ILE cc_start: 0.7697 (mt) cc_final: 0.7306 (mt)
REVERT: E  391 LEU cc_start: 0.9048 (tp) cc_final: 0.8833 (tp)
  outliers start: 26
  outliers final: 8
  residues processed: 747
  average time/residue: 0.4439
  time to fit residues: 472.0541
Evaluate side-chains
  516 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 508
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 197 optimal weight:    6.9990
   chunk 215 optimal weight:    6.9990
   chunk 20 optimal weight:    7.9990
   chunk 132 optimal weight:    6.9990
   chunk 261 optimal weight:    6.9990
   chunk 248 optimal weight:    7.9990
   chunk 207 optimal weight:    9.9990
   chunk 155 optimal weight:    5.9990
   chunk 244 optimal weight:    7.9990
   chunk 183 optimal weight:    7.9990
   chunk 111 optimal weight:    5.9990
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
I  25 GLN
J  16 GLN
J  21 HIS
J  56 HIS
J  59 HIS
** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  99 ASN
** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 334 GLN
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  50 ASN
C 226 ASN
** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  50 ASN
E 393 HIS
** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.100503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.073981 restraints weight = 314022.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.078805 restraints weight = 204309.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.082740 restraints weight = 141655.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.085824 restraints weight = 102430.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.088277 restraints weight = 76841.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.4131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5884
moved from start:          0.3956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.174  22307  Z= 0.296
  Angle     :  0.789  28.139  30216  Z= 0.437
  Chirality :  0.046   0.392   3305
  Planarity :  0.007   0.110   3960
  Dihedral  :  5.175  27.358   3010
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 14.22
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  2.36 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  2.04 %
    Favored  : 97.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.16), residues: 2752
  helix:  1.24 (0.14), residues: 1276
  sheet: -0.30 (0.24), residues: 404
  loop :  0.08 (0.19), residues: 1072

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.001   ARG E 221 
 TYR   0.031   0.002   TYR E 210 
 PHE   0.016   0.002   PHE D 260 
 TRP   0.020   0.002   TRP B 397 
 HIS   0.014   0.002   HIS B 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00629 (22292)
  covalent geometry    : angle       0.78911 (30216)
  hydrogen bonds       : bond        0.06823 ( 1125)
  hydrogen bonds       : angle       5.21405 ( 3213)
  Misc. bond           : bond        0.02010 (   15)

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

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

  5504 Ramachandran restraints generated.
    2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5504 Ramachandran restraints generated.
    2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  552 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 544
  time to evaluate  : 1.248 
Fit side-chains
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REVERT: J   46 PHE cc_start: 0.8748 (m-80) cc_final: 0.7947 (m-80)
REVERT: J   54 PHE cc_start: 0.9199 (t80) cc_final: 0.8927 (t80)
REVERT: J   58 MET cc_start: 0.9660 (tpt) cc_final: 0.9248 (tpp)
REVERT: J   70 PHE cc_start: 0.9110 (t80) cc_final: 0.8115 (t80)
REVERT: J   94 TYR cc_start: 0.9172 (t80) cc_final: 0.8397 (t80)
REVERT: J  142 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8345 (mm-30)
REVERT: B   19 LYS cc_start: 0.9387 (mmtt) cc_final: 0.8918 (tttt)
REVERT: B  137 HIS cc_start: 0.8901 (p-80) cc_final: 0.8666 (p-80)
REVERT: B  266 PHE cc_start: 0.9064 (m-10) cc_final: 0.8750 (m-80)
REVERT: B  292 GLN cc_start: 0.9242 (mt0) cc_final: 0.8987 (tt0)
REVERT: B  330 MET cc_start: 0.8835 (mmm) cc_final: 0.8429 (mmm)
REVERT: B  337 ASN cc_start: 0.9131 (m110) cc_final: 0.8918 (m-40)
REVERT: B  341 PHE cc_start: 0.9096 (m-80) cc_final: 0.8772 (m-80)
REVERT: D  266 PHE cc_start: 0.9427 (m-10) cc_final: 0.8956 (m-80)
REVERT: D  317 PHE cc_start: 0.9495 (m-80) cc_final: 0.9110 (m-10)
REVERT: D  321 MET cc_start: 0.3761 (ptp) cc_final: 0.3549 (pmm)
REVERT: D  408 PHE cc_start: 0.9654 (m-10) cc_final: 0.9398 (m-80)
REVERT: D  412 GLU cc_start: 0.9384 (tm-30) cc_final: 0.8757 (tp30)
REVERT: A   20 CYS cc_start: 0.9311 (m) cc_final: 0.8197 (p)
REVERT: A  101 ASN cc_start: 0.6484 (m-40) cc_final: 0.5725 (p0)
REVERT: A  202 PHE cc_start: 0.9095 (m-80) cc_final: 0.8299 (m-80)
REVERT: A  234 ILE cc_start: 0.8455 (mp) cc_final: 0.8197 (mt)
REVERT: C  168 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8430 (mp0)
REVERT: C  202 PHE cc_start: 0.9362 (m-80) cc_final: 0.8995 (m-80)
REVERT: C  319 TYR cc_start: 0.9353 (m-10) cc_final: 0.9035 (m-80)
REVERT: G   55 GLU cc_start: 0.8711 (pm20) cc_final: 0.8503 (mp0)
REVERT: G  157 LEU cc_start: 0.9129 (mt) cc_final: 0.8838 (mt)
REVERT: G  169 PHE cc_start: 0.9282 (m-80) cc_final: 0.8880 (m-80)
REVERT: G  199 ASP cc_start: 0.9570 (m-30) cc_final: 0.8893 (t0)
REVERT: G  242 LEU cc_start: 0.9579 (mt) cc_final: 0.9289 (mm)
REVERT: G  255 PHE cc_start: 0.9330 (m-80) cc_final: 0.8453 (m-80)
REVERT: G  292 THR cc_start: 0.8770 (p) cc_final: 0.8552 (p)
REVERT: G  313 MET cc_start: 0.5481 (mmp) cc_final: 0.4299 (mmp)
REVERT: E  138 PHE cc_start: 0.8645 (m-80) cc_final: 0.8269 (m-80)
  outliers start: 8
  outliers final: 6
  residues processed: 552
  average time/residue: 0.4590
  time to fit residues: 363.1940
Evaluate side-chains
  448 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 442
  time to evaluate  : 1.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 176 optimal weight:    8.9990
   chunk 251 optimal weight:    6.9990
   chunk 95 optimal weight:   20.0000
   chunk 223 optimal weight:   20.0000
   chunk 267 optimal weight:    9.9990
   chunk 14 optimal weight:   20.0000
   chunk 185 optimal weight:   20.0000
   chunk 162 optimal weight:   10.0000
   chunk 253 optimal weight:   20.0000
   chunk 102 optimal weight:    9.9990
   chunk 134 optimal weight:    4.9990
   overall best weight:    8.1990

