Starting phenix.real_space_refine
on Tue Nov 18 21:08:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6lpb_0940/11_2025/6lpb_0940.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6lpb_0940/11_2025/6lpb_0940.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6lpb_0940/11_2025/6lpb_0940.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6lpb_0940/11_2025/6lpb_0940.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6lpb_0940/11_2025/6lpb_0940.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6lpb_0940/11_2025/6lpb_0940.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S     120      5.16       5
     C   11216      2.51       5
     N    3044      2.21       5
     O    3254      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17634
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "P"
      Number of atoms: 225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 225
          Classifications: {'peptide': 28}
          Link IDs: {'TRANS': 27}
    Chain: "R"
      Number of atoms: 2710
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 2710
          Classifications: {'peptide': 331}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 319}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "B"
      Number of atoms: 2616
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2616
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
    Chain: "A"
      Number of atoms: 1864
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1864
          Classifications: {'peptide': 223}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 216}
          Chain breaks: 1
    Chain: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 973
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "G"
      Number of atoms: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 429
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
  Restraints were copied for chains:
    C, D, E, F, H, I
  Time building chain proxies: 4.61, per 1000 atoms: 0.26
  Number of scatterers: 17634
  At special positions: 0
  Unit cell: (100.413, 191.697, 119.974, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S     120     16.00
     O    3254      8.00
     N    3044      7.00
     C   11216      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  34 " - pdb=" SG  CYS R  63 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  54 " - pdb=" SG  CYS R 118 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  77 " - pdb=" SG  CYS R 134 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 226 " - pdb=" SG  CYS R 296 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  34 " - pdb=" SG  CYS D  63 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  54 " - pdb=" SG  CYS D 118 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  77 " - pdb=" SG  CYS D 134 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 226 " - pdb=" SG  CYS D 296 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.56
  Conformation dependent library (CDL) restraints added in 763.3 milliseconds
  

  4320 Ramachandran restraints generated.
    2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4148

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 24 sheets defined
      39.1% alpha, 17.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'P' and resid 2 through 26
    Processing helix  chain 'R' and resid 27 through 46
    Processing helix  chain 'R' and resid 80 through 85
    Processing helix  chain 'R' and resid 129 through 134
    Processing helix  chain 'R' and resid 147 through 175
    Processing helix  chain 'R' and resid 184 through 211
    Processing helix  chain 'R' and resid 224 through 257
    Processing helix  chain 'R' and resid 263 through 274
      removed outlier: 3.651A  pdb=" N   TYR R 267 " --> pdb=" O   ARG R 263 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   THR R 270 " --> pdb=" O   PHE R 266 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ILE R 271 " --> pdb=" O   TYR R 267 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 276 through 290
    Processing helix  chain 'R' and resid 302 through 307
    Processing helix  chain 'R' and resid 310 through 337
      removed outlier: 4.002A  pdb=" N   SER R 337 " --> pdb=" O   GLN R 333 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 347 through 356
    Processing helix  chain 'R' and resid 358 through 363
    Processing helix  chain 'R' and resid 377 through 387
    Processing helix  chain 'R' and resid 391 through 400
    Processing helix  chain 'R' and resid 405 through 414
      removed outlier: 3.687A  pdb=" N   ALA R 409 " --> pdb=" O   GLY R 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 25
      removed outlier: 3.690A  pdb=" N   LYS B  23 " --> pdb=" O   ARG B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 33
      removed outlier: 3.602A  pdb=" N   GLN B  32 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 13 through 40
      removed outlier: 3.570A  pdb=" N   THR A  40 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 57
      removed outlier: 3.664A  pdb=" N   ILE A  56 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   VAL A  57 " --> pdb=" O   SER A  54 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 53 through 57'
    Processing helix  chain 'A' and resid 235 through 239
      removed outlier: 3.556A  pdb=" N   PHE A 238 " --> pdb=" O   ILE A 235 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 235 through 239'
    Processing helix  chain 'A' and resid 252 through 254
      No H-bonds generated for 'chain 'A' and resid 252 through 254'
    Processing helix  chain 'A' and resid 255 through 268
    Processing helix  chain 'A' and resid 283 through 294
      removed outlier: 3.790A  pdb=" N   LEU A 287 " --> pdb=" O   LYS A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 301
    Processing helix  chain 'A' and resid 321 through 340
    Processing helix  chain 'A' and resid 360 through 379
      removed outlier: 3.690A  pdb=" N   ARG A 364 " --> pdb=" O   GLU A 360 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.501A  pdb=" N   ASP N  90 " --> pdb=" O   LYS N  87 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 87 through 91'
    Processing helix  chain 'G' and resid 8 through 21
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'C' and resid 2 through 26
    Processing helix  chain 'D' and resid 27 through 46
    Processing helix  chain 'D' and resid 80 through 85
    Processing helix  chain 'D' and resid 129 through 134
    Processing helix  chain 'D' and resid 147 through 175
    Processing helix  chain 'D' and resid 184 through 211
    Processing helix  chain 'D' and resid 224 through 257
    Processing helix  chain 'D' and resid 263 through 274
      removed outlier: 3.651A  pdb=" N   TYR D 267 " --> pdb=" O   ARG D 263 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   THR D 270 " --> pdb=" O   PHE D 266 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ILE D 271 " --> pdb=" O   TYR D 267 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 276 through 290
    Processing helix  chain 'D' and resid 302 through 307
    Processing helix  chain 'D' and resid 310 through 337
      removed outlier: 4.002A  pdb=" N   SER D 337 " --> pdb=" O   GLN D 333 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 347 through 356
    Processing helix  chain 'D' and resid 358 through 363
    Processing helix  chain 'D' and resid 377 through 387
    Processing helix  chain 'D' and resid 391 through 400
    Processing helix  chain 'D' and resid 405 through 414
      removed outlier: 3.687A  pdb=" N   ALA D 409 " --> pdb=" O   GLY D 405 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 2 through 25
      removed outlier: 3.690A  pdb=" N   LYS E  23 " --> pdb=" O   ARG E  19 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 29 through 33
      removed outlier: 3.602A  pdb=" N   GLN E  32 " --> pdb=" O   THR E  29 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 13 through 40
      removed outlier: 3.570A  pdb=" N   THR F  40 " --> pdb=" O   VAL F  36 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 53 through 57
      removed outlier: 3.664A  pdb=" N   ILE F  56 " --> pdb=" O   LYS F  53 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   VAL F  57 " --> pdb=" O   SER F  54 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 53 through 57'
    Processing helix  chain 'F' and resid 235 through 239
      removed outlier: 3.556A  pdb=" N   PHE F 238 " --> pdb=" O   ILE F 235 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   ASN F 239 " --> pdb=" O   GLN F 236 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 235 through 239'
    Processing helix  chain 'F' and resid 252 through 254
      No H-bonds generated for 'chain 'F' and resid 252 through 254'
    Processing helix  chain 'F' and resid 255 through 268
    Processing helix  chain 'F' and resid 283 through 294
      removed outlier: 3.790A  pdb=" N   LEU F 287 " --> pdb=" O   LYS F 283 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 297 through 301
    Processing helix  chain 'F' and resid 321 through 340
    Processing helix  chain 'F' and resid 360 through 379
      removed outlier: 3.690A  pdb=" N   ARG F 364 " --> pdb=" O   GLU F 360 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.501A  pdb=" N   ASP H  90 " --> pdb=" O   LYS H  87 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   THR H  91 " --> pdb=" O   PRO H  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 87 through 91'
    Processing helix  chain 'I' and resid 8 through 21
    Processing helix  chain 'I' and resid 29 through 44
    Processing sheet with id=1, first strand: chain 'R' and resid 57 through 58
      removed outlier: 3.578A  pdb=" N   MET R  57 " --> pdb=" O   TRP R  64 " (cutoff:3.500A)
    Processing sheet with id=2, first strand: chain 'R' and resid 72 through 76
    Processing sheet with id=3, first strand: chain 'B' and resid 47 through 49
      removed outlier: 6.858A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
    Processing sheet with id=4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.042A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.812A  pdb=" N   THR B 102 " --> pdb=" O   GLY B 115 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ALA B 104 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   CYS B 121 " --> pdb=" O   LEU B 139 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.742A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.097A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.911A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.602A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 7.430A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.550A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.915A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=9, first strand: chain 'B' and resid 275 through 276
      removed outlier: 3.923A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=10, first strand: chain 'A' and resid 209 through 214
      removed outlier: 6.722A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.050A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   PHE A 280 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 280 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   ASN A 282 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 282 " (cutoff:3.500A)
    Processing sheet with id=11, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=12, first strand: chain 'N' and resid 10 through 11
      removed outlier: 6.182A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.184A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
    Processing sheet with id=13, first strand: chain 'D' and resid 57 through 58
      removed outlier: 3.578A  pdb=" N   MET D  57 " --> pdb=" O   TRP D  64 " (cutoff:3.500A)
    Processing sheet with id=14, first strand: chain 'D' and resid 72 through 76
    Processing sheet with id=15, first strand: chain 'E' and resid 47 through 49
      removed outlier: 6.858A  pdb=" N   ILE E 338 " --> pdb=" O   ARG E  48 " (cutoff:3.500A)
    Processing sheet with id=16, first strand: chain 'E' and resid 58 through 63
      removed outlier: 4.042A  pdb=" N   ALA E  60 " --> pdb=" O   ALA E  73 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   LEU E  79 " --> pdb=" O   ALA E  92 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   ALA E  92 " --> pdb=" O   LEU E  79 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   ILE E  81 " --> pdb=" O   VAL E  90 " (cutoff:3.500A)
    Processing sheet with id=17, first strand: chain 'E' and resid 100 through 105
      removed outlier: 3.812A  pdb=" N   THR E 102 " --> pdb=" O   GLY E 115 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ALA E 104 " --> pdb=" O   ALA E 113 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   CYS E 121 " --> pdb=" O   LEU E 139 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   ASN E 125 " --> pdb=" O   VAL E 135 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   VAL E 135 " --> pdb=" O   ASN E 125 " (cutoff:3.500A)
    Processing sheet with id=18, first strand: chain 'E' and resid 146 through 151
      removed outlier: 3.742A  pdb=" N   CYS E 148 " --> pdb=" O   SER E 160 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   ASP E 170 " --> pdb=" O   GLN E 176 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   GLN E 176 " --> pdb=" O   ASP E 170 " (cutoff:3.500A)
    Processing sheet with id=19, first strand: chain 'E' and resid 187 through 192
      removed outlier: 7.097A  pdb=" N   GLY E 202 " --> pdb=" O   MET E 188 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   LEU E 190 " --> pdb=" O   VAL E 200 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   VAL E 200 " --> pdb=" O   LEU E 190 " (cutoff:3.500A)
      removed outlier: 5.911A  pdb=" N   LEU E 192 " --> pdb=" O   LEU E 198 " (cutoff:3.500A)
      removed outlier: 7.602A  pdb=" N   LEU E 198 " --> pdb=" O   LEU E 192 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   ASP E 212 " --> pdb=" O   CYS E 218 " (cutoff:3.500A)
      removed outlier: 7.430A  pdb=" N   CYS E 218 " --> pdb=" O   ASP E 212 " (cutoff:3.500A)
    Processing sheet with id=20, first strand: chain 'E' and resid 229 through 234
      removed outlier: 6.550A  pdb=" N   ASP E 254 " --> pdb=" O   GLU E 260 " (cutoff:3.500A)
      removed outlier: 5.915A  pdb=" N   GLU E 260 " --> pdb=" O   ASP E 254 " (cutoff:3.500A)
    Processing sheet with id=21, first strand: chain 'E' and resid 275 through 276
      removed outlier: 3.923A  pdb=" N   SER E 275 " --> pdb=" O   GLY E 288 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   ASP E 298 " --> pdb=" O   ARG E 304 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ARG E 304 " --> pdb=" O   ASP E 298 " (cutoff:3.500A)
    Processing sheet with id=22, first strand: chain 'F' and resid 209 through 214
      removed outlier: 6.722A  pdb=" N   HIS F  41 " --> pdb=" O   HIS F 220 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   PHE F 222 " --> pdb=" O   HIS F  41 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   LEU F  43 " --> pdb=" O   PHE F 222 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   VAL F 247 " --> pdb=" O   LEU F  46 " (cutoff:3.500A)
      removed outlier: 6.050A  pdb=" N   ILE F 244 " --> pdb=" O   ILE F 278 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   PHE F 280 " --> pdb=" O   ILE F 244 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   PHE F 246 " --> pdb=" O   PHE F 280 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   ASN F 282 " --> pdb=" O   PHE F 246 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   VAL F 248 " --> pdb=" O   ASN F 282 " (cutoff:3.500A)
    Processing sheet with id=23, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=24, first strand: chain 'H' and resid 10 through 11
      removed outlier: 6.182A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.184A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)

    836 hydrogen bonds defined for protein.
    2412 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.05

  Time building geometry restraints manager: 2.03 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 5658
        1.34 -     1.46: 4576
        1.46 -     1.59: 7616
        1.59 -     1.71: 0
        1.71 -     1.84: 168
  Bond restraints: 18018
  Sorted by residual:
  bond pdb=" CB  TRP R 243 "
       pdb=" CG  TRP R 243 "
    ideal  model  delta    sigma   weight residual
    1.498  1.385  0.113 3.10e-02 1.04e+03 1.34e+01
  bond pdb=" CB  TRP D 243 "
       pdb=" CG  TRP D 243 "
    ideal  model  delta    sigma   weight residual
    1.498  1.385  0.113 3.10e-02 1.04e+03 1.34e+01
  bond pdb=" CB  VAL R 322 "
       pdb=" CG2 VAL R 322 "
    ideal  model  delta    sigma   weight residual
    1.521  1.416  0.105 3.30e-02 9.18e+02 1.01e+01
  bond pdb=" CB  VAL D 322 "
       pdb=" CG2 VAL D 322 "
    ideal  model  delta    sigma   weight residual
    1.521  1.416  0.105 3.30e-02 9.18e+02 1.01e+01
  bond pdb=" CA  PHE A 246 "
       pdb=" CB  PHE A 246 "
    ideal  model  delta    sigma   weight residual
    1.532  1.491  0.042 1.74e-02 3.30e+03 5.69e+00
  ... (remaining 18013 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.48: 23502
        2.48 -     4.95: 800
        4.95 -     7.43: 56
        7.43 -     9.91: 26
        9.91 -    12.39: 4
  Bond angle restraints: 24388
  Sorted by residual:
  angle pdb=" C   PRO D 126 "
        pdb=" N   PHE D 127 "
        pdb=" CA  PHE D 127 "
      ideal   model   delta    sigma   weight residual
     121.57  130.84   -9.27 1.62e+00 3.81e-01 3.28e+01
  angle pdb=" C   PRO R 126 "
        pdb=" N   PHE R 127 "
        pdb=" CA  PHE R 127 "
      ideal   model   delta    sigma   weight residual
     121.57  130.84   -9.27 1.62e+00 3.81e-01 3.28e+01
  angle pdb=" N   ILE E 270 "
        pdb=" CA  ILE E 270 "
        pdb=" C   ILE E 270 "
      ideal   model   delta    sigma   weight residual
     113.20  108.73    4.47 9.60e-01 1.09e+00 2.17e+01
  angle pdb=" N   ILE B 270 "
        pdb=" CA  ILE B 270 "
        pdb=" C   ILE B 270 "
      ideal   model   delta    sigma   weight residual
     113.20  108.73    4.47 9.60e-01 1.09e+00 2.17e+01
  angle pdb=" CA  TYR D 157 "
        pdb=" CB  TYR D 157 "
        pdb=" CG  TYR D 157 "
      ideal   model   delta    sigma   weight residual
     113.90  121.61   -7.71 1.80e+00 3.09e-01 1.83e+01
  ... (remaining 24383 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.62: 9230
       17.62 -    35.23: 1188
       35.23 -    52.85: 196
       52.85 -    70.47: 32
       70.47 -    88.08: 16
  Dihedral angle restraints: 10662
    sinusoidal: 4240
      harmonic: 6422
  Sorted by residual:
  dihedral pdb=" CB  CYS R  54 "
           pdb=" SG  CYS R  54 "
           pdb=" SG  CYS R 118 "
           pdb=" CB  CYS R 118 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -157.05   71.05     1      1.00e+01 1.00e-02 6.48e+01
  dihedral pdb=" CB  CYS D  54 "
           pdb=" SG  CYS D  54 "
           pdb=" SG  CYS D 118 "
           pdb=" CB  CYS D 118 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -157.05   71.05     1      1.00e+01 1.00e-02 6.48e+01
  dihedral pdb=" CB  CYS D  77 "
           pdb=" SG  CYS D  77 "
           pdb=" SG  CYS D 134 "
           pdb=" CB  CYS D 134 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  155.56  -62.56     1      1.00e+01 1.00e-02 5.18e+01
  ... (remaining 10659 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1960
       0.058 -    0.116: 592
       0.116 -    0.175: 118
       0.175 -    0.233: 14
       0.233 -    0.291: 8
  Chirality restraints: 2692
  Sorted by residual:
  chirality pdb=" CB  ILE R 272 "
            pdb=" CA  ILE R 272 "
            pdb=" CG1 ILE R 272 "
            pdb=" CG2 ILE R 272 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" CB  ILE D 272 "
            pdb=" CA  ILE D 272 "
            pdb=" CG1 ILE D 272 "
            pdb=" CG2 ILE D 272 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" CB  ILE E 157 "
            pdb=" CA  ILE E 157 "
            pdb=" CG1 ILE E 157 "
            pdb=" CG2 ILE E 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.28 2.00e-01 2.50e+01 1.93e+00
  ... (remaining 2689 not shown)

  Planarity restraints: 3106
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY D 311 "   -0.055 5.00e-02 4.00e+02   8.29e-02 1.10e+01
        pdb=" N   PRO D 312 "    0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO D 312 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO D 312 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 311 "    0.055 5.00e-02 4.00e+02   8.29e-02 1.10e+01
        pdb=" N   PRO R 312 "   -0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO R 312 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO R 312 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE D 127 "    0.045 5.00e-02 4.00e+02   6.81e-02 7.42e+00
        pdb=" N   PRO D 128 "   -0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO D 128 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO D 128 "    0.038 5.00e-02 4.00e+02
  ... (remaining 3103 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 3726
        2.77 -     3.30: 15358
        3.30 -     3.83: 28749
        3.83 -     4.37: 31837
        4.37 -     4.90: 56606
  Nonbonded interactions: 136276
  Sorted by model distance:
  nonbonded pdb=" O   ALA A  48 "
            pdb=" OG  SER A  51 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   ALA F  48 "
            pdb=" OG  SER F  51 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OG  SER C   2 "
            pdb=" OE1 GLU D 385 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" OG  SER P   2 "
            pdb=" OE1 GLU R 385 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" OG  SER E 161 "
            pdb=" OG1 THR E 165 "
     model   vdw
     2.276 3.040
  ... (remaining 136271 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'P'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'R'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'N'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'I'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.450
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
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      :  0.009   0.113  18028  Z= 0.392
  Angle     :  1.056  12.387  24408  Z= 0.600
  Chirality :  0.058   0.291   2692
  Planarity :  0.007   0.083   3106
  Dihedral  : 15.620  88.082   6484
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 13.72 %
    Favored  : 85.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -3.86 (0.15), residues: 2160
  helix: -2.93 (0.12), residues: 804
  sheet: -1.36 (0.23), residues: 492
  loop : -2.73 (0.18), residues: 864

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 116 
 TYR   0.031   0.003   TYR R 157 
 PHE   0.031   0.003   PHE B 234 
 TRP   0.028   0.004   TRP B 297 
 HIS   0.008   0.002   HIS E 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00913 (18018)
  covalent geometry    : angle       1.05465 (24388)
  SS BOND              : bond        0.00211 (   10)
  SS BOND              : angle       1.96429 (   20)
  hydrogen bonds       : bond        0.17019 (  836)
  hydrogen bonds       : angle       7.34337 ( 2412)