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

Flipped N/Q/H residues before XYZ refinement:
** J  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  25 GLN
** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 347 ASN
B 414 ASN
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 414 ASN
D 423 GLN
** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.094651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.069313 restraints weight = 321082.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.073849 restraints weight = 207308.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.077484 restraints weight = 143690.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.080395 restraints weight = 104217.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.082720 restraints weight = 78289.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.4053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6092
moved from start:          0.5324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.216  22307  Z= 0.278
  Angle     :  0.774  28.895  30216  Z= 0.424
  Chirality :  0.043   0.234   3305
  Planarity :  0.008   0.211   3960
  Dihedral  :  5.216  38.114   3010
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 15.20
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.38 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  1.83 %
    Favored  : 98.09 %
  Cbeta Deviations :  0.16 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.15), residues: 2752
  helix:  0.99 (0.13), residues: 1270
  sheet: -0.25 (0.24), residues: 388
  loop : -0.27 (0.19), residues: 1094

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG G 221 
 TYR   0.028   0.002   TYR G 224 
 PHE   0.027   0.002   PHE C 138 
 TRP   0.023   0.002   TRP C 346 
 HIS   0.022   0.002   HIS G 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00566 (22292)
  covalent geometry    : angle       0.77413 (30216)
  hydrogen bonds       : bond        0.06178 ( 1125)
  hydrogen bonds       : angle       5.08216 ( 3213)
  Misc. bond           : bond        0.02208 (   15)

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

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

  5504 Ramachandran restraints generated.
    2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5504 Ramachandran restraints generated.
    2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  487 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 485
  time to evaluate  : 1.088 
Fit side-chains
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REVERT: J   45 MET cc_start: 0.2537 (ptp) cc_final: 0.2314 (tpt)
REVERT: J   46 PHE cc_start: 0.8711 (m-80) cc_final: 0.7679 (m-80)
REVERT: J   54 PHE cc_start: 0.9206 (t80) cc_final: 0.8885 (t80)
REVERT: J   58 MET cc_start: 0.9654 (tpt) cc_final: 0.9452 (tpp)
REVERT: J   65 LEU cc_start: 0.8416 (tp) cc_final: 0.8069 (tt)
REVERT: J   70 PHE cc_start: 0.9141 (t80) cc_final: 0.8019 (t80)
REVERT: J   94 TYR cc_start: 0.9277 (t80) cc_final: 0.8651 (t80)
REVERT: J  116 MET cc_start: 0.9237 (tmm) cc_final: 0.9018 (tmm)
REVERT: J  137 LEU cc_start: 0.9680 (mt) cc_final: 0.9321 (mt)
REVERT: J  142 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8337 (mm-30)
REVERT: B  318 ARG cc_start: 0.8748 (mtp180) cc_final: 0.8334 (mmm160)
REVERT: D   66 VAL cc_start: 0.8895 (t) cc_final: 0.8541 (m)
REVERT: D  317 PHE cc_start: 0.9617 (m-80) cc_final: 0.9108 (m-10)
REVERT: D  330 MET cc_start: 0.9013 (mmm) cc_final: 0.8245 (mmm)
REVERT: D  408 PHE cc_start: 0.9732 (m-10) cc_final: 0.9498 (m-80)
REVERT: A  101 ASN cc_start: 0.6506 (m-40) cc_final: 0.5126 (t0)
REVERT: A  169 PHE cc_start: 0.8797 (m-80) cc_final: 0.8127 (m-80)
REVERT: A  202 PHE cc_start: 0.8812 (m-80) cc_final: 0.8369 (m-80)
REVERT: A  255 PHE cc_start: 0.9297 (m-80) cc_final: 0.8929 (m-80)
REVERT: A  417 GLU cc_start: 0.9377 (mt-10) cc_final: 0.9018 (tp30)
REVERT: A  425 MET cc_start: 0.9217 (mmp) cc_final: 0.8796 (mmp)
REVERT: C  168 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8451 (mp0)
REVERT: C  169 PHE cc_start: 0.9063 (m-10) cc_final: 0.8627 (m-80)
REVERT: C  253 THR cc_start: 0.9178 (m) cc_final: 0.8926 (p)
REVERT: C  255 PHE cc_start: 0.8881 (m-80) cc_final: 0.8309 (m-80)
REVERT: C  292 THR cc_start: 0.9356 (p) cc_final: 0.9026 (p)
REVERT: C  313 MET cc_start: 0.3439 (mmp) cc_final: 0.2509 (mmp)
REVERT: C  319 TYR cc_start: 0.9397 (m-10) cc_final: 0.9092 (m-80)
REVERT: C  339 ARG cc_start: 0.4008 (mpt90) cc_final: 0.3461 (mmt180)
REVERT: G   55 GLU cc_start: 0.8808 (pm20) cc_final: 0.8594 (mp0)
REVERT: G  157 LEU cc_start: 0.9187 (mt) cc_final: 0.8858 (mt)
REVERT: G  169 PHE cc_start: 0.9362 (m-80) cc_final: 0.8742 (m-80)
REVERT: G  199 ASP cc_start: 0.9586 (m-30) cc_final: 0.9057 (t0)
REVERT: G  313 MET cc_start: 0.5921 (mmp) cc_final: 0.4622 (mmp)
REVERT: G  319 TYR cc_start: 0.9413 (m-10) cc_final: 0.9096 (m-80)
REVERT: E  255 PHE cc_start: 0.8744 (m-80) cc_final: 0.8180 (m-80)
REVERT: E  296 PHE cc_start: 0.9200 (m-80) cc_final: 0.8881 (t80)
  outliers start: 2
  outliers final: 2
  residues processed: 487
  average time/residue: 0.4043
  time to fit residues: 285.4698
Evaluate side-chains
  405 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 403
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 220 optimal weight:   20.0000
   chunk 41 optimal weight:    6.9990
   chunk 52 optimal weight:   30.0000
   chunk 203 optimal weight:    6.9990
   chunk 137 optimal weight:   30.0000
   chunk 181 optimal weight:   10.0000
   chunk 104 optimal weight:   20.0000
   chunk 14 optimal weight:    6.9990
   chunk 190 optimal weight:    2.9990
   chunk 259 optimal weight:    0.9990
   chunk 182 optimal weight:    6.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
I  25 GLN
** J  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  99 ASN
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  50 ASN
C  91 GLN
** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 406 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.094459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.069074 restraints weight = 320705.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.073580 restraints weight = 208400.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.077262 restraints weight = 144487.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.080200 restraints weight = 104733.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.082521 restraints weight = 78659.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6056
moved from start:          0.5821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.168  22307  Z= 0.223
  Angle     :  0.665  23.332  30216  Z= 0.370
  Chirality :  0.042   0.218   3305
  Planarity :  0.007   0.225   3960
  Dihedral  :  5.027  39.250   3010
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  3.09 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.48 (0.16), residues: 2752
  helix:  1.09 (0.14), residues: 1287
  sheet: -0.66 (0.24), residues: 408
  loop : -0.08 (0.19), residues: 1057