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

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

  4320 Ramachandran restraints generated.
    2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4320 Ramachandran restraints generated.
    2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  369 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 345
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P   17 MET cc_start: 0.7200 (ttm) cc_final: 0.6807 (ttp)
REVERT: R   82 ARG cc_start: 0.6088 (mtt90) cc_final: 0.5197 (ptm160)
REVERT: R  300 ASN cc_start: 0.8770 (m-40) cc_final: 0.8566 (m110)
REVERT: R  356 LEU cc_start: 0.8490 (tt) cc_final: 0.8038 (tp)
REVERT: B  218 CYS cc_start: 0.8394 (t) cc_final: 0.7448 (p)
REVERT: B  258 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6580 (t70)
REVERT: B  289 TYR cc_start: 0.8928 (m-80) cc_final: 0.8714 (m-80)
REVERT: A  231 ARG cc_start: 0.8456 (ptt90) cc_final: 0.6041 (mpt-90)
REVERT: A  255 ARG cc_start: 0.7770 (mtp180) cc_final: 0.7526 (mtp85)
REVERT: A  320 GLU cc_start: 0.6381 (mp0) cc_final: 0.5865 (mp0)
REVERT: A  376 MET cc_start: 0.8120 (tmm) cc_final: 0.7346 (ttt)
REVERT: N   70 ILE cc_start: 0.7182 (pt) cc_final: 0.6553 (pt)
REVERT: N   82 GLN cc_start: 0.6638 (mt0) cc_final: 0.6421 (mt0)
REVERT: C   17 MET cc_start: 0.7202 (ttm) cc_final: 0.6811 (ttp)
REVERT: D   82 ARG cc_start: 0.6089 (mtt90) cc_final: 0.5200 (ptm160)
REVERT: D  300 ASN cc_start: 0.8771 (m-40) cc_final: 0.8566 (m110)
REVERT: D  356 LEU cc_start: 0.8491 (tt) cc_final: 0.8038 (tp)
REVERT: E  218 CYS cc_start: 0.8402 (t) cc_final: 0.7447 (p)
REVERT: E  258 ASP cc_start: 0.7083 (OUTLIER) cc_final: 0.6586 (t70)
REVERT: E  289 TYR cc_start: 0.8928 (m-80) cc_final: 0.8713 (m-80)
REVERT: F  231 ARG cc_start: 0.8454 (ptt90) cc_final: 0.6039 (mpt-90)
REVERT: F  255 ARG cc_start: 0.7769 (mtp180) cc_final: 0.7528 (mtp85)
REVERT: F  320 GLU cc_start: 0.6384 (mp0) cc_final: 0.5868 (mp0)
REVERT: F  376 MET cc_start: 0.8122 (tmm) cc_final: 0.7346 (ttt)
REVERT: H   70 ILE cc_start: 0.7184 (pt) cc_final: 0.6558 (pt)
REVERT: H   82 GLN cc_start: 0.6638 (mt0) cc_final: 0.6417 (mt0)
  outliers start: 24
  outliers final: 14
  residues processed: 365
  average time/residue: 0.1596
  time to fit residues: 84.6418
Evaluate side-chains
  269 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 253
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   62 THR
Chi-restraints excluded: chain R residue  231 VAL
Chi-restraints excluded: chain R residue  347 ILE
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  258 ASP
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain D residue  347 ILE
Chi-restraints excluded: chain E residue   47 THR
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  258 ASP
Chi-restraints excluded: chain F residue   45 LEU
Chi-restraints excluded: chain H residue    2 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 194 optimal weight:    3.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    0.3980
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    1.9990
   chunk 200 optimal weight:   10.0000
   chunk 212 optimal weight:    0.0970
   chunk 77 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
R  68 HIS
R 129 HIS
R 234 HIS
R 333 GLN
R 365 HIS
B  88 ASN
B 142 HIS
B 220 GLN
B 340 ASN
A  23 ASN
A 257 GLN
A 347 HIS
N 123 GLN
D  68 HIS
D 129 HIS
D 234 HIS
D 333 GLN
D 365 HIS
E 142 HIS
E 220 GLN
E 340 ASN
F  23 ASN
F 257 GLN
F 347 HIS
H 123 GLN

Total number of N/Q/H flips: 25

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.184513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.159646 restraints weight = 19101.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.157631 restraints weight = 35160.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 72)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.153392 restraints weight = 34081.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.149376 restraints weight = 27440.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.149440 restraints weight = 25765.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  18028  Z= 0.117
  Angle     :  0.547   7.112  24408  Z= 0.298
  Chirality :  0.041   0.146   2692
  Planarity :  0.005   0.054   3106
  Dihedral  :  6.305  84.997   2438
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 18.22 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.88 (0.16), residues: 2160
  helix: -0.26 (0.17), residues: 820
  sheet: -1.21 (0.23), residues: 456
  loop : -2.15 (0.18), residues: 884

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 255 
 TYR   0.019   0.001   TYR R 157 
 PHE   0.028   0.001   PHE N  29 
 TRP   0.017   0.002   TRP D 243 
 HIS   0.003   0.001   HIS R 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (18018)
  covalent geometry    : angle       0.54684 (24388)
  SS BOND              : bond        0.00173 (   10)
  SS BOND              : angle       1.02245 (   20)
  hydrogen bonds       : bond        0.04549 (  836)
  hydrogen bonds       : angle       4.91138 ( 2412)

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

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

  4320 Ramachandran restraints generated.
    2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4320 Ramachandran restraints generated.
    2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  346 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 292
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   82 ARG cc_start: 0.6441 (mtt90) cc_final: 0.5370 (ptm160)
REVERT: R  300 ASN cc_start: 0.8375 (m-40) cc_final: 0.8145 (m-40)
REVERT: R  356 LEU cc_start: 0.8419 (tt) cc_final: 0.8010 (tp)
REVERT: B  118 ASP cc_start: 0.6928 (m-30) cc_final: 0.6667 (m-30)
REVERT: B  212 ASP cc_start: 0.7187 (m-30) cc_final: 0.5503 (m-30)
REVERT: B  218 CYS cc_start: 0.8601 (t) cc_final: 0.7607 (p)
REVERT: B  219 ARG cc_start: 0.6414 (mmt180) cc_final: 0.6053 (ttm170)
REVERT: A  231 ARG cc_start: 0.8517 (ptt90) cc_final: 0.6667 (mpt-90)
REVERT: A  249 ASP cc_start: 0.7845 (p0) cc_final: 0.7645 (p0)
REVERT: A  260 LEU cc_start: 0.8576 (mt) cc_final: 0.8369 (mm)
REVERT: N   70 ILE cc_start: 0.7285 (OUTLIER) cc_final: 0.6506 (pt)
REVERT: D   82 ARG cc_start: 0.6431 (mtt90) cc_final: 0.5364 (ptm160)
REVERT: D  300 ASN cc_start: 0.8400 (m-40) cc_final: 0.8170 (m-40)
REVERT: D  356 LEU cc_start: 0.8414 (tt) cc_final: 0.8000 (tp)
REVERT: E  118 ASP cc_start: 0.6924 (m-30) cc_final: 0.6660 (m-30)
REVERT: E  212 ASP cc_start: 0.7198 (m-30) cc_final: 0.5508 (m-30)
REVERT: E  218 CYS cc_start: 0.8601 (t) cc_final: 0.7605 (p)
REVERT: E  219 ARG cc_start: 0.6411 (mmt180) cc_final: 0.6030 (ttm170)
REVERT: F  231 ARG cc_start: 0.8516 (ptt90) cc_final: 0.6658 (mpt-90)
REVERT: F  260 LEU cc_start: 0.8584 (mt) cc_final: 0.8373 (mm)
REVERT: H   70 ILE cc_start: 0.7299 (OUTLIER) cc_final: 0.6519 (pt)
  outliers start: 54
  outliers final: 36
  residues processed: 334
  average time/residue: 0.1429
  time to fit residues: 71.3965
Evaluate side-chains
  290 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 252
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    7 THR
Chi-restraints excluded: chain P residue    8 ASP
Chi-restraints excluded: chain R residue   62 THR
Chi-restraints excluded: chain R residue  305 LEU
Chi-restraints excluded: chain R residue  347 ILE
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue    8 ASP
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  347 ILE
Chi-restraints excluded: chain E residue    7 LEU
Chi-restraints excluded: chain E residue   47 THR
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain E residue  173 THR
Chi-restraints excluded: chain E residue  317 CYS
Chi-restraints excluded: chain F residue   45 LEU
Chi-restraints excluded: chain F residue  210 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   19 ARG
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue  107 CYS
Chi-restraints excluded: chain I residue   28 ILE
Chi-restraints excluded: chain I residue   36 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 86 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 53 optimal weight:    6.9990
   chunk 93 optimal weight:    5.9990
   chunk 192 optimal weight:    0.0770
   chunk 111 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 165 optimal weight:    9.9990
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
R  68 HIS
B 225 HIS
N  82 GLN
D  68 HIS
H  82 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.194339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.169493 restraints weight = 20839.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.167123 restraints weight = 38670.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.166990 restraints weight = 40044.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.166233 restraints weight = 26315.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.166766 restraints weight = 20805.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.2589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  18028  Z= 0.102
  Angle     :  0.505   7.036  24408  Z= 0.273
  Chirality :  0.040   0.137   2692
  Planarity :  0.004   0.048   3106
  Dihedral  :  5.567  82.470   2432
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 18.59 %
    Favored  : 77.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.92 (0.17), residues: 2160
  helix:  0.89 (0.18), residues: 822
  sheet: -1.06 (0.23), residues: 456
  loop : -1.79 (0.19), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  96 
 TYR   0.021   0.001   TYR R 157 
 PHE   0.017   0.001   PHE H  29 
 TRP   0.029   0.002   TRP F 271 
 HIS   0.002   0.001   HIS I  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 (18018)
  covalent geometry    : angle       0.50426 (24388)
  SS BOND              : bond        0.00147 (   10)
  SS BOND              : angle       0.90609 (   20)
  hydrogen bonds       : bond        0.04078 (  836)
  hydrogen bonds       : angle       4.41852 ( 2412)

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

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

  4320 Ramachandran restraints generated.
    2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4320 Ramachandran restraints generated.
    2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  374 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 302
  time to evaluate  : 0.673 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   82 ARG cc_start: 0.6516 (mtt90) cc_final: 0.5415 (ptm160)
REVERT: R  190 MET cc_start: 0.7540 (mmt) cc_final: 0.7069 (mmt)
REVERT: R  356 LEU cc_start: 0.8374 (tt) cc_final: 0.7975 (tp)
REVERT: R  371 PHE cc_start: 0.4901 (p90) cc_final: 0.4673 (p90)
REVERT: B  218 CYS cc_start: 0.8392 (t) cc_final: 0.7404 (p)
REVERT: A  231 ARG cc_start: 0.8543 (ptt90) cc_final: 0.6615 (mmt90)
REVERT: A  308 TYR cc_start: 0.6272 (t80) cc_final: 0.6009 (t80)
REVERT: N   70 ILE cc_start: 0.7226 (OUTLIER) cc_final: 0.6595 (pt)
REVERT: D   82 ARG cc_start: 0.6510 (mtt90) cc_final: 0.5415 (ptm160)
REVERT: D  190 MET cc_start: 0.7533 (mmt) cc_final: 0.7068 (mmt)
REVERT: D  356 LEU cc_start: 0.8365 (tt) cc_final: 0.7967 (tp)
REVERT: D  371 PHE cc_start: 0.4900 (p90) cc_final: 0.4676 (p90)
REVERT: E  218 CYS cc_start: 0.8389 (t) cc_final: 0.7408 (p)
REVERT: F  231 ARG cc_start: 0.8556 (ptt90) cc_final: 0.6622 (mmt90)
REVERT: F  308 TYR cc_start: 0.6277 (t80) cc_final: 0.6015 (t80)
REVERT: H   70 ILE cc_start: 0.7225 (OUTLIER) cc_final: 0.6598 (pt)
  outliers start: 72
  outliers final: 45
  residues processed: 348
  average time/residue: 0.1358
  time to fit residues: 72.3346
Evaluate side-chains
  313 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 266
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    7 THR
Chi-restraints excluded: chain R residue   62 THR
Chi-restraints excluded: chain R residue  223 THR
Chi-restraints excluded: chain R residue  246 ILE
Chi-restraints excluded: chain R residue  254 LEU
Chi-restraints excluded: chain R residue  305 LEU
Chi-restraints excluded: chain R residue  316 SER
Chi-restraints excluded: chain R residue  347 ILE
Chi-restraints excluded: chain R residue  388 LEU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue   39 GLN
Chi-restraints excluded: chain N residue   58 ILE
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue  223 THR
Chi-restraints excluded: chain D residue  246 ILE
Chi-restraints excluded: chain D residue  254 LEU
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  316 SER
Chi-restraints excluded: chain D residue  347 ILE
Chi-restraints excluded: chain D residue  388 LEU
Chi-restraints excluded: chain E residue   47 THR
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain E residue  173 THR
Chi-restraints excluded: chain E residue  245 SER
Chi-restraints excluded: chain E residue  317 CYS
Chi-restraints excluded: chain E residue  336 LEU
Chi-restraints excluded: chain F residue   45 LEU
Chi-restraints excluded: chain F residue  210 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   19 ARG
Chi-restraints excluded: chain H residue   39 GLN
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain I residue   36 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 72 optimal weight:    4.9990
   chunk 60 optimal weight:    9.9990
   chunk 116 optimal weight:   20.0000
   chunk 162 optimal weight:    0.9980
   chunk 186 optimal weight:    8.9990
   chunk 113 optimal weight:    0.0050
   chunk 142 optimal weight:    4.9990
   chunk 156 optimal weight:    6.9990
   chunk 144 optimal weight:    2.9990
   chunk 93 optimal weight:    9.9990
   chunk 69 optimal weight:    7.9990
   overall best weight:    2.8000

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

Flipped N/Q/H residues before XYZ refinement:
R  31 GLN
R  42 ASN
R  68 HIS
B 268 ASN
N  82 GLN
D  31 GLN
D  42 ASN
D  68 HIS
** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  88 ASN
E 225 HIS
E 268 ASN
H  82 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.175445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.152724 restraints weight = 19914.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.151466 restraints weight = 36971.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.148401 restraints weight = 27575.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.147140 restraints weight = 30752.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.146292 restraints weight = 26683.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.2593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  18028  Z= 0.224
  Angle     :  0.633   8.368  24408  Z= 0.341
  Chirality :  0.044   0.163   2692
  Planarity :  0.004   0.055   3106
  Dihedral  :  6.058  85.585   2430
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  6.86 %
    Allowed  : 20.68 %
    Favored  : 72.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.95 (0.17), residues: 2160
  helix:  0.85 (0.18), residues: 824
  sheet: -1.08 (0.24), residues: 420
  loop : -1.77 (0.18), residues: 916

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  14 
 TYR   0.035   0.002   TYR R 157 
 PHE   0.017   0.002   PHE B 292 
 TRP   0.025   0.002   TRP D 243 
 HIS   0.007   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00531 (18018)
  covalent geometry    : angle       0.63306 (24388)
  SS BOND              : bond        0.00584 (   10)
  SS BOND              : angle       0.97165 (   20)
  hydrogen bonds       : bond        0.05278 (  836)
  hydrogen bonds       : angle       4.70575 ( 2412)

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

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

  4320 Ramachandran restraints generated.
    2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4320 Ramachandran restraints generated.
    2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  406 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 131
    poor density    : 275
  time to evaluate  : 0.638 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P    8 ASP cc_start: 0.8953 (OUTLIER) cc_final: 0.8468 (t0)
REVERT: R   82 ARG cc_start: 0.6500 (mtt90) cc_final: 0.5500 (ptm160)
REVERT: R  190 MET cc_start: 0.7777 (mmt) cc_final: 0.7127 (mmt)
REVERT: R  356 LEU cc_start: 0.8678 (tt) cc_final: 0.8234 (tp)
REVERT: R  371 PHE cc_start: 0.4972 (p90) cc_final: 0.4758 (p90)
REVERT: B   66 ASP cc_start: 0.6687 (p0) cc_final: 0.6235 (p0)
REVERT: B  218 CYS cc_start: 0.8402 (t) cc_final: 0.7567 (p)
REVERT: B  258 ASP cc_start: 0.6554 (t0) cc_final: 0.6207 (t0)
REVERT: A  231 ARG cc_start: 0.8693 (ptt90) cc_final: 0.6905 (mmt90)
REVERT: A  338 ILE cc_start: 0.8509 (mm) cc_final: 0.8270 (mt)
REVERT: A  376 MET cc_start: 0.8246 (tmm) cc_final: 0.7370 (ttt)
REVERT: N   34 MET cc_start: 0.8623 (mmt) cc_final: 0.8381 (mmt)
REVERT: N   70 ILE cc_start: 0.7142 (OUTLIER) cc_final: 0.6515 (pt)
REVERT: N   77 ASN cc_start: 0.7243 (m-40) cc_final: 0.6819 (m-40)
REVERT: C    8 ASP cc_start: 0.8959 (OUTLIER) cc_final: 0.8474 (t0)
REVERT: D   82 ARG cc_start: 0.6507 (mtt90) cc_final: 0.5508 (ptm160)
REVERT: D  190 MET cc_start: 0.7786 (mmt) cc_final: 0.7131 (mmt)
REVERT: D  356 LEU cc_start: 0.8688 (tt) cc_final: 0.8240 (tp)
REVERT: D  371 PHE cc_start: 0.4873 (p90) cc_final: 0.4661 (p90)
REVERT: E   66 ASP cc_start: 0.6701 (p0) cc_final: 0.6244 (p0)
REVERT: E  218 CYS cc_start: 0.8395 (t) cc_final: 0.7560 (p)
REVERT: E  258 ASP cc_start: 0.6550 (t0) cc_final: 0.6207 (t0)
REVERT: F  231 ARG cc_start: 0.8687 (ptt90) cc_final: 0.6898 (mmt90)
REVERT: F  338 ILE cc_start: 0.8500 (mm) cc_final: 0.8264 (mt)
REVERT: F  376 MET cc_start: 0.8217 (tmm) cc_final: 0.7340 (ttt)
REVERT: H   34 MET cc_start: 0.8628 (mmt) cc_final: 0.8388 (mmt)
REVERT: H   70 ILE cc_start: 0.7154 (OUTLIER) cc_final: 0.6528 (pt)
REVERT: H   77 ASN cc_start: 0.7246 (m-40) cc_final: 0.6824 (m-40)
  outliers start: 131
  outliers final: 97
  residues processed: 362
  average time/residue: 0.1313
  time to fit residues: 74.2796
Evaluate side-chains
  367 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 101
    poor density    : 266
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    7 THR
Chi-restraints excluded: chain P residue    8 ASP
Chi-restraints excluded: chain P residue   19 VAL
Chi-restraints excluded: chain P residue   23 LEU
Chi-restraints excluded: chain R residue   62 THR
Chi-restraints excluded: chain R residue  223 THR
Chi-restraints excluded: chain R residue  246 ILE
Chi-restraints excluded: chain R residue  254 LEU
Chi-restraints excluded: chain R residue  255 LEU
Chi-restraints excluded: chain R residue  282 THR
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  305 LEU
Chi-restraints excluded: chain R residue  316 SER
Chi-restraints excluded: chain R residue  325 ILE
Chi-restraints excluded: chain R residue  328 ILE
Chi-restraints excluded: chain R residue  347 ILE
Chi-restraints excluded: chain R residue  359 ILE
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   16 ASN
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue   39 GLN
Chi-restraints excluded: chain N residue   58 ILE
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue   80 TYR
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue    8 ASP
Chi-restraints excluded: chain C residue   19 VAL
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue  223 THR
Chi-restraints excluded: chain D residue  246 ILE
Chi-restraints excluded: chain D residue  254 LEU
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  282 THR
Chi-restraints excluded: chain D residue  296 CYS
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  316 SER
Chi-restraints excluded: chain D residue  325 ILE
Chi-restraints excluded: chain D residue  328 ILE
Chi-restraints excluded: chain D residue  347 ILE
Chi-restraints excluded: chain D residue  359 ILE
Chi-restraints excluded: chain E residue    7 LEU
Chi-restraints excluded: chain E residue   16 ASN
Chi-restraints excluded: chain E residue   38 ASP
Chi-restraints excluded: chain E residue   47 THR
Chi-restraints excluded: chain E residue   65 THR
Chi-restraints excluded: chain E residue   70 LEU
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain E residue  157 ILE
Chi-restraints excluded: chain E residue  173 THR
Chi-restraints excluded: chain E residue  189 SER
Chi-restraints excluded: chain E residue  227 SER
Chi-restraints excluded: chain E residue  228 ASP
Chi-restraints excluded: chain E residue  233 CYS
Chi-restraints excluded: chain E residue  245 SER
Chi-restraints excluded: chain E residue  268 ASN
Chi-restraints excluded: chain E residue  317 CYS
Chi-restraints excluded: chain E residue  325 MET
Chi-restraints excluded: chain E residue  336 LEU
Chi-restraints excluded: chain F residue   45 LEU
Chi-restraints excluded: chain F residue   56 ILE
Chi-restraints excluded: chain F residue  210 THR
Chi-restraints excluded: chain F residue  217 VAL
Chi-restraints excluded: chain F residue  256 LEU
Chi-restraints excluded: chain F residue  277 VAL
Chi-restraints excluded: chain H residue   19 ARG
Chi-restraints excluded: chain H residue   39 GLN
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   80 TYR
Chi-restraints excluded: chain H residue  111 THR
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain I residue   36 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 7 optimal weight:    0.0980
   chunk 104 optimal weight:    6.9990
   chunk 45 optimal weight:    5.9990
   chunk 131 optimal weight:    3.9990
   chunk 112 optimal weight:   20.0000
   chunk 18 optimal weight:    0.5980
   chunk 71 optimal weight:    5.9990
   chunk 160 optimal weight:    0.4980
   chunk 207 optimal weight:    7.9990
   chunk 106 optimal weight:    8.9990
   chunk 167 optimal weight:    4.9990
   overall best weight:    2.0384

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

Flipped N/Q/H residues before XYZ refinement:
R  31 GLN
R  68 HIS
R 234 HIS
D  31 GLN
D  68 HIS
D 234 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.185832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.161166 restraints weight = 21139.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.160316 restraints weight = 46278.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.159873 restraints weight = 42098.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.158412 restraints weight = 30686.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.159027 restraints weight = 25637.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.2790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  18028  Z= 0.173
  Angle     :  0.582   7.916  24408  Z= 0.311
  Chirality :  0.042   0.145   2692
  Planarity :  0.004   0.052   3106
  Dihedral  :  5.866  83.844   2428
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 23.09 %
    Favored  : 70.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.79 (0.18), residues: 2160
  helix:  1.04 (0.18), residues: 824
  sheet: -1.00 (0.24), residues: 418
  loop : -1.75 (0.19), residues: 918

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  14 
 TYR   0.028   0.002   TYR R 157 
 PHE   0.029   0.002   PHE N  29 
 TRP   0.030   0.002   TRP A 271 
 HIS   0.005   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (18018)
  covalent geometry    : angle       0.58156 (24388)
  SS BOND              : bond        0.00289 (   10)
  SS BOND              : angle       0.97012 (   20)
  hydrogen bonds       : bond        0.04795 (  836)
  hydrogen bonds       : angle       4.56248 ( 2412)