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 121 
 TYR   0.037   0.002   TYR E 210 
 PHE   0.022   0.002   PHE E 138 
 TRP   0.021   0.002   TRP D 397 
 HIS   0.016   0.002   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 (22292)
  covalent geometry    : angle       0.66472 (30216)
  hydrogen bonds       : bond        0.05633 ( 1125)
  hydrogen bonds       : angle       4.94990 ( 3213)
  Misc. bond           : bond        0.01460 (   15)

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

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

  5504 Ramachandran restraints generated.
    2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5504 Ramachandran restraints generated.
    2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  464 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 464
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
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REVERT: J   45 MET cc_start: 0.2307 (ptp) cc_final: 0.1939 (tpt)
REVERT: J   58 MET cc_start: 0.9756 (tpt) cc_final: 0.9416 (tpp)
REVERT: J   65 LEU cc_start: 0.7868 (tp) cc_final: 0.7554 (tt)
REVERT: J   70 PHE cc_start: 0.9087 (t80) cc_final: 0.7951 (t80)
REVERT: J   74 PHE cc_start: 0.6905 (m-10) cc_final: 0.6360 (m-10)
REVERT: J   94 TYR cc_start: 0.9289 (t80) cc_final: 0.8668 (t80)
REVERT: J   98 LEU cc_start: 0.9794 (mt) cc_final: 0.9434 (mt)
REVERT: J  137 LEU cc_start: 0.9585 (mt) cc_final: 0.9298 (mt)
REVERT: J  142 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8340 (mm-30)
REVERT: B  198 GLU cc_start: 0.9680 (mt-10) cc_final: 0.9468 (mt-10)
REVERT: B  340 TYR cc_start: 0.9348 (m-80) cc_final: 0.9131 (m-10)
REVERT: D  128 ASP cc_start: 0.7992 (m-30) cc_final: 0.7753 (m-30)
REVERT: D  317 PHE cc_start: 0.9591 (m-80) cc_final: 0.9155 (m-10)
REVERT: D  330 MET cc_start: 0.8962 (mmm) cc_final: 0.8236 (mmm)
REVERT: A  101 ASN cc_start: 0.5874 (m-40) cc_final: 0.4564 (t0)
REVERT: A  139 HIS cc_start: 0.8522 (p90) cc_final: 0.7703 (p90)
REVERT: A  169 PHE cc_start: 0.8918 (m-80) cc_final: 0.8421 (m-80)
REVERT: A  202 PHE cc_start: 0.8766 (m-80) cc_final: 0.8320 (m-80)
REVERT: A  238 ILE cc_start: 0.9044 (mt) cc_final: 0.8842 (mt)
REVERT: A  255 PHE cc_start: 0.9364 (m-80) cc_final: 0.8996 (m-80)
REVERT: A  296 PHE cc_start: 0.9284 (m-80) cc_final: 0.9016 (m-10)
REVERT: A  386 GLU cc_start: 0.9099 (mp0) cc_final: 0.8718 (mp0)
REVERT: A  417 GLU cc_start: 0.9424 (mt-10) cc_final: 0.9040 (tp30)
REVERT: A  425 MET cc_start: 0.9218 (mmp) cc_final: 0.8770 (mmm)
REVERT: C  169 PHE cc_start: 0.8927 (m-10) cc_final: 0.8655 (m-80)
REVERT: C  253 THR cc_start: 0.9081 (m) cc_final: 0.8771 (p)
REVERT: C  255 PHE cc_start: 0.9096 (m-80) cc_final: 0.8414 (m-80)
REVERT: C  319 TYR cc_start: 0.9319 (m-10) cc_final: 0.9115 (m-80)
REVERT: G   55 GLU cc_start: 0.8840 (pm20) cc_final: 0.8622 (mp0)
REVERT: G  157 LEU cc_start: 0.9163 (mt) cc_final: 0.8939 (mt)
REVERT: G  169 PHE cc_start: 0.9372 (m-80) cc_final: 0.8736 (m-80)
REVERT: G  199 ASP cc_start: 0.9674 (m-30) cc_final: 0.9038 (t0)
REVERT: G  255 PHE cc_start: 0.9353 (m-80) cc_final: 0.8575 (m-80)
REVERT: G  319 TYR cc_start: 0.9442 (m-10) cc_final: 0.9145 (m-80)
REVERT: E  255 PHE cc_start: 0.8830 (m-80) cc_final: 0.8293 (m-80)
REVERT: E  296 PHE cc_start: 0.9183 (m-80) cc_final: 0.8910 (t80)
REVERT: E  377 MET cc_start: 0.5244 (ttp) cc_final: 0.4830 (ttp)
REVERT: E  398 MET cc_start: 0.9260 (mtt) cc_final: 0.8686 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 464
  average time/residue: 0.3973
  time to fit residues: 268.1428
Evaluate side-chains
  402 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 402
  time to evaluate  : 1.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 57 optimal weight:    9.9990
   chunk 1 optimal weight:    1.9990
   chunk 56 optimal weight:   20.0000
   chunk 60 optimal weight:   20.0000
   chunk 48 optimal weight:    8.9990
   chunk 130 optimal weight:    4.9990
   chunk 113 optimal weight:   20.0000
   chunk 182 optimal weight:   20.0000
   chunk 213 optimal weight:    6.9990
   chunk 172 optimal weight:   10.0000
   chunk 47 optimal weight:    9.9990
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
** J  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 124 ASN
** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   8 GLN
** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  91 GLN
G 406 HIS
E  50 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.091146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.066645 restraints weight = 329226.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.071033 restraints weight = 213633.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.074585 restraints weight = 147912.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.077427 restraints weight = 106893.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.079625 restraints weight = 79971.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6286
moved from start:          0.6416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.168  22307  Z= 0.239
  Angle     :  0.673  22.048  30216  Z= 0.376
  Chirality :  0.041   0.218   3305
  Planarity :  0.007   0.223   3960
  Dihedral  :  4.983  33.259   3010
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 15.36
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  3.67 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.16), residues: 2752
  helix:  1.04 (0.14), residues: 1257
  sheet: -0.92 (0.24), residues: 396
  loop : -0.11 (0.19), residues: 1099