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

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

  4320 Ramachandran restraints generated.
    2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4320 Ramachandran restraints generated.
    2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  385 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 116
    poor density    : 269
  time to evaluate  : 0.688 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: P    8 ASP cc_start: 0.8938 (OUTLIER) cc_final: 0.8725 (t0)
REVERT: R   82 ARG cc_start: 0.6429 (mtt90) cc_final: 0.5520 (ptm160)
REVERT: R   88 GLN cc_start: 0.3798 (OUTLIER) cc_final: 0.3535 (mt0)
REVERT: R  356 LEU cc_start: 0.8643 (tt) cc_final: 0.8174 (tp)
REVERT: R  371 PHE cc_start: 0.4945 (p90) cc_final: 0.4676 (p90)
REVERT: B   66 ASP cc_start: 0.6788 (p0) cc_final: 0.6434 (p0)
REVERT: B  218 CYS cc_start: 0.8325 (t) cc_final: 0.7764 (p)
REVERT: B  258 ASP cc_start: 0.6788 (t0) cc_final: 0.6485 (t0)
REVERT: B  268 ASN cc_start: 0.7352 (t0) cc_final: 0.7049 (t0)
REVERT: A  231 ARG cc_start: 0.8638 (ptt90) cc_final: 0.6750 (mmt90)
REVERT: A  338 ILE cc_start: 0.8457 (mm) cc_final: 0.8220 (mt)
REVERT: A  376 MET cc_start: 0.8132 (tmm) cc_final: 0.7179 (ttt)
REVERT: N   70 ILE cc_start: 0.7146 (OUTLIER) cc_final: 0.6484 (pt)
REVERT: C    8 ASP cc_start: 0.8972 (OUTLIER) cc_final: 0.8758 (t0)
REVERT: D   82 ARG cc_start: 0.6443 (mtt90) cc_final: 0.5528 (ptm160)
REVERT: D   88 GLN cc_start: 0.3787 (OUTLIER) cc_final: 0.3530 (mt0)
REVERT: D  356 LEU cc_start: 0.8653 (tt) cc_final: 0.8182 (tp)
REVERT: D  371 PHE cc_start: 0.4942 (p90) cc_final: 0.4677 (p90)
REVERT: E   66 ASP cc_start: 0.6793 (p0) cc_final: 0.6438 (p0)
REVERT: E  218 CYS cc_start: 0.8317 (t) cc_final: 0.7761 (p)
REVERT: E  258 ASP cc_start: 0.6777 (t0) cc_final: 0.6477 (t0)
REVERT: E  268 ASN cc_start: 0.7359 (t0) cc_final: 0.7049 (t0)
REVERT: F  231 ARG cc_start: 0.8631 (ptt90) cc_final: 0.6758 (mmt90)
REVERT: F  338 ILE cc_start: 0.8455 (mm) cc_final: 0.8216 (mt)
REVERT: F  376 MET cc_start: 0.8128 (tmm) cc_final: 0.7164 (ttt)
REVERT: H   70 ILE cc_start: 0.7145 (OUTLIER) cc_final: 0.6482 (pt)
  outliers start: 116
  outliers final: 84
  residues processed: 355
  average time/residue: 0.1382
  time to fit residues: 75.2756
Evaluate side-chains
  355 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 90
    poor density    : 265
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    7 THR
Chi-restraints excluded: chain P residue    8 ASP
Chi-restraints excluded: chain P residue   19 VAL
Chi-restraints excluded: chain P residue   23 LEU
Chi-restraints excluded: chain R residue   62 THR
Chi-restraints excluded: chain R residue   88 GLN
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  223 THR
Chi-restraints excluded: chain R residue  224 VAL
Chi-restraints excluded: chain R residue  239 SER
Chi-restraints excluded: chain R residue  246 ILE
Chi-restraints excluded: chain R residue  254 LEU
Chi-restraints excluded: chain R residue  255 LEU
Chi-restraints excluded: chain R residue  258 THR
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  305 LEU
Chi-restraints excluded: chain R residue  316 SER
Chi-restraints excluded: chain R residue  325 ILE
Chi-restraints excluded: chain R residue  328 ILE
Chi-restraints excluded: chain R residue  347 ILE
Chi-restraints excluded: chain R residue  364 ILE
Chi-restraints excluded: chain R residue  388 LEU
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   16 ASN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain N residue   58 ILE
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue    8 ASP
Chi-restraints excluded: chain C residue   19 VAL
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue   88 GLN
Chi-restraints excluded: chain D residue  205 ILE
Chi-restraints excluded: chain D residue  223 THR
Chi-restraints excluded: chain D residue  224 VAL
Chi-restraints excluded: chain D residue  239 SER
Chi-restraints excluded: chain D residue  246 ILE
Chi-restraints excluded: chain D residue  254 LEU
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  258 THR
Chi-restraints excluded: chain D residue  296 CYS
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  316 SER
Chi-restraints excluded: chain D residue  325 ILE
Chi-restraints excluded: chain D residue  328 ILE
Chi-restraints excluded: chain D residue  347 ILE
Chi-restraints excluded: chain D residue  364 ILE
Chi-restraints excluded: chain D residue  388 LEU
Chi-restraints excluded: chain E residue    7 LEU
Chi-restraints excluded: chain E residue   16 ASN
Chi-restraints excluded: chain E residue   47 THR
Chi-restraints excluded: chain E residue   65 THR
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain E residue  164 THR
Chi-restraints excluded: chain E residue  173 THR
Chi-restraints excluded: chain E residue  227 SER
Chi-restraints excluded: chain E residue  228 ASP
Chi-restraints excluded: chain E residue  233 CYS
Chi-restraints excluded: chain E residue  245 SER
Chi-restraints excluded: chain E residue  317 CYS
Chi-restraints excluded: chain E residue  336 LEU
Chi-restraints excluded: chain F residue   45 LEU
Chi-restraints excluded: chain F residue   56 ILE
Chi-restraints excluded: chain F residue  210 THR
Chi-restraints excluded: chain F residue  256 LEU
Chi-restraints excluded: chain F residue  277 VAL
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue  111 THR
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain I residue   36 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 214 optimal weight:    9.9990
   chunk 19 optimal weight:    1.9990
   chunk 6 optimal weight:   10.0000
   chunk 153 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9980
   chunk 137 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 196 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0070
   chunk 215 optimal weight:    0.0570
   chunk 184 optimal weight:    0.9990
   overall best weight:    0.5916

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

Flipped N/Q/H residues before XYZ refinement:
R  31 GLN
B 268 ASN
N  39 GLN
N  82 GLN
D  31 GLN
E 220 GLN
E 268 ASN
H  39 GLN
H  82 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.193172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.175593 restraints weight = 20870.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.173466 restraints weight = 41291.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.156755 restraints weight = 42518.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.152340 restraints weight = 31048.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.152157 restraints weight = 26821.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.3189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  18028  Z= 0.101
  Angle     :  0.506   6.940  24408  Z= 0.268
  Chirality :  0.040   0.133   2692
  Planarity :  0.004   0.047   3106
  Dihedral  :  5.420  83.533   2428
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 24.66 %
    Favored  : 70.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.18), residues: 2160
  helix:  1.54 (0.18), residues: 824
  sheet: -0.58 (0.25), residues: 424
  loop : -1.66 (0.19), residues: 912

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 379 
 TYR   0.017   0.001   TYR R 157 
 PHE   0.018   0.001   PHE N  29 
 TRP   0.017   0.001   TRP A 271 
 HIS   0.002   0.000   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 (18018)
  covalent geometry    : angle       0.50558 (24388)
  SS BOND              : bond        0.00109 (   10)
  SS BOND              : angle       0.90061 (   20)
  hydrogen bonds       : bond        0.03913 (  836)
  hydrogen bonds       : angle       4.15819 ( 2412)

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

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

  4320 Ramachandran restraints generated.
    2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4320 Ramachandran restraints generated.
    2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  364 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 87
    poor density    : 277
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   82 ARG cc_start: 0.6228 (mtt90) cc_final: 0.5099 (ptm160)
REVERT: R  190 MET cc_start: 0.7421 (mmt) cc_final: 0.6911 (mmt)
REVERT: R  328 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8494 (tp)
REVERT: R  356 LEU cc_start: 0.8538 (tt) cc_final: 0.8083 (tp)
REVERT: B   66 ASP cc_start: 0.6894 (p0) cc_final: 0.6535 (p0)
REVERT: B  218 CYS cc_start: 0.8433 (t) cc_final: 0.7793 (p)
REVERT: B  235 PHE cc_start: 0.6039 (OUTLIER) cc_final: 0.4869 (t80)
REVERT: B  258 ASP cc_start: 0.6783 (t0) cc_final: 0.6471 (t0)
REVERT: B  268 ASN cc_start: 0.7522 (OUTLIER) cc_final: 0.7131 (t0)
REVERT: A  231 ARG cc_start: 0.8615 (ptt90) cc_final: 0.6905 (mmt90)
REVERT: A  308 TYR cc_start: 0.6115 (t80) cc_final: 0.5896 (t80)
REVERT: N   19 ARG cc_start: 0.6817 (OUTLIER) cc_final: 0.5457 (tmm-80)
REVERT: N   70 ILE cc_start: 0.7051 (OUTLIER) cc_final: 0.6432 (pt)
REVERT: N   83 MET cc_start: 0.7385 (mtm) cc_final: 0.7182 (ptp)
REVERT: D   82 ARG cc_start: 0.6258 (mtt90) cc_final: 0.5116 (ptm160)
REVERT: D  190 MET cc_start: 0.7401 (mmt) cc_final: 0.6899 (mmt)
REVERT: D  328 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8493 (tp)
REVERT: D  356 LEU cc_start: 0.8536 (tt) cc_final: 0.8079 (tp)
REVERT: E  218 CYS cc_start: 0.8420 (t) cc_final: 0.7796 (p)
REVERT: E  249 THR cc_start: 0.8627 (p) cc_final: 0.8424 (p)
REVERT: E  258 ASP cc_start: 0.6776 (t0) cc_final: 0.6465 (t0)
REVERT: E  268 ASN cc_start: 0.7518 (OUTLIER) cc_final: 0.7127 (t0)
REVERT: F  231 ARG cc_start: 0.8606 (ptt90) cc_final: 0.6907 (mmt90)
REVERT: F  308 TYR cc_start: 0.6118 (t80) cc_final: 0.5898 (t80)
REVERT: H   19 ARG cc_start: 0.6788 (OUTLIER) cc_final: 0.5520 (tmm-80)
REVERT: H   70 ILE cc_start: 0.7063 (OUTLIER) cc_final: 0.6435 (pt)
  outliers start: 87
  outliers final: 65
  residues processed: 343
  average time/residue: 0.1374
  time to fit residues: 72.0179
Evaluate side-chains
  337 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 263
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    8 ASP
Chi-restraints excluded: chain P residue   23 LEU
Chi-restraints excluded: chain R residue   62 THR
Chi-restraints excluded: chain R residue  223 THR
Chi-restraints excluded: chain R residue  239 SER
Chi-restraints excluded: chain R residue  255 LEU
Chi-restraints excluded: chain R residue  258 THR
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  305 LEU
Chi-restraints excluded: chain R residue  316 SER
Chi-restraints excluded: chain R residue  328 ILE
Chi-restraints excluded: chain R residue  347 ILE
Chi-restraints excluded: chain R residue  364 ILE
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  240 ASP
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue   39 GLN
Chi-restraints excluded: chain N residue   58 ILE
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain C residue    8 ASP
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue  223 THR
Chi-restraints excluded: chain D residue  239 SER
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  258 THR
Chi-restraints excluded: chain D residue  296 CYS
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  316 SER
Chi-restraints excluded: chain D residue  328 ILE
Chi-restraints excluded: chain D residue  347 ILE
Chi-restraints excluded: chain D residue  364 ILE
Chi-restraints excluded: chain E residue    7 LEU
Chi-restraints excluded: chain E residue   38 ASP
Chi-restraints excluded: chain E residue   47 THR
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain E residue  164 THR
Chi-restraints excluded: chain E residue  173 THR
Chi-restraints excluded: chain E residue  228 ASP
Chi-restraints excluded: chain E residue  233 CYS
Chi-restraints excluded: chain E residue  268 ASN
Chi-restraints excluded: chain E residue  300 LEU
Chi-restraints excluded: chain E residue  317 CYS
Chi-restraints excluded: chain E residue  336 LEU
Chi-restraints excluded: chain F residue   45 LEU
Chi-restraints excluded: chain F residue  210 THR
Chi-restraints excluded: chain F residue  240 ASP
Chi-restraints excluded: chain F residue  256 LEU
Chi-restraints excluded: chain H residue   19 ARG
Chi-restraints excluded: chain H residue   39 GLN
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue  111 THR
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain I residue   36 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 5 optimal weight:    7.9990
   chunk 140 optimal weight:    0.8980
   chunk 107 optimal weight:    0.0270
   chunk 78 optimal weight:    9.9990
   chunk 110 optimal weight:    5.9990
   chunk 57 optimal weight:    8.9990
   chunk 141 optimal weight:    0.5980
   chunk 179 optimal weight:    1.9990
   chunk 181 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.6638

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

Flipped N/Q/H residues before XYZ refinement:
R  31 GLN
R  68 HIS
B  75 GLN
B 225 HIS
N  39 GLN
D  31 GLN
D  68 HIS
E  75 GLN
E 225 HIS
H  39 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.193530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.167678 restraints weight = 20799.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.164941 restraints weight = 41639.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.164833 restraints weight = 41139.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.163940 restraints weight = 26660.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.164975 restraints weight = 23027.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.3326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  18028  Z= 0.103
  Angle     :  0.529  11.478  24408  Z= 0.276
  Chirality :  0.040   0.183   2692
  Planarity :  0.003   0.047   3106
  Dihedral  :  5.332  83.609   2428
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 25.13 %
    Favored  : 70.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.15 (0.18), residues: 2160
  helix:  1.65 (0.18), residues: 836
  sheet: -0.51 (0.25), residues: 424
  loop : -1.60 (0.19), residues: 900

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  14 
 TYR   0.017   0.001   TYR R 157 
 PHE   0.021   0.001   PHE N 108 
 TRP   0.017   0.001   TRP A 271 
 HIS   0.005   0.001   HIS E 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (18018)
  covalent geometry    : angle       0.52541 (24388)
  SS BOND              : bond        0.00302 (   10)
  SS BOND              : angle       2.27930 (   20)
  hydrogen bonds       : bond        0.03893 (  836)
  hydrogen bonds       : angle       4.09897 ( 2412)

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

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

  4320 Ramachandran restraints generated.
    2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4320 Ramachandran restraints generated.
    2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  360 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 274
  time to evaluate  : 0.673 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   82 ARG cc_start: 0.6522 (mtt90) cc_final: 0.5479 (ptm160)
REVERT: R  190 MET cc_start: 0.7148 (mmt) cc_final: 0.6675 (mmt)
REVERT: R  356 LEU cc_start: 0.8378 (tt) cc_final: 0.7909 (tp)
REVERT: B   66 ASP cc_start: 0.6541 (p0) cc_final: 0.6248 (p0)
REVERT: B  218 CYS cc_start: 0.8207 (t) cc_final: 0.7531 (p)
REVERT: B  233 CYS cc_start: 0.6533 (m) cc_final: 0.5995 (m)
REVERT: B  258 ASP cc_start: 0.6673 (t0) cc_final: 0.6432 (t0)
REVERT: B  268 ASN cc_start: 0.7200 (t0) cc_final: 0.6869 (t0)
REVERT: A  231 ARG cc_start: 0.8623 (ptt90) cc_final: 0.6858 (mmt90)
REVERT: A  308 TYR cc_start: 0.6310 (t80) cc_final: 0.6107 (t80)
REVERT: N   19 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.5636 (tmm-80)
REVERT: N   70 ILE cc_start: 0.7237 (OUTLIER) cc_final: 0.6540 (pt)
REVERT: N   83 MET cc_start: 0.6832 (mtm) cc_final: 0.6308 (ptp)
REVERT: D   82 ARG cc_start: 0.6533 (mtt90) cc_final: 0.5489 (ptm160)
REVERT: D  190 MET cc_start: 0.7142 (mmt) cc_final: 0.6674 (mmt)
REVERT: D  356 LEU cc_start: 0.8375 (tt) cc_final: 0.7907 (tp)
REVERT: E   66 ASP cc_start: 0.6549 (p0) cc_final: 0.6231 (p0)
REVERT: E  218 CYS cc_start: 0.8207 (t) cc_final: 0.7531 (p)
REVERT: E  233 CYS cc_start: 0.6544 (m) cc_final: 0.5993 (m)
REVERT: E  235 PHE cc_start: 0.6539 (OUTLIER) cc_final: 0.5395 (t80)
REVERT: E  258 ASP cc_start: 0.6677 (t0) cc_final: 0.6394 (t0)
REVERT: E  268 ASN cc_start: 0.7205 (t0) cc_final: 0.6870 (t0)
REVERT: F  231 ARG cc_start: 0.8603 (ptt90) cc_final: 0.6810 (mmt90)
REVERT: H   19 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.5613 (tmm-80)
REVERT: H   70 ILE cc_start: 0.7168 (OUTLIER) cc_final: 0.6523 (pt)
  outliers start: 86
  outliers final: 68
  residues processed: 340
  average time/residue: 0.1401
  time to fit residues: 72.4098
Evaluate side-chains
  339 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 266
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    8 ASP
Chi-restraints excluded: chain P residue   23 LEU
Chi-restraints excluded: chain R residue   62 THR
Chi-restraints excluded: chain R residue  157 TYR
Chi-restraints excluded: chain R residue  223 THR
Chi-restraints excluded: chain R residue  239 SER
Chi-restraints excluded: chain R residue  255 LEU
Chi-restraints excluded: chain R residue  258 THR
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  305 LEU
Chi-restraints excluded: chain R residue  316 SER
Chi-restraints excluded: chain R residue  325 ILE
Chi-restraints excluded: chain R residue  347 ILE
Chi-restraints excluded: chain R residue  364 ILE
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  240 ASP
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue   39 GLN
Chi-restraints excluded: chain N residue   58 ILE
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain C residue    8 ASP
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue  157 TYR
Chi-restraints excluded: chain D residue  223 THR
Chi-restraints excluded: chain D residue  239 SER
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  258 THR
Chi-restraints excluded: chain D residue  296 CYS
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  316 SER
Chi-restraints excluded: chain D residue  325 ILE
Chi-restraints excluded: chain D residue  347 ILE
Chi-restraints excluded: chain D residue  364 ILE
Chi-restraints excluded: chain E residue    7 LEU
Chi-restraints excluded: chain E residue   38 ASP
Chi-restraints excluded: chain E residue   47 THR
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain E residue  164 THR
Chi-restraints excluded: chain E residue  173 THR
Chi-restraints excluded: chain E residue  189 SER
Chi-restraints excluded: chain E residue  228 ASP
Chi-restraints excluded: chain E residue  235 PHE
Chi-restraints excluded: chain E residue  300 LEU
Chi-restraints excluded: chain E residue  317 CYS
Chi-restraints excluded: chain E residue  336 LEU
Chi-restraints excluded: chain F residue   45 LEU
Chi-restraints excluded: chain F residue  210 THR
Chi-restraints excluded: chain F residue  240 ASP
Chi-restraints excluded: chain F residue  256 LEU
Chi-restraints excluded: chain H residue   19 ARG
Chi-restraints excluded: chain H residue   39 GLN
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue  111 THR
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain I residue   36 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 123 optimal weight:    2.9990
   chunk 213 optimal weight:    8.9990
   chunk 96 optimal weight:   10.0000
   chunk 130 optimal weight:    2.9990
   chunk 119 optimal weight:    0.8980
   chunk 84 optimal weight:    5.9990
   chunk 129 optimal weight:    0.9990
   chunk 64 optimal weight:    7.9990
   chunk 43 optimal weight:    4.9990
   chunk 150 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
R  31 GLN
R 146 GLN
R 300 ASN
G  11 GLN
D  31 GLN
D 300 ASN
** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  82 GLN
I  11 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.186172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.169777 restraints weight = 21052.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.168751 restraints weight = 43547.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.165994 restraints weight = 34999.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.162382 restraints weight = 42090.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.161360 restraints weight = 40423.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.3182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  18028  Z= 0.195
  Angle     :  0.612   7.538  24408  Z= 0.324
  Chirality :  0.043   0.174   2692
  Planarity :  0.004   0.052   3106
  Dihedral  :  5.769  87.382   2428
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 24.71 %
    Favored  : 69.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.37 (0.18), residues: 2160
  helix:  1.42 (0.18), residues: 824
  sheet: -0.83 (0.24), residues: 442
  loop : -1.52 (0.19), residues: 894

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  96 
 TYR   0.032   0.002   TYR D 157 
 PHE   0.014   0.002   PHE H  29 
 TRP   0.023   0.002   TRP R 243 
 HIS   0.002   0.001   HIS I  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 (18018)
  covalent geometry    : angle       0.61052 (24388)
  SS BOND              : bond        0.00485 (   10)
  SS BOND              : angle       1.69773 (   20)
  hydrogen bonds       : bond        0.04846 (  836)
  hydrogen bonds       : angle       4.37687 ( 2412)