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B   2 
 TYR   0.027   0.002   TYR E 210 
 PHE   0.042   0.002   PHE J 129 
 TRP   0.016   0.002   TRP C 346 
 HIS   0.011   0.002   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 (22292)
  covalent geometry    : angle       0.67292 (30216)
  hydrogen bonds       : bond        0.05548 ( 1125)
  hydrogen bonds       : angle       4.96845 ( 3213)
  Misc. bond           : bond        0.01567 (   15)

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

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

  5504 Ramachandran restraints generated.
    2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5504 Ramachandran restraints generated.
    2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  462 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 462
  time to evaluate  : 1.107 
Fit side-chains
   revert: symmetry clash
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REVERT: J   45 MET cc_start: 0.1988 (ptp) cc_final: 0.1588 (tpt)
REVERT: J   58 MET cc_start: 0.9668 (tpt) cc_final: 0.9377 (tpp)
REVERT: J   65 LEU cc_start: 0.8320 (tp) cc_final: 0.7718 (tt)
REVERT: J   70 PHE cc_start: 0.9015 (t80) cc_final: 0.7949 (t80)
REVERT: J   74 PHE cc_start: 0.8088 (m-10) cc_final: 0.7161 (m-10)
REVERT: J   94 TYR cc_start: 0.9310 (t80) cc_final: 0.8675 (t80)
REVERT: J  137 LEU cc_start: 0.9586 (mt) cc_final: 0.9365 (mt)
REVERT: B  198 GLU cc_start: 0.9679 (mt-10) cc_final: 0.9356 (mt-10)
REVERT: B  337 ASN cc_start: 0.9282 (m-40) cc_final: 0.9081 (m-40)
REVERT: D   68 LEU cc_start: 0.9071 (mm) cc_final: 0.8709 (mm)
REVERT: D  111 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8325 (mt-10)
REVERT: D  128 ASP cc_start: 0.7851 (m-30) cc_final: 0.7636 (m-30)
REVERT: D  389 PHE cc_start: 0.8598 (t80) cc_final: 0.8377 (t80)
REVERT: D  408 PHE cc_start: 0.9589 (m-80) cc_final: 0.9370 (m-80)
REVERT: A  169 PHE cc_start: 0.9016 (m-80) cc_final: 0.8580 (m-80)
REVERT: A  202 PHE cc_start: 0.8796 (m-80) cc_final: 0.8290 (m-80)
REVERT: A  234 ILE cc_start: 0.8595 (mt) cc_final: 0.8366 (mt)
REVERT: A  238 ILE cc_start: 0.9011 (mt) cc_final: 0.8773 (mt)
REVERT: A  255 PHE cc_start: 0.9342 (m-80) cc_final: 0.8967 (m-80)
REVERT: A  296 PHE cc_start: 0.9341 (m-80) cc_final: 0.9041 (m-10)
REVERT: A  417 GLU cc_start: 0.9401 (mt-10) cc_final: 0.9138 (tp30)
REVERT: A  425 MET cc_start: 0.9160 (mmp) cc_final: 0.8929 (mmm)
REVERT: C  169 PHE cc_start: 0.8930 (m-10) cc_final: 0.8633 (m-80)
REVERT: C  202 PHE cc_start: 0.9247 (m-80) cc_final: 0.8962 (m-80)
REVERT: C  255 PHE cc_start: 0.9116 (m-80) cc_final: 0.8513 (m-80)
REVERT: C  313 MET cc_start: 0.4688 (mmp) cc_final: 0.3115 (mmp)
REVERT: G  137 VAL cc_start: 0.9301 (t) cc_final: 0.9041 (p)
REVERT: G  154 MET cc_start: 0.9386 (mmm) cc_final: 0.9019 (mmm)
REVERT: G  169 PHE cc_start: 0.9316 (m-80) cc_final: 0.8624 (m-80)
REVERT: G  199 ASP cc_start: 0.9569 (m-30) cc_final: 0.8937 (t0)
REVERT: G  313 MET cc_start: 0.5970 (mmp) cc_final: 0.4724 (mmp)
REVERT: G  319 TYR cc_start: 0.9368 (m-10) cc_final: 0.9074 (m-80)
REVERT: E  255 PHE cc_start: 0.8728 (m-80) cc_final: 0.8111 (m-80)
REVERT: E  398 MET cc_start: 0.9160 (mtt) cc_final: 0.8618 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 462
  average time/residue: 0.4143
  time to fit residues: 276.8158
Evaluate side-chains
  387 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 387
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 2 optimal weight:    8.9990
   chunk 228 optimal weight:    9.9990
   chunk 53 optimal weight:   10.0000
   chunk 120 optimal weight:    9.9990
   chunk 59 optimal weight:    7.9990
   chunk 78 optimal weight:    1.9990
   chunk 213 optimal weight:    9.9990
   chunk 21 optimal weight:    9.9990
   chunk 14 optimal weight:   20.0000
   chunk 164 optimal weight:    9.9990
   chunk 271 optimal weight:   20.0000
   overall best weight:    7.7990

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

Flipped N/Q/H residues before XYZ refinement:
** J  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 163 ASN
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 186 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.089379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.066341 restraints weight = 340034.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.070483 restraints weight = 219513.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.073798 restraints weight = 151912.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.076446 restraints weight = 110416.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.078530 restraints weight = 83128.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6333
moved from start:          0.7048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.169  22307  Z= 0.253
  Angle     :  0.699  20.855  30216  Z= 0.390
  Chirality :  0.042   0.238   3305
  Planarity :  0.007   0.231   3960
  Dihedral  :  5.155  48.451   3010
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 16.76
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.11 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.04 %
    Allowed  :  0.68 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.15), residues: 2752
  helix:  0.77 (0.14), residues: 1269
  sheet: -0.62 (0.25), residues: 366
  loop : -0.41 (0.19), residues: 1117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG J 161 
 TYR   0.029   0.002   TYR E 210 
 PHE   0.037   0.002   PHE J 129 
 TRP   0.014   0.002   TRP C 346 
 HIS   0.020   0.002   HIS E   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 (22292)
  covalent geometry    : angle       0.69897 (30216)
  hydrogen bonds       : bond        0.05466 ( 1125)
  hydrogen bonds       : angle       5.05443 ( 3213)
  Misc. bond           : bond        0.01819 (   15)

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

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

  5504 Ramachandran restraints generated.
    2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5504 Ramachandran restraints generated.
    2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  447 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 446
  time to evaluate  : 1.218 
Fit side-chains
   revert: symmetry clash
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REVERT: J   45 MET cc_start: 0.2857 (ptp) cc_final: 0.2007 (tpt)
REVERT: J   58 MET cc_start: 0.9644 (tpp) cc_final: 0.9380 (tpp)
REVERT: J   64 LEU cc_start: 0.8609 (mp) cc_final: 0.8402 (mp)
REVERT: J   65 LEU cc_start: 0.8417 (tp) cc_final: 0.7887 (tt)
REVERT: J   70 PHE cc_start: 0.9048 (t80) cc_final: 0.8093 (t80)
REVERT: J   74 PHE cc_start: 0.8392 (m-10) cc_final: 0.7731 (m-10)
REVERT: J   94 TYR cc_start: 0.9302 (t80) cc_final: 0.8695 (t80)
REVERT: J  116 MET cc_start: 0.9151 (tmm) cc_final: 0.8871 (tmm)
REVERT: J  159 MET cc_start: 0.8237 (mpp) cc_final: 0.7786 (mpp)
REVERT: B   67 ASP cc_start: 0.6708 (t0) cc_final: 0.5503 (p0)
REVERT: B  198 GLU cc_start: 0.9744 (mt-10) cc_final: 0.9471 (mt-10)
REVERT: B  318 ARG cc_start: 0.8446 (mtp180) cc_final: 0.7736 (mmm-85)
REVERT: B  331 LEU cc_start: 0.9715 (mt) cc_final: 0.9457 (mt)
REVERT: D  128 ASP cc_start: 0.7951 (m-30) cc_final: 0.7739 (m-30)
REVERT: D  165 ASN cc_start: 0.9411 (t0) cc_final: 0.8572 (t0)
REVERT: D  200 TYR cc_start: 0.9464 (m-80) cc_final: 0.9201 (m-80)
REVERT: D  293 MET cc_start: 0.9197 (ttt) cc_final: 0.8376 (tmm)
REVERT: D  389 PHE cc_start: 0.8411 (t80) cc_final: 0.8146 (t80)
REVERT: A  138 PHE cc_start: 0.9014 (m-80) cc_final: 0.8648 (m-80)
REVERT: A  169 PHE cc_start: 0.9147 (m-80) cc_final: 0.8814 (m-80)
REVERT: A  202 PHE cc_start: 0.8742 (m-80) cc_final: 0.8249 (m-80)
REVERT: A  255 PHE cc_start: 0.9385 (m-80) cc_final: 0.8994 (m-80)
REVERT: A  267 PHE cc_start: 0.8962 (m-80) cc_final: 0.8689 (m-80)
REVERT: A  417 GLU cc_start: 0.9428 (mt-10) cc_final: 0.9156 (tp30)
REVERT: A  425 MET cc_start: 0.9226 (mmp) cc_final: 0.8740 (mmp)
REVERT: C  202 PHE cc_start: 0.9244 (m-80) cc_final: 0.9016 (m-80)
REVERT: C  313 MET cc_start: 0.5270 (mmp) cc_final: 0.3705 (mmp)
REVERT: C  339 ARG cc_start: 0.1674 (mpt180) cc_final: 0.1442 (mpt180)
REVERT: G  137 VAL cc_start: 0.9356 (t) cc_final: 0.9109 (p)
REVERT: G  154 MET cc_start: 0.9461 (mmm) cc_final: 0.9117 (mmm)
REVERT: G  169 PHE cc_start: 0.9404 (m-80) cc_final: 0.8751 (m-80)
REVERT: G  199 ASP cc_start: 0.9579 (m-30) cc_final: 0.9022 (t0)
REVERT: G  313 MET cc_start: 0.6257 (mmp) cc_final: 0.4980 (mmp)
REVERT: G  319 TYR cc_start: 0.9439 (m-10) cc_final: 0.9147 (m-80)
REVERT: E  255 PHE cc_start: 0.8745 (m-80) cc_final: 0.8165 (m-80)
REVERT: E  377 MET cc_start: 0.5123 (ttp) cc_final: 0.4918 (ttp)
REVERT: E  398 MET cc_start: 0.9189 (mtt) cc_final: 0.8738 (mtp)
  outliers start: 1
  outliers final: 1
  residues processed: 446
  average time/residue: 0.4391
  time to fit residues: 285.0340
Evaluate side-chains
  392 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 391
  time to evaluate  : 1.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 137 optimal weight:   40.0000
   chunk 203 optimal weight:   10.0000
   chunk 253 optimal weight:    0.8980
   chunk 128 optimal weight:    8.9990
   chunk 49 optimal weight:    5.9990
   chunk 38 optimal weight:    0.8980
   chunk 178 optimal weight:   10.0000
   chunk 117 optimal weight:    9.9990
   chunk 261 optimal weight:    0.0570
   chunk 62 optimal weight:   20.0000
   chunk 177 optimal weight:    5.9990
   overall best weight:    2.7702

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

Flipped N/Q/H residues before XYZ refinement:
** J  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 163 ASN
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 186 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.091154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.067827 restraints weight = 336784.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.072133 restraints weight = 215793.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.075610 restraints weight = 148186.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.078330 restraints weight = 106486.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.080458 restraints weight = 79486.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6239
moved from start:          0.7157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.170  22307  Z= 0.192
  Angle     :  0.623  20.747  30216  Z= 0.347
  Chirality :  0.041   0.249   3305
  Planarity :  0.007   0.263   3960
  Dihedral  :  4.991  52.207   3010
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 14.10
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.67 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.16), residues: 2752
  helix:  1.28 (0.14), residues: 1257
  sheet: -0.99 (0.25), residues: 388
  loop : -0.13 (0.19), residues: 1107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.039   0.001   ARG G 221 
 TYR   0.023   0.001   TYR E 210 
 PHE   0.032   0.002   PHE D 167 
 TRP   0.012   0.001   TRP B 344 
 HIS   0.008   0.001   HIS G 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (22292)
  covalent geometry    : angle       0.62323 (30216)
  hydrogen bonds       : bond        0.05094 ( 1125)
  hydrogen bonds       : angle       4.81081 ( 3213)
  Misc. bond           : bond        0.01648 (   15)