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

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

  4320 Ramachandran restraints generated.
    2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4320 Ramachandran restraints generated.
    2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  367 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 102
    poor density    : 265
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: P    8 ASP cc_start: 0.9032 (OUTLIER) cc_final: 0.8396 (t0)
REVERT: R   82 ARG cc_start: 0.6407 (mtt90) cc_final: 0.5649 (ptm160)
REVERT: R   88 GLN cc_start: 0.3504 (OUTLIER) cc_final: 0.3206 (mt0)
REVERT: R  190 MET cc_start: 0.7445 (mmt) cc_final: 0.6943 (mmt)
REVERT: R  300 ASN cc_start: 0.7845 (m110) cc_final: 0.7439 (m110)
REVERT: R  356 LEU cc_start: 0.8600 (tt) cc_final: 0.8118 (tp)
REVERT: B   42 ARG cc_start: 0.7021 (tpp80) cc_final: 0.6667 (tpp80)
REVERT: B   66 ASP cc_start: 0.6367 (p0) cc_final: 0.6108 (p0)
REVERT: B  218 CYS cc_start: 0.8186 (t) cc_final: 0.7472 (p)
REVERT: B  233 CYS cc_start: 0.6505 (m) cc_final: 0.6038 (m)
REVERT: B  235 PHE cc_start: 0.6725 (OUTLIER) cc_final: 0.5607 (t80)
REVERT: B  251 ARG cc_start: 0.7903 (mtt180) cc_final: 0.7676 (mtt180)
REVERT: A  231 ARG cc_start: 0.8760 (ptt90) cc_final: 0.7140 (mmt90)
REVERT: A  308 TYR cc_start: 0.6280 (t80) cc_final: 0.6079 (t80)
REVERT: A  376 MET cc_start: 0.8120 (tmm) cc_final: 0.7217 (ttt)
REVERT: N   19 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.5812 (tmm-80)
REVERT: N   70 ILE cc_start: 0.7338 (OUTLIER) cc_final: 0.6633 (pt)
REVERT: N   83 MET cc_start: 0.6630 (mtm) cc_final: 0.6364 (ptp)
REVERT: C    8 ASP cc_start: 0.9012 (OUTLIER) cc_final: 0.8373 (t0)
REVERT: D   82 ARG cc_start: 0.6414 (mtt90) cc_final: 0.5657 (ptm160)
REVERT: D   88 GLN cc_start: 0.3498 (OUTLIER) cc_final: 0.3198 (mt0)
REVERT: D  190 MET cc_start: 0.7471 (mmt) cc_final: 0.6965 (mmt)
REVERT: D  300 ASN cc_start: 0.7814 (m110) cc_final: 0.7410 (m110)
REVERT: D  356 LEU cc_start: 0.8598 (tt) cc_final: 0.8116 (tp)
REVERT: E   42 ARG cc_start: 0.7022 (tpp80) cc_final: 0.6668 (tpp80)
REVERT: E   66 ASP cc_start: 0.6373 (p0) cc_final: 0.6112 (p0)
REVERT: E  218 CYS cc_start: 0.8176 (t) cc_final: 0.7477 (p)
REVERT: E  233 CYS cc_start: 0.6503 (OUTLIER) cc_final: 0.6029 (m)
REVERT: E  235 PHE cc_start: 0.6717 (OUTLIER) cc_final: 0.5594 (t80)
REVERT: E  258 ASP cc_start: 0.6682 (t0) cc_final: 0.6476 (t0)
REVERT: F  231 ARG cc_start: 0.8777 (ptt90) cc_final: 0.7209 (mmt90)
REVERT: F  376 MET cc_start: 0.8113 (tmm) cc_final: 0.7201 (ttt)
REVERT: H   19 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.5757 (tmm-80)
REVERT: H   70 ILE cc_start: 0.7234 (OUTLIER) cc_final: 0.6576 (pt)
  outliers start: 102
  outliers final: 82
  residues processed: 341
  average time/residue: 0.1378
  time to fit residues: 72.3544
Evaluate side-chains
  354 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 93
    poor density    : 261
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    7 THR
Chi-restraints excluded: chain P residue    8 ASP
Chi-restraints excluded: chain P residue   19 VAL
Chi-restraints excluded: chain P residue   23 LEU
Chi-restraints excluded: chain R residue   62 THR
Chi-restraints excluded: chain R residue   88 GLN
Chi-restraints excluded: chain R residue  223 THR
Chi-restraints excluded: chain R residue  231 VAL
Chi-restraints excluded: chain R residue  236 CYS
Chi-restraints excluded: chain R residue  239 SER
Chi-restraints excluded: chain R residue  246 ILE
Chi-restraints excluded: chain R residue  255 LEU
Chi-restraints excluded: chain R residue  258 THR
Chi-restraints excluded: chain R residue  282 THR
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  305 LEU
Chi-restraints excluded: chain R residue  316 SER
Chi-restraints excluded: chain R residue  325 ILE
Chi-restraints excluded: chain R residue  347 ILE
Chi-restraints excluded: chain R residue  364 ILE
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  240 ASP
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue   58 ILE
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue    8 ASP
Chi-restraints excluded: chain C residue   19 VAL
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue   88 GLN
Chi-restraints excluded: chain D residue  223 THR
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain D residue  236 CYS
Chi-restraints excluded: chain D residue  239 SER
Chi-restraints excluded: chain D residue  246 ILE
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  258 THR
Chi-restraints excluded: chain D residue  282 THR
Chi-restraints excluded: chain D residue  296 CYS
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  316 SER
Chi-restraints excluded: chain D residue  325 ILE
Chi-restraints excluded: chain D residue  347 ILE
Chi-restraints excluded: chain D residue  364 ILE
Chi-restraints excluded: chain E residue    7 LEU
Chi-restraints excluded: chain E residue   38 ASP
Chi-restraints excluded: chain E residue   47 THR
Chi-restraints excluded: chain E residue   65 THR
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain E residue  157 ILE
Chi-restraints excluded: chain E residue  161 SER
Chi-restraints excluded: chain E residue  164 THR
Chi-restraints excluded: chain E residue  173 THR
Chi-restraints excluded: chain E residue  189 SER
Chi-restraints excluded: chain E residue  228 ASP
Chi-restraints excluded: chain E residue  233 CYS
Chi-restraints excluded: chain E residue  235 PHE
Chi-restraints excluded: chain E residue  300 LEU
Chi-restraints excluded: chain E residue  317 CYS
Chi-restraints excluded: chain E residue  336 LEU
Chi-restraints excluded: chain F residue   45 LEU
Chi-restraints excluded: chain F residue  210 THR
Chi-restraints excluded: chain F residue  240 ASP
Chi-restraints excluded: chain F residue  256 LEU
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   19 ARG
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue  111 THR
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain I residue   36 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 182 optimal weight:    0.9990
   chunk 106 optimal weight:    5.9990
   chunk 151 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0970
   chunk 42 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 77 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 115 optimal weight:    7.9990
   chunk 204 optimal weight:    9.9990
   chunk 187 optimal weight:    0.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
R  31 GLN
B 220 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  31 GLN
** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 220 HIS ** 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 = 0.4110 r_free = 0.4110 target = 0.192194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 90)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.158450 restraints weight = 20859.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.152747 restraints weight = 26325.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.153012 restraints weight = 25969.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.153464 restraints weight = 21407.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.153603 restraints weight = 18695.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.3467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  18028  Z= 0.110
  Angle     :  0.541   8.046  24408  Z= 0.283
  Chirality :  0.040   0.165   2692
  Planarity :  0.004   0.048   3106
  Dihedral  :  5.453  85.803   2428
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 25.60 %
    Favored  : 69.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.16 (0.18), residues: 2160
  helix:  1.61 (0.18), residues: 838
  sheet: -0.65 (0.24), residues: 442
  loop : -1.51 (0.19), residues: 880

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  96 
 TYR   0.022   0.001   TYR F 308 
 PHE   0.013   0.001   PHE H  29 
 TRP   0.012   0.001   TRP A 271 
 HIS   0.003   0.000   HIS E 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (18018)
  covalent geometry    : angle       0.53883 (24388)
  SS BOND              : bond        0.00384 (   10)
  SS BOND              : angle       1.68189 (   20)
  hydrogen bonds       : bond        0.04035 (  836)
  hydrogen bonds       : angle       4.10374 ( 2412)

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

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

  4320 Ramachandran restraints generated.
    2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4320 Ramachandran restraints generated.
    2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  359 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 271
  time to evaluate  : 0.677 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   82 ARG cc_start: 0.6428 (mtt90) cc_final: 0.5272 (ptm160)
REVERT: R  190 MET cc_start: 0.7185 (mmt) cc_final: 0.6730 (mmt)
REVERT: R  356 LEU cc_start: 0.8549 (tt) cc_final: 0.8133 (tp)
REVERT: B   42 ARG cc_start: 0.6847 (tpp80) cc_final: 0.6511 (tpp80)
REVERT: B   66 ASP cc_start: 0.6516 (p0) cc_final: 0.6280 (p0)
REVERT: B  218 CYS cc_start: 0.8337 (t) cc_final: 0.7667 (p)
REVERT: B  233 CYS cc_start: 0.6553 (m) cc_final: 0.5922 (m)
REVERT: B  235 PHE cc_start: 0.6392 (OUTLIER) cc_final: 0.5192 (t80)
REVERT: B  251 ARG cc_start: 0.7832 (mtt180) cc_final: 0.7476 (mtt180)
REVERT: A  231 ARG cc_start: 0.8672 (ptt90) cc_final: 0.6985 (mmt90)
REVERT: A  308 TYR cc_start: 0.6326 (t80) cc_final: 0.6054 (t80)
REVERT: A  376 MET cc_start: 0.8096 (tmm) cc_final: 0.7035 (ttt)
REVERT: N   19 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.5647 (tmm-80)
REVERT: N   70 ILE cc_start: 0.7217 (OUTLIER) cc_final: 0.6557 (pt)
REVERT: D   82 ARG cc_start: 0.6428 (mtt90) cc_final: 0.5276 (ptm160)
REVERT: D  190 MET cc_start: 0.7210 (mmt) cc_final: 0.6751 (mmt)
REVERT: D  356 LEU cc_start: 0.8534 (tt) cc_final: 0.8113 (tp)
REVERT: E   42 ARG cc_start: 0.6850 (tpp80) cc_final: 0.6514 (tpp80)
REVERT: E   66 ASP cc_start: 0.6522 (p0) cc_final: 0.6277 (p0)
REVERT: E  218 CYS cc_start: 0.8349 (t) cc_final: 0.7649 (p)
REVERT: E  233 CYS cc_start: 0.6535 (m) cc_final: 0.5919 (m)
REVERT: E  235 PHE cc_start: 0.6389 (OUTLIER) cc_final: 0.5185 (t80)
REVERT: E  258 ASP cc_start: 0.6775 (t0) cc_final: 0.6511 (t0)
REVERT: F  231 ARG cc_start: 0.8662 (ptt90) cc_final: 0.6964 (mmt90)
REVERT: F  260 LEU cc_start: 0.8364 (mt) cc_final: 0.8156 (mm)
REVERT: F  376 MET cc_start: 0.8102 (tmm) cc_final: 0.7085 (ttt)
REVERT: H   19 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.5540 (tmm-80)
REVERT: H   70 ILE cc_start: 0.7131 (OUTLIER) cc_final: 0.6579 (pt)
  outliers start: 88
  outliers final: 75
  residues processed: 336
  average time/residue: 0.1382
  time to fit residues: 71.7241
Evaluate side-chains
  345 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 264
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    7 THR
Chi-restraints excluded: chain P residue    8 ASP
Chi-restraints excluded: chain P residue   23 LEU
Chi-restraints excluded: chain R residue   62 THR
Chi-restraints excluded: chain R residue  223 THR
Chi-restraints excluded: chain R residue  231 VAL
Chi-restraints excluded: chain R residue  239 SER
Chi-restraints excluded: chain R residue  246 ILE
Chi-restraints excluded: chain R residue  255 LEU
Chi-restraints excluded: chain R residue  258 THR
Chi-restraints excluded: chain R residue  282 THR
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  305 LEU
Chi-restraints excluded: chain R residue  316 SER
Chi-restraints excluded: chain R residue  347 ILE
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  240 ASP
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue   39 GLN
Chi-restraints excluded: chain N residue   58 ILE
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue    8 ASP
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue  223 THR
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain D residue  239 SER
Chi-restraints excluded: chain D residue  246 ILE
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  258 THR
Chi-restraints excluded: chain D residue  282 THR
Chi-restraints excluded: chain D residue  296 CYS
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  316 SER
Chi-restraints excluded: chain D residue  347 ILE
Chi-restraints excluded: chain E residue    7 LEU
Chi-restraints excluded: chain E residue   38 ASP
Chi-restraints excluded: chain E residue   47 THR
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain E residue  157 ILE
Chi-restraints excluded: chain E residue  161 SER
Chi-restraints excluded: chain E residue  164 THR
Chi-restraints excluded: chain E residue  173 THR
Chi-restraints excluded: chain E residue  189 SER
Chi-restraints excluded: chain E residue  228 ASP
Chi-restraints excluded: chain E residue  235 PHE
Chi-restraints excluded: chain E residue  300 LEU
Chi-restraints excluded: chain E residue  317 CYS
Chi-restraints excluded: chain E residue  336 LEU
Chi-restraints excluded: chain F residue   45 LEU
Chi-restraints excluded: chain F residue  210 THR
Chi-restraints excluded: chain F residue  240 ASP
Chi-restraints excluded: chain F residue  256 LEU
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   19 ARG
Chi-restraints excluded: chain H residue   39 GLN
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue  111 THR
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain I residue   36 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 105 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   chunk 136 optimal weight:    0.0470
   chunk 178 optimal weight:    3.9990
   chunk 177 optimal weight:    9.9990
   chunk 211 optimal weight:    0.9980
   chunk 154 optimal weight:    0.9980
   chunk 150 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 8 optimal weight:   20.0000
   chunk 145 optimal weight:   20.0000
   overall best weight:    1.0082