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

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

  5504 Ramachandran restraints generated.
    2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5504 Ramachandran restraints generated.
    2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  454 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 454
  time to evaluate  : 1.115 
Fit side-chains
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REVERT: J   46 PHE cc_start: 0.8891 (m-80) cc_final: 0.8642 (m-80)
REVERT: J   58 MET cc_start: 0.9617 (tpp) cc_final: 0.9308 (tpp)
REVERT: J   65 LEU cc_start: 0.8317 (tp) cc_final: 0.7836 (tt)
REVERT: J   70 PHE cc_start: 0.8924 (t80) cc_final: 0.7901 (t80)
REVERT: J   74 PHE cc_start: 0.8110 (m-10) cc_final: 0.7290 (m-10)
REVERT: J   94 TYR cc_start: 0.9252 (t80) cc_final: 0.8624 (t80)
REVERT: B  198 GLU cc_start: 0.9759 (mt-10) cc_final: 0.9522 (mt-10)
REVERT: B  330 MET cc_start: 0.9034 (ttp) cc_final: 0.8331 (mmm)
REVERT: D  128 ASP cc_start: 0.7915 (m-30) cc_final: 0.7704 (m-30)
REVERT: A  238 ILE cc_start: 0.8945 (mt) cc_final: 0.8688 (mt)
REVERT: A  255 PHE cc_start: 0.9345 (m-80) cc_final: 0.8963 (m-80)
REVERT: A  267 PHE cc_start: 0.8954 (m-80) cc_final: 0.8690 (m-80)
REVERT: A  417 GLU cc_start: 0.9437 (mt-10) cc_final: 0.9149 (tp30)
REVERT: A  425 MET cc_start: 0.9201 (mmp) cc_final: 0.8766 (mmm)
REVERT: C  202 PHE cc_start: 0.9203 (m-80) cc_final: 0.8908 (m-80)
REVERT: C  313 MET cc_start: 0.5340 (mmp) cc_final: 0.3796 (mmp)
REVERT: G  137 VAL cc_start: 0.9357 (t) cc_final: 0.9104 (p)
REVERT: G  154 MET cc_start: 0.9438 (mmm) cc_final: 0.9068 (mmm)
REVERT: G  169 PHE cc_start: 0.9371 (m-80) cc_final: 0.8711 (m-80)
REVERT: G  199 ASP cc_start: 0.9585 (m-30) cc_final: 0.9062 (t0)
REVERT: G  313 MET cc_start: 0.6276 (mmp) cc_final: 0.5019 (mmp)
REVERT: G  319 TYR cc_start: 0.9432 (m-10) cc_final: 0.9132 (m-80)
REVERT: E  255 PHE cc_start: 0.8737 (m-80) cc_final: 0.8160 (m-80)
REVERT: E  296 PHE cc_start: 0.9310 (m-80) cc_final: 0.8688 (t80)
REVERT: E  398 MET cc_start: 0.9051 (mtt) cc_final: 0.8632 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 454
  average time/residue: 0.4387
  time to fit residues: 290.8835
Evaluate side-chains
  390 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 390
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 184 optimal weight:   20.0000
   chunk 42 optimal weight:    9.9990
   chunk 174 optimal weight:   10.0000
   chunk 133 optimal weight:    9.9990
   chunk 74 optimal weight:   10.0000
   chunk 7 optimal weight:    0.0770
   chunk 123 optimal weight:   20.0000
   chunk 190 optimal weight:   30.0000
   chunk 138 optimal weight:   20.0000
   chunk 81 optimal weight:   10.0000
   overall best weight:    7.2148

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

Flipped N/Q/H residues before XYZ refinement:
** J  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  86 ASN
J  97 HIS
J 102 HIS
** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 105 HIS
** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 247 ASN
D 416 ASN
** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 186 ASN
** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.086882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.064567 restraints weight = 346543.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.068701 restraints weight = 220390.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.071991 restraints weight = 150946.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.074568 restraints weight = 108591.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.076574 restraints weight = 81109.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6390
moved from start:          0.7745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.168  22307  Z= 0.246
  Angle     :  0.688  21.033  30216  Z= 0.388
  Chirality :  0.042   0.271   3305
  Planarity :  0.007   0.234   3960
  Dihedral  :  5.177  50.651   3010
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 18.22
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.43 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.59 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.16), residues: 2752
  helix:  0.89 (0.14), residues: 1257
  sheet: -0.72 (0.25), residues: 366
  loop : -0.45 (0.19), residues: 1129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.028   0.001   ARG G 221 
 TYR   0.032   0.002   TYR E 210 
 PHE   0.025   0.002   PHE A 202 
 TRP   0.019   0.002   TRP B 344 
 HIS   0.015   0.002   HIS C 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 (22292)
  covalent geometry    : angle       0.68820 (30216)
  hydrogen bonds       : bond        0.05372 ( 1125)
  hydrogen bonds       : angle       5.02423 ( 3213)
  Misc. bond           : bond        0.01574 (   15)

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

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

  5504 Ramachandran restraints generated.
    2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5504 Ramachandran restraints generated.
    2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  441 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 441
  time to evaluate  : 1.137 
Fit side-chains
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REVERT: J   46 PHE cc_start: 0.8774 (m-80) cc_final: 0.8491 (m-80)
REVERT: J   58 MET cc_start: 0.9652 (tpp) cc_final: 0.9354 (tpp)
REVERT: J   65 LEU cc_start: 0.8393 (tp) cc_final: 0.7937 (tt)
REVERT: J   70 PHE cc_start: 0.9019 (t80) cc_final: 0.8148 (t80)
REVERT: J   74 PHE cc_start: 0.8546 (m-10) cc_final: 0.7947 (m-10)
REVERT: J   94 TYR cc_start: 0.9368 (t80) cc_final: 0.8867 (t80)
REVERT: B   67 ASP cc_start: 0.7272 (t0) cc_final: 0.5129 (p0)
REVERT: B  203 ASP cc_start: 0.7520 (t70) cc_final: 0.7015 (m-30)
REVERT: B  233 MET cc_start: 0.8187 (mtp) cc_final: 0.7982 (mtp)
REVERT: B  298 ASN cc_start: 0.9528 (m110) cc_final: 0.9161 (t0)
REVERT: B  330 MET cc_start: 0.9100 (ttp) cc_final: 0.8534 (mmm)
REVERT: D  197 ASP cc_start: 0.9595 (m-30) cc_final: 0.8961 (t70)
REVERT: D  265 PHE cc_start: 0.9340 (m-80) cc_final: 0.8927 (m-80)
REVERT: D  418 LEU cc_start: 0.9290 (tp) cc_final: 0.9039 (tp)
REVERT: A  255 PHE cc_start: 0.9374 (m-80) cc_final: 0.8994 (m-80)
REVERT: A  425 MET cc_start: 0.9205 (mmp) cc_final: 0.8734 (mmm)
REVERT: C   36 MET cc_start: 0.4196 (ttt) cc_final: 0.3953 (ttt)
REVERT: C  202 PHE cc_start: 0.9301 (m-80) cc_final: 0.9050 (m-80)
REVERT: C  313 MET cc_start: 0.6059 (mmp) cc_final: 0.4300 (mmp)
REVERT: G  137 VAL cc_start: 0.9368 (t) cc_final: 0.9110 (p)
REVERT: G  157 LEU cc_start: 0.9291 (mt) cc_final: 0.9054 (mt)
REVERT: G  169 PHE cc_start: 0.9441 (m-80) cc_final: 0.8819 (m-80)
REVERT: G  199 ASP cc_start: 0.9571 (m-30) cc_final: 0.9098 (t0)
REVERT: G  313 MET cc_start: 0.6508 (mmp) cc_final: 0.5211 (mmp)
REVERT: G  319 TYR cc_start: 0.9455 (m-10) cc_final: 0.9173 (m-80)
REVERT: E  255 PHE cc_start: 0.8846 (m-80) cc_final: 0.8273 (m-80)
REVERT: E  358 GLU cc_start: 0.9091 (tp30) cc_final: 0.8697 (mt-10)
REVERT: E  398 MET cc_start: 0.9205 (mtt) cc_final: 0.8727 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 441
  average time/residue: 0.3990
  time to fit residues: 255.3160
Evaluate side-chains
  384 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 384
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 129 optimal weight:    8.9990
   chunk 9 optimal weight:    3.9990
   chunk 112 optimal weight:    9.9990
   chunk 43 optimal weight:   20.0000
   chunk 19 optimal weight:   20.0000
   chunk 262 optimal weight:    7.9990
   chunk 60 optimal weight:   10.0000
   chunk 28 optimal weight:   20.0000
   chunk 188 optimal weight:   20.0000
   chunk 263 optimal weight:    7.9990
   chunk 205 optimal weight:    4.9990
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
** J  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 247 ASN
** D   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 186 ASN
** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.085785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.063698 restraints weight = 350954.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.067841 restraints weight = 222380.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.071068 restraints weight = 151607.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.073616 restraints weight = 108893.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.075591 restraints weight = 81266.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6441
moved from start:          0.8131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.169  22307  Z= 0.224
  Angle     :  0.658  21.218  30216  Z= 0.370
  Chirality :  0.042   0.227   3305
  Planarity :  0.007   0.233   3960
  Dihedral  :  5.213  53.302   3010
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 17.83
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.47 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.59 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.01 (0.16), residues: 2752
  helix:  0.83 (0.14), residues: 1265
  sheet: -0.85 (0.25), residues: 374
  loop : -0.51 (0.19), residues: 1113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.001   ARG G 221 
 TYR   0.019   0.002   TYR G 224 
 PHE   0.038   0.002   PHE D 167 
 TRP   0.015   0.001   TRP B 344 
 HIS   0.010   0.002   HIS G 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 (22292)
  covalent geometry    : angle       0.65840 (30216)
  hydrogen bonds       : bond        0.05241 ( 1125)
  hydrogen bonds       : angle       5.06527 ( 3213)
  Misc. bond           : bond        0.01448 (   15)

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

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

  5504 Ramachandran restraints generated.
    2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5504 Ramachandran restraints generated.
    2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  442 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 442
  time to evaluate  : 1.163 
Fit side-chains
   revert: symmetry clash
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REVERT: J   58 MET cc_start: 0.9650 (tpp) cc_final: 0.9345 (tpp)
REVERT: J   65 LEU cc_start: 0.8470 (tp) cc_final: 0.7990 (tt)
REVERT: J   70 PHE cc_start: 0.8931 (t80) cc_final: 0.8094 (t80)
REVERT: J   74 PHE cc_start: 0.8711 (m-10) cc_final: 0.8055 (m-10)
REVERT: J   94 TYR cc_start: 0.9291 (t80) cc_final: 0.8904 (t80)
REVERT: B   67 ASP cc_start: 0.7260 (t0) cc_final: 0.5942 (p0)
REVERT: B   77 ARG cc_start: 0.8132 (ttm110) cc_final: 0.6954 (tpt170)
REVERT: B  105 HIS cc_start: 0.8974 (t70) cc_final: 0.8725 (t70)
REVERT: B  203 ASP cc_start: 0.7464 (t70) cc_final: 0.6932 (m-30)
REVERT: B  233 MET cc_start: 0.8191 (mtp) cc_final: 0.7973 (mtp)
REVERT: B  298 ASN cc_start: 0.9551 (m110) cc_final: 0.9119 (t0)
REVERT: B  330 MET cc_start: 0.9204 (ttp) cc_final: 0.8583 (mmm)
REVERT: D  128 ASP cc_start: 0.8095 (m-30) cc_final: 0.7892 (m-30)
REVERT: D  197 ASP cc_start: 0.9563 (m-30) cc_final: 0.8937 (t70)
REVERT: D  265 PHE cc_start: 0.9391 (m-80) cc_final: 0.9004 (m-80)
REVERT: D  389 PHE cc_start: 0.8361 (t80) cc_final: 0.8134 (t80)
REVERT: D  418 LEU cc_start: 0.9283 (tp) cc_final: 0.9016 (tp)
REVERT: A  255 PHE cc_start: 0.9360 (m-80) cc_final: 0.8982 (m-80)
REVERT: A  267 PHE cc_start: 0.8871 (m-80) cc_final: 0.8652 (m-80)
REVERT: A  425 MET cc_start: 0.9184 (mmp) cc_final: 0.8723 (mmm)
REVERT: C  202 PHE cc_start: 0.9343 (m-80) cc_final: 0.9010 (m-80)
REVERT: C  313 MET cc_start: 0.6150 (mmp) cc_final: 0.4348 (mmp)
REVERT: G  137 VAL cc_start: 0.9372 (t) cc_final: 0.9109 (p)
REVERT: G  157 LEU cc_start: 0.9249 (mt) cc_final: 0.9015 (mt)
REVERT: G  169 PHE cc_start: 0.9436 (m-80) cc_final: 0.8812 (m-80)
REVERT: G  199 ASP cc_start: 0.9568 (m-30) cc_final: 0.9110 (t0)
REVERT: G  313 MET cc_start: 0.6504 (mmp) cc_final: 0.5210 (mmp)
REVERT: G  319 TYR cc_start: 0.9461 (m-10) cc_final: 0.9155 (m-80)
REVERT: E  255 PHE cc_start: 0.8898 (m-80) cc_final: 0.8400 (m-80)
REVERT: E  358 GLU cc_start: 0.9134 (tp30) cc_final: 0.8755 (mt-10)
REVERT: E  398 MET cc_start: 0.9183 (mtt) cc_final: 0.8701 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 442
  average time/residue: 0.3985
  time to fit residues: 257.5560
Evaluate side-chains
  372 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 372
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 228 optimal weight:    8.9990
   chunk 43 optimal weight:    1.9990
   chunk 210 optimal weight:    6.9990
   chunk 251 optimal weight:   10.0000
   chunk 35 optimal weight:   20.0000
   chunk 132 optimal weight:    5.9990
   chunk 86 optimal weight:    6.9990
   chunk 241 optimal weight:    5.9990
   chunk 225 optimal weight:   20.0000
   chunk 51 optimal weight:    9.9990
   chunk 159 optimal weight:   10.0000
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
** J  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   8 GLN
** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  31 GLN
** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 186 ASN
** E 258 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 = 0.4015 r_free = 0.4015 target = 0.085469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.063265 restraints weight = 347112.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.067383 restraints weight = 219898.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.070607 restraints weight = 150191.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.073162 restraints weight = 108119.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.075150 restraints weight = 80848.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6474
moved from start:          0.8426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.168  22307  Z= 0.212
  Angle     :  0.645  20.969  30216  Z= 0.361
  Chirality :  0.042   0.215   3305
  Planarity :  0.007   0.227   3960
  Dihedral  :  5.222  53.509   3010
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 17.24
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.91 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.59 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.06 (0.16), residues: 2752
  helix:  0.93 (0.14), residues: 1259
  sheet: -0.96 (0.25), residues: 374
  loop : -0.50 (0.19), residues: 1119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG G 221 
 TYR   0.024   0.002   TYR B 422 
 PHE   0.021   0.002   PHE J 129 
 TRP   0.015   0.001   TRP B 344 
 HIS   0.010   0.002   HIS G 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 (22292)
  covalent geometry    : angle       0.64497 (30216)
  hydrogen bonds       : bond        0.05191 ( 1125)
  hydrogen bonds       : angle       5.01124 ( 3213)
  Misc. bond           : bond        0.01449 (   15)