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

Flipped N/Q/H residues before XYZ refinement:
R  31 GLN
** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  31 GLN
** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 268 ASN
** F 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.191491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.173409 restraints weight = 20797.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.172153 restraints weight = 40931.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.163640 restraints weight = 38850.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.156540 restraints weight = 31947.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.155629 restraints weight = 31931.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.3569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  18028  Z= 0.119
  Angle     :  0.548   8.133  24408  Z= 0.288
  Chirality :  0.041   0.164   2692
  Planarity :  0.004   0.048   3106
  Dihedral  :  5.434  87.375   2428
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 26.07 %
    Favored  : 69.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.18), residues: 2160
  helix:  1.68 (0.18), residues: 838
  sheet: -0.61 (0.24), residues: 430
  loop : -1.50 (0.19), residues: 892

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 379 
 TYR   0.023   0.001   TYR F 308 
 PHE   0.014   0.001   PHE N  29 
 TRP   0.019   0.002   TRP A 271 
 HIS   0.003   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (18018)
  covalent geometry    : angle       0.54681 (24388)
  SS BOND              : bond        0.00182 (   10)
  SS BOND              : angle       1.56447 (   20)
  hydrogen bonds       : bond        0.04073 (  836)
  hydrogen bonds       : angle       4.12202 ( 2412)

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

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

  4320 Ramachandran restraints generated.
    2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4320 Ramachandran restraints generated.
    2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  351 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 265
  time to evaluate  : 0.685 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   82 ARG cc_start: 0.6451 (mtt90) cc_final: 0.5291 (ptm160)
REVERT: R  190 MET cc_start: 0.7231 (mmt) cc_final: 0.6758 (mmt)
REVERT: R  356 LEU cc_start: 0.8534 (tt) cc_final: 0.8114 (tp)
REVERT: B   42 ARG cc_start: 0.6855 (tpp80) cc_final: 0.6570 (tpp80)
REVERT: B   66 ASP cc_start: 0.6603 (p0) cc_final: 0.6327 (p0)
REVERT: B  190 LEU cc_start: 0.8942 (mt) cc_final: 0.8664 (mt)
REVERT: B  218 CYS cc_start: 0.8277 (t) cc_final: 0.7612 (p)
REVERT: B  233 CYS cc_start: 0.6644 (m) cc_final: 0.6286 (m)
REVERT: B  235 PHE cc_start: 0.6494 (OUTLIER) cc_final: 0.5295 (t80)
REVERT: B  268 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7750 (t0)
REVERT: A  231 ARG cc_start: 0.8638 (ptt90) cc_final: 0.6899 (mmt90)
REVERT: A  308 TYR cc_start: 0.6322 (t80) cc_final: 0.6074 (t80)
REVERT: A  376 MET cc_start: 0.8082 (tmm) cc_final: 0.7053 (ttt)
REVERT: N   19 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.5579 (tmm-80)
REVERT: N   70 ILE cc_start: 0.7182 (OUTLIER) cc_final: 0.6568 (pt)
REVERT: D   82 ARG cc_start: 0.6434 (mtt90) cc_final: 0.5285 (ptm160)
REVERT: D  190 MET cc_start: 0.7243 (mmt) cc_final: 0.6785 (mmt)
REVERT: D  356 LEU cc_start: 0.8543 (tt) cc_final: 0.8129 (tp)
REVERT: E   42 ARG cc_start: 0.6849 (tpp80) cc_final: 0.6565 (tpp80)
REVERT: E   66 ASP cc_start: 0.6603 (p0) cc_final: 0.6324 (p0)
REVERT: E  190 LEU cc_start: 0.8949 (mt) cc_final: 0.8669 (mt)
REVERT: E  218 CYS cc_start: 0.8295 (t) cc_final: 0.7614 (p)
REVERT: E  233 CYS cc_start: 0.6821 (m) cc_final: 0.6483 (m)
REVERT: E  235 PHE cc_start: 0.6498 (OUTLIER) cc_final: 0.5306 (t80)
REVERT: E  258 ASP cc_start: 0.6778 (t0) cc_final: 0.6545 (t0)
REVERT: E  268 ASN cc_start: 0.8126 (OUTLIER) cc_final: 0.7769 (t0)
REVERT: F  231 ARG cc_start: 0.8559 (ptt90) cc_final: 0.6910 (mmt90)
REVERT: F  376 MET cc_start: 0.8062 (tmm) cc_final: 0.7014 (ttt)
REVERT: H   19 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.5602 (tmm-80)
REVERT: H   70 ILE cc_start: 0.7181 (OUTLIER) cc_final: 0.6502 (pt)
REVERT: H   83 MET cc_start: 0.7203 (mpp) cc_final: 0.6510 (ptp)
  outliers start: 86
  outliers final: 76
  residues processed: 329
  average time/residue: 0.1362
  time to fit residues: 68.9436
Evaluate side-chains
  346 residues out of total 1912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 84
    poor density    : 262
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    7 THR
Chi-restraints excluded: chain P residue    8 ASP
Chi-restraints excluded: chain P residue   23 LEU
Chi-restraints excluded: chain R residue   62 THR
Chi-restraints excluded: chain R residue  223 THR
Chi-restraints excluded: chain R residue  231 VAL
Chi-restraints excluded: chain R residue  239 SER
Chi-restraints excluded: chain R residue  255 LEU
Chi-restraints excluded: chain R residue  258 THR
Chi-restraints excluded: chain R residue  282 THR
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  305 LEU
Chi-restraints excluded: chain R residue  316 SER
Chi-restraints excluded: chain R residue  347 ILE
Chi-restraints excluded: chain R residue  376 VAL
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  235 PHE
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  240 ASP
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain N residue   19 ARG
Chi-restraints excluded: chain N residue   39 GLN
Chi-restraints excluded: chain N residue   58 ILE
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain C residue    7 THR
Chi-restraints excluded: chain C residue    8 ASP
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue  223 THR
Chi-restraints excluded: chain D residue  231 VAL
Chi-restraints excluded: chain D residue  239 SER
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  258 THR
Chi-restraints excluded: chain D residue  282 THR
Chi-restraints excluded: chain D residue  296 CYS
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  316 SER
Chi-restraints excluded: chain D residue  347 ILE
Chi-restraints excluded: chain D residue  376 VAL
Chi-restraints excluded: chain E residue    7 LEU
Chi-restraints excluded: chain E residue   38 ASP
Chi-restraints excluded: chain E residue   47 THR
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain E residue  157 ILE
Chi-restraints excluded: chain E residue  161 SER
Chi-restraints excluded: chain E residue  164 THR
Chi-restraints excluded: chain E residue  173 THR
Chi-restraints excluded: chain E residue  189 SER
Chi-restraints excluded: chain E residue  228 ASP
Chi-restraints excluded: chain E residue  235 PHE
Chi-restraints excluded: chain E residue  268 ASN
Chi-restraints excluded: chain E residue  300 LEU
Chi-restraints excluded: chain E residue  317 CYS
Chi-restraints excluded: chain E residue  336 LEU
Chi-restraints excluded: chain F residue   45 LEU
Chi-restraints excluded: chain F residue  210 THR
Chi-restraints excluded: chain F residue  240 ASP
Chi-restraints excluded: chain F residue  256 LEU
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   19 ARG
Chi-restraints excluded: chain H residue   39 GLN
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue  111 THR
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain I residue   36 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 137 optimal weight:    0.8980
   chunk 127 optimal weight:    0.6980
   chunk 170 optimal weight:    0.2980
   chunk 126 optimal weight:    0.9990
   chunk 182 optimal weight:    0.0870
   chunk 112 optimal weight:    9.9990
   chunk 141 optimal weight:    3.9990
   chunk 151 optimal weight:    0.9990
   chunk 178 optimal weight:    5.9990
   chunk 186 optimal weight:    6.9990
   chunk 106 optimal weight:    7.9990
   overall best weight:    0.5960

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

Flipped N/Q/H residues before XYZ refinement:
R  31 GLN
** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  39 GLN
D  31 GLN
** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.194354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.159400 restraints weight = 20638.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.150694 restraints weight = 22951.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.151408 restraints weight = 22931.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.151461 restraints weight = 19057.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.151461 restraints weight = 18692.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.3715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  18028  Z= 0.103
  Angle     :  0.534   8.374  24408  Z= 0.278
  Chirality :  0.040   0.161   2692
  Planarity :  0.004   0.054   3106
  Dihedral  :  5.367  89.063   2428
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 25.97 %
    Favored  : 69.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.18), residues: 2160
  helix:  1.88 (0.18), residues: 832
  sheet: -0.61 (0.24), residues: 430
  loop : -1.49 (0.19), residues: 898

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 379 
 TYR   0.026   0.001   TYR F 308 
 PHE   0.013   0.001   PHE H  29 
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS E 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (18018)
  covalent geometry    : angle       0.53267 (24388)
  SS BOND              : bond        0.00191 (   10)
  SS BOND              : angle       1.56704 (   20)
  hydrogen bonds       : bond        0.03815 (  836)
  hydrogen bonds       : angle       4.02681 ( 2412)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2741.03 seconds
wall clock time: 48 minutes 33.95 seconds (2913.95 seconds total)