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

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

  5504 Ramachandran restraints generated.
    2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5504 Ramachandran restraints generated.
    2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  435 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 435
  time to evaluate  : 1.173 
Fit side-chains
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REVERT: J   58 MET cc_start: 0.9635 (tpp) cc_final: 0.9331 (tpp)
REVERT: J   65 LEU cc_start: 0.8402 (tp) cc_final: 0.7865 (tt)
REVERT: J   70 PHE cc_start: 0.8867 (t80) cc_final: 0.8018 (t80)
REVERT: J   74 PHE cc_start: 0.8826 (m-10) cc_final: 0.8066 (m-10)
REVERT: J   94 TYR cc_start: 0.9275 (t80) cc_final: 0.8876 (t80)
REVERT: B   67 ASP cc_start: 0.7654 (t0) cc_final: 0.5948 (p0)
REVERT: B   77 ARG cc_start: 0.8159 (ttm110) cc_final: 0.6995 (tpt170)
REVERT: B  233 MET cc_start: 0.8186 (mtp) cc_final: 0.7953 (mtp)
REVERT: B  298 ASN cc_start: 0.9575 (m110) cc_final: 0.9102 (t0)
REVERT: B  331 LEU cc_start: 0.9773 (mt) cc_final: 0.9567 (mt)
REVERT: D  128 ASP cc_start: 0.8105 (m-30) cc_final: 0.7888 (m-30)
REVERT: D  265 PHE cc_start: 0.9432 (m-80) cc_final: 0.9036 (m-80)
REVERT: D  389 PHE cc_start: 0.8330 (t80) cc_final: 0.8097 (t80)
REVERT: D  418 LEU cc_start: 0.9278 (tp) cc_final: 0.9007 (tp)
REVERT: A    1 MET cc_start: 0.7254 (tpt) cc_final: 0.7048 (tpt)
REVERT: A  255 PHE cc_start: 0.9389 (m-80) cc_final: 0.9009 (m-80)
REVERT: A  267 PHE cc_start: 0.8883 (m-80) cc_final: 0.8674 (m-80)
REVERT: A  425 MET cc_start: 0.9177 (mmp) cc_final: 0.8718 (mmm)
REVERT: C  202 PHE cc_start: 0.9330 (m-80) cc_final: 0.8919 (m-80)
REVERT: C  313 MET cc_start: 0.6295 (mmp) cc_final: 0.4492 (mmp)
REVERT: G  137 VAL cc_start: 0.9382 (t) cc_final: 0.9131 (p)
REVERT: G  169 PHE cc_start: 0.9428 (m-80) cc_final: 0.8784 (m-80)
REVERT: G  199 ASP cc_start: 0.9557 (m-30) cc_final: 0.9128 (t0)
REVERT: G  313 MET cc_start: 0.6566 (mmp) cc_final: 0.5268 (mmp)
REVERT: G  319 TYR cc_start: 0.9440 (m-10) cc_final: 0.9114 (m-80)
REVERT: E  255 PHE cc_start: 0.8868 (m-80) cc_final: 0.8353 (m-80)
REVERT: E  358 GLU cc_start: 0.9154 (tp30) cc_final: 0.8767 (mt-10)
REVERT: E  398 MET cc_start: 0.9119 (mtt) cc_final: 0.8633 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 435
  average time/residue: 0.4214
  time to fit residues: 267.0953
Evaluate side-chains
  374 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 374
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 272
   random chunks:
   chunk 52 optimal weight:    7.9990
   chunk 62 optimal weight:    9.9990
   chunk 64 optimal weight:    8.9990
   chunk 119 optimal weight:    5.9990
   chunk 87 optimal weight:    5.9990
   chunk 253 optimal weight:   20.0000
   chunk 258 optimal weight:    6.9990
   chunk 152 optimal weight:   10.0000
   chunk 91 optimal weight:    5.9990
   chunk 186 optimal weight:    7.9990
   chunk 81 optimal weight:    6.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
I  29 HIS
** J  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 226 ASN
** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 186 ASN
** E 258 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 = 0.3989 r_free = 0.3989 target = 0.083915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.062176 restraints weight = 355989.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.066234 restraints weight = 224345.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.069443 restraints weight = 152623.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.071952 restraints weight = 109433.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.073884 restraints weight = 81586.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6534
moved from start:          0.8792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.169  22307  Z= 0.228
  Angle     :  0.664  20.895  30216  Z= 0.375
  Chirality :  0.042   0.215   3305
  Planarity :  0.008   0.282   3960
  Dihedral  :  5.364  54.408   3010
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 18.66
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.27 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.59 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.16), residues: 2752
  helix:  0.86 (0.14), residues: 1249
  sheet: -0.93 (0.26), residues: 374
  loop : -0.57 (0.19), residues: 1129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.037   0.001   ARG E 221 
 TYR   0.020   0.002   TYR G 224 
 PHE   0.030   0.002   PHE D 167 
 TRP   0.016   0.002   TRP B 344 
 HIS   0.013   0.002   HIS G 393 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 (22292)
  covalent geometry    : angle       0.66437 (30216)
  hydrogen bonds       : bond        0.05310 ( 1125)
  hydrogen bonds       : angle       5.06145 ( 3213)
  Misc. bond           : bond        0.01465 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7764.16 seconds
wall clock time: 133 minutes 27.02 seconds (8007.02 seconds total)